├── .gitignore ├── README.md ├── abstracts ├── 01-introduction-phylogenetic-comparative-method.md ├── 02-working-tree-life-comparative-studies-build-tailor-phylogenies-interspecific-datasets.md ├── 03-introduction-supertree-construction-partitioned-phylogenetic-analyses-view-toward-distinction-gene-trees-species-trees.md ├── 04-graphical-methods-visualizing-comparative-data-phylogenies.md ├── 05-primer-phylogenetic-generalised-least-squares.md ├── 06-statistical-issues-assumptions-phylogenetic-generalised-least-squares.md ├── 07-uncertainties-due-within-species-variation-comparative-studies-measurement-errors-statistical-weights.md ├── 08-introduction-phylogenetic-path-analysis.md ├── 09-phylogenetic-logistic-regression-binary-dependent-variables.md ├── 10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md ├── 11-general-quantitative-genetic-methods-comparative-biology.md ├── 12-multimodel-inference-comparative-analyses.md ├── 13-simulation-phylogenetic-data.md ├── 14-use-misuse-comparative-methods-study-adaptation.md ├── 15-modelling-stabilising-selection-attraction-ornstein-uhlenbeck-models.md ├── 16-hidden-markov-models-studying-evolution-binary-morphological-characters.md ├── 17-detecting-phenotypic-selection-approximate-bayesian-computation-abc-phylogenetic-comparative-methods.md ├── 18-phylogenetic-comparative-methods-studying-clade-wide-convergence.md ├── 19-metrics-models-community-phylogenetics.md ├── 20-event-based-cophylogenetic-comparative-analysis.md ├── 21-phylogenetic-prediction-identify-evolutionary-singularities.md ├── 22-preparing-paleontological-datasets-phylogenetic-comparative-methods.md └── README.md ├── authors.md ├── backup ├── additional_files │ ├── ch10 │ │ ├── ch10_figures.md │ │ ├── unnamed-chunk-1.png │ │ ├── unnamed-chunk-10.png │ │ ├── unnamed-chunk-11.png │ │ ├── unnamed-chunk-12.png │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-4.png │ │ ├── unnamed-chunk-5.png │ │ ├── unnamed-chunk-6.png │ │ ├── unnamed-chunk-7.png │ │ ├── unnamed-chunk-8.png │ │ └── unnamed-chunk-9.png │ ├── ch11 │ │ ├── ch11_figures.md │ │ ├── unnamed-chunk-1.png │ │ ├── unnamed-chunk-2.png │ │ └── unnamed-chunk-3.png │ ├── ch12 │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-4.png │ │ ├── unnamed-chunk-7.png │ │ └── unnamed-chunk-9.png │ ├── ch13 │ │ ├── unnamed-chunk-15.png │ │ └── unnamed-chunk-16.png │ ├── ch17 │ │ └── image001.png │ ├── ch2 │ │ ├── ch2_figures.md │ │ ├── unnamed-chunk-10.png │ │ ├── unnamed-chunk-11.png │ │ ├── unnamed-chunk-17.png │ │ ├── unnamed-chunk-181.png │ │ ├── unnamed-chunk-182.png │ │ ├── unnamed-chunk-20.png │ │ ├── unnamed-chunk-221.png │ │ ├── unnamed-chunk-222.png │ │ ├── unnamed-chunk-223.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-41.png │ │ ├── unnamed-chunk-42.png │ │ ├── unnamed-chunk-61.png │ │ ├── unnamed-chunk-62.png │ │ ├── unnamed-chunk-63.png │ │ ├── unnamed-chunk-64.png │ │ ├── unnamed-chunk-7.png │ │ └── unnamed-chunk-9.png │ ├── ch21 │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-31.png │ │ ├── unnamed-chunk-32.png │ │ ├── unnamed-chunk-33.png │ │ ├── unnamed-chunk-34.png │ │ └── unnamed-chunk-35.png │ ├── ch22 │ │ ├── unnamed-chunk-10.png │ │ ├── unnamed-chunk-11.png │ │ ├── unnamed-chunk-13.png │ │ ├── unnamed-chunk-14.png │ │ ├── unnamed-chunk-17.png │ │ ├── unnamed-chunk-181.png │ │ ├── unnamed-chunk-182.png │ │ ├── unnamed-chunk-20.png │ │ ├── unnamed-chunk-221.png │ │ ├── unnamed-chunk-222.png │ │ ├── unnamed-chunk-223.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-41.png │ │ ├── unnamed-chunk-42.png │ │ ├── unnamed-chunk-6.png │ │ ├── unnamed-chunk-61.png │ │ ├── unnamed-chunk-62.png │ │ ├── unnamed-chunk-63.png │ │ ├── unnamed-chunk-64.png │ │ ├── unnamed-chunk-7.png │ │ ├── unnamed-chunk-8.png │ │ └── unnamed-chunk-9.png │ ├── ch4 │ │ ├── ch4_figures.md │ │ ├── unnamed-chunk-1.png │ │ ├── unnamed-chunk-10.png │ │ ├── unnamed-chunk-11.png │ │ ├── unnamed-chunk-12.png │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-4.png │ │ ├── unnamed-chunk-5.png │ │ ├── unnamed-chunk-6.png │ │ ├── unnamed-chunk-7.png │ │ ├── unnamed-chunk-8.png │ │ └── unnamed-chunk-9.png │ ├── ch5 │ │ ├── ch5_figures.md │ │ ├── unnamed-chunk-1.png │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-4.png │ │ ├── unnamed-chunk-5.png │ │ └── unnamed-chunk-6.png │ ├── ch6 │ │ ├── ch6_figures.md │ │ ├── unnamed-chunk-1.png │ │ ├── unnamed-chunk-31.png │ │ ├── unnamed-chunk-32.png │ │ ├── unnamed-chunk-33.png │ │ ├── unnamed-chunk-34.png │ │ ├── unnamed-chunk-35.png │ │ ├── unnamed-chunk-36.png │ │ ├── unnamed-chunk-61.png │ │ ├── unnamed-chunk-62.png │ │ ├── unnamed-chunk-63.png │ │ └── unnamed-chunk-64.png │ ├── ch7 │ │ ├── ch7_figures.md │ │ ├── unnamed-chunk-1.png │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-4.png │ │ └── unnamed-chunk-6.png │ └── ch8 │ │ ├── ch8_figures.md │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-36.png │ │ ├── unnamed-chunk-4.png │ │ └── unnamed-chunk-5.png ├── book-sections.md ├── book │ └── CHAPTERS │ │ ├── 1-introduction-phylogenetic-comparative-method.md │ │ ├── 10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md │ │ ├── 11-general-quantitative-genetic-methods-comparative-biology.md │ │ ├── 12-multimodel-inference-comparative-analyses.md │ │ ├── 13-simulation-phylogenetic-data.md │ │ ├── 14-use-misuse-comparative-methods-study-adaptation.md │ │ ├── 15-modelling-stabilising-selection-attraction-ornstein-uhlenbeck-models.md │ │ ├── 16-hidden-markov-models-studying-evolution-binary-morphological-characters.md │ │ ├── 17-detecting-phenotypic-selection-approximate-bayesian-computation-abc-phylogenetic-comparative-methods.md │ │ ├── 18-phylogenetic-comparative-methods-studying-clade-wide-convergence.md │ │ ├── 19-metrics-models-community-phylogenetics.md │ │ ├── 2-working-tree-life-comparative-studies-build-tailor-phylogenies-interspecific-datasets.md │ │ ├── 20-event-based-cophylogenetic-comparative-analysis.md │ │ ├── 21-phylogenetic-prediction-identify-evolutionary-singularities.md │ │ ├── 22-preparing-paleontological-datasets-phylogenetic-comparative-methods.md │ │ ├── 3-introduction-supertree-construction-partitioned-phylogenetic-analyses-view-toward-distinction-gene-trees-species-trees.md │ │ ├── 4-graphical-methods-visualizing-comparative-data-phylogenies.md │ │ ├── 5-primer-phylogenetic-generalised-least-squares.md │ │ ├── 6-statistical-issues-assumptions-phylogenetic-generalised-least-squares.md │ │ ├── 7-uncertainties-due-within-species-variation-comparative-studies-measurement-errors-statistical-weights.md │ │ ├── 8-introduction-phylogenetic-path-analysis.md │ │ └── 9-phylogenetic-logistic-regression-binary-dependent-variables.md ├── data_files │ ├── ch10 │ │ ├── Primates.trees │ │ ├── Primates.txt │ │ └── ch10_data.md │ ├── ch11 │ │ ├── ch11_data.md │ │ ├── data_effect.txt │ │ ├── data_pois.txt │ │ ├── data_pois_missing.txt │ │ ├── data_repeat.txt │ │ ├── data_simple.txt │ │ └── phylo.nex │ ├── ch12 │ │ ├── 10kTrees_Primates.nex │ │ ├── consensusTre_Primates.nex │ │ ├── primate_data.txt │ │ ├── primate_spec.txt │ │ └── primate_tree.nex │ ├── ch17 │ │ └── ABC_PCM.c │ ├── ch19 │ │ ├── figures.R │ │ ├── functions.R │ │ ├── metrics.R │ │ ├── pglmm.R │ │ └── tables.pdf │ ├── ch2 │ │ ├── Bird_tree5.nex │ │ ├── Bird_tree7.tre │ │ ├── bird_trees.tre │ │ ├── ch2_data.md │ │ ├── primate_spec.txt │ │ └── primate_tree.phy │ ├── ch21 │ │ ├── BayesModelS_v22.R │ │ ├── e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt │ │ └── e.dataIMI_corrected.csv │ ├── ch4 │ │ ├── Centrarchidae.tre │ │ ├── anole.data.csv │ │ ├── ch4_data.md │ │ ├── elopomorph.csv │ │ └── elopomorph.tre │ ├── ch5 │ │ ├── ch5_data.md │ │ └── vcv2phylo.R │ ├── ch6 │ │ ├── ch6_data.md │ │ ├── covariates.txt │ │ ├── fict_phylo.nex │ │ └── pgls_check_fncs.r │ ├── ch7 │ │ ├── GLSME.R │ │ ├── ch7_data.md │ │ ├── primate_ind.txt │ │ ├── primate_spec.txt │ │ └── primate_tree.phy │ └── ch8 │ │ ├── ch8_data.md │ │ ├── rhino.csv │ │ ├── rhino.tree │ │ └── storks.csv ├── modern-phylogenetic-comparative-methods-application-evolutionary-biology-concepts-practice.md ├── part-ii-handling-phylogenies-different-statistical-designs.md ├── part-iii-specific-models-studying-evolutionary-mechanisms.md └── part-introduction.md └── online_practical_material ├── 02-chapter.md ├── README.md ├── additional_files ├── ch10 │ ├── ch10_figures.md │ ├── unnamed-chunk-1.png │ ├── unnamed-chunk-10.png │ ├── unnamed-chunk-11.png │ ├── unnamed-chunk-12.png │ ├── unnamed-chunk-2.png │ ├── unnamed-chunk-3.png │ ├── unnamed-chunk-4.png │ ├── unnamed-chunk-5.png │ ├── unnamed-chunk-6.png │ ├── unnamed-chunk-7.png │ ├── unnamed-chunk-8.png │ └── unnamed-chunk-9.png ├── ch11 │ ├── ch11_figures.md │ ├── unnamed-chunk-1.png │ ├── unnamed-chunk-2.png │ └── unnamed-chunk-3.png ├── ch12 │ ├── unnamed-chunk-2.png │ ├── unnamed-chunk-4.png │ ├── unnamed-chunk-7.png │ └── unnamed-chunk-9.png ├── ch13 │ ├── unnamed-chunk-15.png │ └── unnamed-chunk-16.png ├── ch17 │ └── image001.png ├── ch2 │ ├── ch2_figures.md │ ├── unnamed-chunk-10.png │ ├── unnamed-chunk-11.png │ ├── unnamed-chunk-17.png │ ├── unnamed-chunk-181.png │ ├── unnamed-chunk-182.png │ ├── unnamed-chunk-20.png │ ├── unnamed-chunk-221.png │ ├── unnamed-chunk-222.png │ ├── unnamed-chunk-223.png │ ├── unnamed-chunk-3.png │ ├── unnamed-chunk-41.png │ ├── unnamed-chunk-42.png │ ├── unnamed-chunk-61.png │ ├── unnamed-chunk-62.png │ ├── unnamed-chunk-63.png │ ├── unnamed-chunk-64.png │ ├── unnamed-chunk-7.png │ └── unnamed-chunk-9.png ├── ch21 │ ├── unnamed-chunk-2.png │ ├── unnamed-chunk-31.png │ ├── unnamed-chunk-32.png │ ├── unnamed-chunk-33.png │ ├── unnamed-chunk-34.png │ └── unnamed-chunk-35.png ├── ch22 │ ├── unnamed-chunk-10.png │ ├── unnamed-chunk-11.png │ ├── unnamed-chunk-13.png │ ├── unnamed-chunk-14.png │ ├── unnamed-chunk-17.png │ ├── unnamed-chunk-181.png │ ├── unnamed-chunk-182.png │ ├── unnamed-chunk-20.png │ ├── unnamed-chunk-221.png │ ├── unnamed-chunk-222.png │ ├── unnamed-chunk-223.png │ ├── unnamed-chunk-3.png │ ├── unnamed-chunk-41.png │ ├── unnamed-chunk-42.png │ ├── unnamed-chunk-6.png │ ├── unnamed-chunk-61.png │ ├── unnamed-chunk-62.png │ ├── unnamed-chunk-63.png │ ├── unnamed-chunk-64.png │ ├── unnamed-chunk-7.png │ ├── unnamed-chunk-8.png │ └── unnamed-chunk-9.png ├── ch4 │ ├── ch4_figures.md │ ├── unnamed-chunk-1.png │ ├── unnamed-chunk-10.png │ ├── unnamed-chunk-11.png │ ├── unnamed-chunk-12.png │ ├── unnamed-chunk-2.png │ ├── unnamed-chunk-3.png │ ├── unnamed-chunk-4.png │ ├── unnamed-chunk-5.png │ ├── unnamed-chunk-6.png │ ├── unnamed-chunk-7.png │ ├── unnamed-chunk-8.png │ └── unnamed-chunk-9.png ├── ch5 │ ├── ch5_figures.md │ ├── unnamed-chunk-1.png │ ├── unnamed-chunk-2.png │ ├── unnamed-chunk-3.png │ ├── unnamed-chunk-4.png │ ├── unnamed-chunk-5.png │ └── unnamed-chunk-6.png ├── ch6 │ ├── ch6_figures.md │ ├── unnamed-chunk-1.png │ ├── unnamed-chunk-31.png │ ├── unnamed-chunk-32.png │ ├── unnamed-chunk-33.png │ ├── unnamed-chunk-34.png │ ├── unnamed-chunk-35.png │ ├── unnamed-chunk-36.png │ ├── unnamed-chunk-61.png │ ├── unnamed-chunk-62.png │ ├── unnamed-chunk-63.png │ └── unnamed-chunk-64.png ├── ch7 │ ├── ch7_figures.md │ ├── unnamed-chunk-1.png │ ├── unnamed-chunk-2.png │ ├── unnamed-chunk-3.png │ ├── unnamed-chunk-4.png │ └── unnamed-chunk-6.png └── ch8 │ ├── ch8_figures.md │ ├── unnamed-chunk-2.png │ ├── unnamed-chunk-36.png │ ├── unnamed-chunk-4.png │ └── unnamed-chunk-5.png ├── data_files ├── ch10 │ ├── Primates.trees │ ├── Primates.txt │ └── ch10_data.md ├── ch11 │ ├── ch11_data.md │ ├── data_effect.txt │ ├── data_pois.txt │ ├── data_pois_missing.txt │ ├── data_repeat.txt │ ├── data_simple.txt │ └── phylo.nex ├── ch12 │ ├── 10kTrees_Primates.nex │ ├── consensusTre_Primates.nex │ ├── primate_data.txt │ ├── primate_spec.txt │ └── primate_tree.nex ├── ch17 │ └── ABC_PCM.c ├── ch19 │ ├── figures.R │ ├── functions.R │ ├── metrics.R │ ├── pglmm.R │ └── tables.pdf ├── ch2 │ ├── Bird_tree5.nex │ ├── Bird_tree7.tre │ ├── bird_trees.tre │ ├── ch2_data.md │ ├── primate_spec.txt │ └── primate_tree.phy ├── ch21 │ ├── BayesModelS_v22.R │ ├── e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt │ └── e.dataIMI_corrected.csv ├── ch4 │ ├── Centrarchidae.tre │ ├── anole.data.csv │ ├── ch4_data.md │ ├── elopomorph.csv │ └── elopomorph.tre ├── ch5 │ ├── ch5_data.md │ └── vcv2phylo.R ├── ch6 │ ├── ch6_data.md │ ├── covariates.txt │ ├── fict_phylo.nex │ └── pgls_check_fncs.r ├── ch7 │ ├── GLSME.R │ ├── ch7_data.md │ ├── primate_ind.txt │ ├── primate_spec.txt │ └── primate_tree.phy └── ch8 │ ├── ch8_data.md │ ├── rhino.csv │ ├── rhino.tree │ └── storks.csv ├── exercises_and_tutorials ├── chapter-10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md ├── chapter-11-1-simple-model-mcmcglmm.md ├── chapter-11-2-multiple-measurements-model-mcmcglmm.md ├── chapter-11-3-example-meta-analysis-fishers-transformation-r-zr.md ├── chapter-11-4-example-non-gaussian-trait-using-count-data.md ├── chapter-11-bibliography.md ├── chapter-11-example-mar-comparative-data.md ├── chapter-12-1-evolutionary-models-different-combinations-predictors.md ├── chapter-12-2-dealing-phylogenetic-uncertainty-inference-across-models-considering-different-phylogenetic-hypotheses.md ├── chapter-12-3-playing-statistical-weights-adjusting-omega-parameter.md ├── chapter-12-4-multimodel-inference-exploring-multidimensional-parameter-space-simultaneously-varying-lambda-omega.md ├── chapter-13-1-trees.md ├── chapter-13-2-traits.md ├── chapter-13-3-trees-traits.md ├── chapter-17-1-brief-description-program-code.md ├── chapter-19-1-calculating-community-phylogenetic-metrics-opm.md ├── chapter-2-1-exercises-building-manipulating-phylogenetic-trees.md ├── chapter-21-1-exercises-analyses-displaying-results.md ├── chapter-22-1-example-time-scaling-using-r-package-paleotree.md ├── chapter-4-1-codes-used-produce-twelve-figures-chapter.md ├── chapter-6-1exercises-testing-assumptions-statistical-issues-framework-phylogenetic-generalized-least-squares.md ├── chapter-7-1-repeatability-opm.md ├── chapter-7-2-data-opm.md ├── chapter-7-3-weighted-regr-opm.md ├── chapter-7-4-univariate-opm.md ├── chapter-7-5-bivariate-opm.md ├── chapter-8-1-baby-delivering-storks-example.md └── chapter-8-2-step-step-guide-phylogenetic-path-analysis-using-d-sep-method-rhinograds-example.md ├── iframe ├── Chapter10_OPM │ ├── OPM_chap10.doc │ ├── OPM_chap10.pdf │ ├── Primates.trees │ └── Primates.txt ├── Chapter11_OPM │ ├── 1_simple.html │ ├── 2_multi.html │ ├── 3_fisher.html │ ├── 4_nongaussian.html │ ├── 5_missing.html │ ├── VCV.png │ ├── biblio.html │ ├── data.zip │ ├── fixed.png │ ├── funnel.png │ ├── img1.png │ ├── img10.png │ ├── img11.old │ ├── img11.png │ ├── img12.png │ ├── img13.png │ ├── img14.png │ ├── img15.png │ ├── img16.png │ ├── img17.png │ ├── img2.png │ ├── img3.png │ ├── img4.png │ ├── img5.png │ ├── img6.png │ ├── img7.png │ ├── img8.old │ ├── img8.png │ ├── img9.old │ ├── img9.png │ ├── internals.pl │ ├── labels.pl │ ├── opm.css │ └── opm.html ├── Chapter12_OPM │ ├── 1_multi_predictors_OUT.html │ ├── 1_multi_predictors_OUT_corr.html │ ├── 2_phylo_uncertainity_OUT.html │ ├── 3_weights_OUT.html │ ├── 4_weight&lambda_OUT.html │ ├── download │ │ ├── 10kTrees_Primates.nex │ │ ├── consensusTre_Primates.nex │ │ ├── primate_data.txt │ │ ├── primate_spec.txt │ │ └── primate_tree.nex │ └── figure │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-4.png │ │ ├── unnamed-chunk-7.png │ │ └── unnamed-chunk-9.png ├── Chapter13_OPM │ ├── 1_Trees.html │ ├── 2_Traits.html │ ├── 3_Trees_and_traits.html │ └── figure │ │ ├── unnamed-chunk-15.png │ │ └── unnamed-chunk-16.png ├── Chapter17_OPM │ ├── download │ │ └── ABC_PCM.c │ ├── figure │ │ └── image001.png │ └── html_frame_chap17.html ├── Chapter19_OPM │ ├── 1_Calculating_community_phylogenetic_metrics_OPM.html │ └── download │ │ ├── figures.R │ │ ├── functions.R │ │ ├── metrics.R │ │ ├── pglmm.R │ │ └── tables.pdf ├── Chapter21_OPM │ ├── download │ │ ├── BayesModelS_v22.R │ │ ├── e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt │ │ └── e.dataIMI_corrected.csv │ ├── figures for IMI OPM │ │ ├── Thumbs.db │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-31.png │ │ ├── unnamed-chunk-32.png │ │ ├── unnamed-chunk-33.png │ │ ├── unnamed-chunk-34.png │ │ └── unnamed-chunk-35.png │ └── html_frame_chap21.html ├── Chapter22_OPM │ ├── figure │ │ ├── unnamed-chunk-10.png │ │ ├── unnamed-chunk-11.png │ │ ├── unnamed-chunk-13.png │ │ ├── unnamed-chunk-14.png │ │ ├── unnamed-chunk-17.png │ │ ├── unnamed-chunk-181.png │ │ ├── unnamed-chunk-182.png │ │ ├── unnamed-chunk-20.png │ │ ├── unnamed-chunk-221.png │ │ ├── unnamed-chunk-222.png │ │ ├── unnamed-chunk-223.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-41.png │ │ ├── unnamed-chunk-42.png │ │ ├── unnamed-chunk-6.png │ │ ├── unnamed-chunk-61.png │ │ ├── unnamed-chunk-62.png │ │ ├── unnamed-chunk-63.png │ │ ├── unnamed-chunk-64.png │ │ ├── unnamed-chunk-7.png │ │ ├── unnamed-chunk-8.png │ │ └── unnamed-chunk-9.png │ └── html_frame_chap22_OUT.html ├── Chapter2_OPM │ ├── download │ │ ├── bird_trees.tre │ │ ├── primate_spec.txt │ │ └── primate_tree.phy │ ├── figure │ │ ├── unnamed-chunk-10.png │ │ ├── unnamed-chunk-11.png │ │ ├── unnamed-chunk-17.png │ │ ├── unnamed-chunk-181.png │ │ ├── unnamed-chunk-182.png │ │ ├── unnamed-chunk-20.png │ │ ├── unnamed-chunk-221.png │ │ ├── unnamed-chunk-222.png │ │ ├── unnamed-chunk-223.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-41.png │ │ ├── unnamed-chunk-42.png │ │ ├── unnamed-chunk-61.png │ │ ├── unnamed-chunk-62.png │ │ ├── unnamed-chunk-63.png │ │ ├── unnamed-chunk-64.png │ │ ├── unnamed-chunk-7.png │ │ └── unnamed-chunk-9.png │ └── html_frame_chap2_OUT.html ├── Chapter4_OPM │ ├── Centrarchidae.tre │ ├── Revell_Chapter4_OPM_mod1.html │ ├── anole.data.csv │ ├── elopomorph.csv │ └── elopomorph.tre ├── Chapter5_OPM │ ├── OPM_chap5.pdf │ └── download │ │ └── vcv2phylo.R ├── Chapter6_OPM │ ├── download │ │ ├── covariates.txt │ │ ├── fict_phylo.nex │ │ └── pgls_check_fncs.r │ ├── figure │ │ ├── unnamed-chunk-1.png │ │ ├── unnamed-chunk-31.png │ │ ├── unnamed-chunk-32.png │ │ ├── unnamed-chunk-33.png │ │ ├── unnamed-chunk-34.png │ │ ├── unnamed-chunk-35.png │ │ ├── unnamed-chunk-36.png │ │ ├── unnamed-chunk-61.png │ │ ├── unnamed-chunk-62.png │ │ ├── unnamed-chunk-63.png │ │ └── unnamed-chunk-64.png │ └── html_frame_chap6.html ├── Chapter7_OPM │ ├── 1_repeatability_OPM.html │ ├── 2_data_OPM.html │ ├── 3_weighted_regr_OPM.html │ ├── 4_univariate_OPM.html │ ├── 5_bivariate_OPM.html │ ├── download │ │ ├── GLSME.R │ │ ├── primate_ind.txt │ │ ├── primate_spec.txt │ │ └── primate_tree.phy │ └── figure │ │ ├── unnamed-chunk-1.png │ │ ├── unnamed-chunk-2.png │ │ ├── unnamed-chunk-3.png │ │ ├── unnamed-chunk-4.png │ │ └── unnamed-chunk-6.png └── Chapter8_OPM │ ├── Rhinograds example.html │ ├── Storks example.html │ └── download │ ├── rhino.csv │ ├── rhino.tree │ └── storks.csv ├── online-practical-material-chapter-11.md ├── online-practical-material-chapter-12.md ├── online-practical-material-chapter-13.md ├── online-practical-material-chapter-17.md ├── online-practical-material-chapter-19.md ├── online-practical-material-chapter-21.md ├── online-practical-material-chapter-22.md ├── online-practical-material-chapter-4.md ├── online-practical-material-chapter-5.md ├── online-practical-material-chapter-6.md ├── online-practical-material-chapter-7.md └── online-practical-material-chapter-8.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/README.md -------------------------------------------------------------------------------- /abstracts/01-introduction-phylogenetic-comparative-method.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/01-introduction-phylogenetic-comparative-method.md -------------------------------------------------------------------------------- /abstracts/02-working-tree-life-comparative-studies-build-tailor-phylogenies-interspecific-datasets.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/02-working-tree-life-comparative-studies-build-tailor-phylogenies-interspecific-datasets.md -------------------------------------------------------------------------------- /abstracts/03-introduction-supertree-construction-partitioned-phylogenetic-analyses-view-toward-distinction-gene-trees-species-trees.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/03-introduction-supertree-construction-partitioned-phylogenetic-analyses-view-toward-distinction-gene-trees-species-trees.md -------------------------------------------------------------------------------- /abstracts/04-graphical-methods-visualizing-comparative-data-phylogenies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/04-graphical-methods-visualizing-comparative-data-phylogenies.md -------------------------------------------------------------------------------- /abstracts/05-primer-phylogenetic-generalised-least-squares.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/05-primer-phylogenetic-generalised-least-squares.md -------------------------------------------------------------------------------- /abstracts/06-statistical-issues-assumptions-phylogenetic-generalised-least-squares.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/06-statistical-issues-assumptions-phylogenetic-generalised-least-squares.md -------------------------------------------------------------------------------- /abstracts/07-uncertainties-due-within-species-variation-comparative-studies-measurement-errors-statistical-weights.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/07-uncertainties-due-within-species-variation-comparative-studies-measurement-errors-statistical-weights.md -------------------------------------------------------------------------------- /abstracts/08-introduction-phylogenetic-path-analysis.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/08-introduction-phylogenetic-path-analysis.md -------------------------------------------------------------------------------- /abstracts/09-phylogenetic-logistic-regression-binary-dependent-variables.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/09-phylogenetic-logistic-regression-binary-dependent-variables.md -------------------------------------------------------------------------------- /abstracts/10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md -------------------------------------------------------------------------------- /abstracts/11-general-quantitative-genetic-methods-comparative-biology.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/11-general-quantitative-genetic-methods-comparative-biology.md -------------------------------------------------------------------------------- /abstracts/12-multimodel-inference-comparative-analyses.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/12-multimodel-inference-comparative-analyses.md -------------------------------------------------------------------------------- /abstracts/13-simulation-phylogenetic-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/13-simulation-phylogenetic-data.md -------------------------------------------------------------------------------- /abstracts/14-use-misuse-comparative-methods-study-adaptation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/14-use-misuse-comparative-methods-study-adaptation.md -------------------------------------------------------------------------------- /abstracts/15-modelling-stabilising-selection-attraction-ornstein-uhlenbeck-models.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/15-modelling-stabilising-selection-attraction-ornstein-uhlenbeck-models.md -------------------------------------------------------------------------------- /abstracts/16-hidden-markov-models-studying-evolution-binary-morphological-characters.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/16-hidden-markov-models-studying-evolution-binary-morphological-characters.md -------------------------------------------------------------------------------- /abstracts/17-detecting-phenotypic-selection-approximate-bayesian-computation-abc-phylogenetic-comparative-methods.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/17-detecting-phenotypic-selection-approximate-bayesian-computation-abc-phylogenetic-comparative-methods.md -------------------------------------------------------------------------------- /abstracts/18-phylogenetic-comparative-methods-studying-clade-wide-convergence.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/18-phylogenetic-comparative-methods-studying-clade-wide-convergence.md -------------------------------------------------------------------------------- /abstracts/19-metrics-models-community-phylogenetics.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/19-metrics-models-community-phylogenetics.md -------------------------------------------------------------------------------- /abstracts/20-event-based-cophylogenetic-comparative-analysis.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/20-event-based-cophylogenetic-comparative-analysis.md -------------------------------------------------------------------------------- /abstracts/21-phylogenetic-prediction-identify-evolutionary-singularities.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/21-phylogenetic-prediction-identify-evolutionary-singularities.md -------------------------------------------------------------------------------- /abstracts/22-preparing-paleontological-datasets-phylogenetic-comparative-methods.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/22-preparing-paleontological-datasets-phylogenetic-comparative-methods.md -------------------------------------------------------------------------------- /abstracts/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/abstracts/README.md -------------------------------------------------------------------------------- /authors.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/authors.md -------------------------------------------------------------------------------- /backup/additional_files/ch10/ch10_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 10. 2 | -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-1.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-10.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-11.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-12.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-2.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-3.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-4.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-5.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-6.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-7.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-8.png -------------------------------------------------------------------------------- /backup/additional_files/ch10/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch10/unnamed-chunk-9.png -------------------------------------------------------------------------------- /backup/additional_files/ch11/ch11_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 11. 2 | -------------------------------------------------------------------------------- /backup/additional_files/ch11/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch11/unnamed-chunk-1.png -------------------------------------------------------------------------------- /backup/additional_files/ch11/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch11/unnamed-chunk-2.png -------------------------------------------------------------------------------- /backup/additional_files/ch11/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch11/unnamed-chunk-3.png -------------------------------------------------------------------------------- /backup/additional_files/ch12/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch12/unnamed-chunk-2.png -------------------------------------------------------------------------------- /backup/additional_files/ch12/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch12/unnamed-chunk-4.png -------------------------------------------------------------------------------- /backup/additional_files/ch12/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch12/unnamed-chunk-7.png -------------------------------------------------------------------------------- /backup/additional_files/ch12/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch12/unnamed-chunk-9.png -------------------------------------------------------------------------------- /backup/additional_files/ch13/unnamed-chunk-15.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch13/unnamed-chunk-15.png -------------------------------------------------------------------------------- /backup/additional_files/ch13/unnamed-chunk-16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch13/unnamed-chunk-16.png -------------------------------------------------------------------------------- /backup/additional_files/ch17/image001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch17/image001.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/ch2_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 2. 2 | -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-10.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-11.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-17.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-17.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-181.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-181.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-182.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-182.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-20.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-221.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-221.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-222.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-222.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-223.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-223.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-3.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-41.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-41.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-42.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-42.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-61.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-62.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-63.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-64.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-7.png -------------------------------------------------------------------------------- /backup/additional_files/ch2/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch2/unnamed-chunk-9.png -------------------------------------------------------------------------------- /backup/additional_files/ch21/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch21/unnamed-chunk-2.png -------------------------------------------------------------------------------- /backup/additional_files/ch21/unnamed-chunk-31.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch21/unnamed-chunk-31.png -------------------------------------------------------------------------------- /backup/additional_files/ch21/unnamed-chunk-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch21/unnamed-chunk-32.png -------------------------------------------------------------------------------- /backup/additional_files/ch21/unnamed-chunk-33.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch21/unnamed-chunk-33.png -------------------------------------------------------------------------------- /backup/additional_files/ch21/unnamed-chunk-34.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch21/unnamed-chunk-34.png -------------------------------------------------------------------------------- /backup/additional_files/ch21/unnamed-chunk-35.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch21/unnamed-chunk-35.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-10.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-11.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-13.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-13.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-14.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-14.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-17.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-17.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-181.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-181.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-182.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-182.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-20.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-221.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-221.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-222.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-222.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-223.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-223.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-3.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-41.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-41.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-42.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-42.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-6.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-61.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-62.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-63.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-64.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-7.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-8.png -------------------------------------------------------------------------------- /backup/additional_files/ch22/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch22/unnamed-chunk-9.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/ch4_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 4. 2 | -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-1.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-10.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-11.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-12.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-2.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-3.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-4.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-5.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-6.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-7.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-8.png -------------------------------------------------------------------------------- /backup/additional_files/ch4/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch4/unnamed-chunk-9.png -------------------------------------------------------------------------------- /backup/additional_files/ch5/ch5_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 5. 2 | -------------------------------------------------------------------------------- /backup/additional_files/ch5/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch5/unnamed-chunk-1.png -------------------------------------------------------------------------------- /backup/additional_files/ch5/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch5/unnamed-chunk-2.png -------------------------------------------------------------------------------- /backup/additional_files/ch5/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch5/unnamed-chunk-3.png -------------------------------------------------------------------------------- /backup/additional_files/ch5/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch5/unnamed-chunk-4.png -------------------------------------------------------------------------------- /backup/additional_files/ch5/unnamed-chunk-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch5/unnamed-chunk-5.png -------------------------------------------------------------------------------- /backup/additional_files/ch5/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch5/unnamed-chunk-6.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/ch6_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 6. 2 | -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-1.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-31.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-31.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-32.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-33.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-33.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-34.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-34.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-35.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-35.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-36.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-36.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-61.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-62.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-63.png -------------------------------------------------------------------------------- /backup/additional_files/ch6/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch6/unnamed-chunk-64.png -------------------------------------------------------------------------------- /backup/additional_files/ch7/ch7_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 7. 2 | -------------------------------------------------------------------------------- /backup/additional_files/ch7/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch7/unnamed-chunk-1.png -------------------------------------------------------------------------------- /backup/additional_files/ch7/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch7/unnamed-chunk-2.png -------------------------------------------------------------------------------- /backup/additional_files/ch7/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch7/unnamed-chunk-3.png -------------------------------------------------------------------------------- /backup/additional_files/ch7/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch7/unnamed-chunk-4.png -------------------------------------------------------------------------------- /backup/additional_files/ch7/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch7/unnamed-chunk-6.png -------------------------------------------------------------------------------- /backup/additional_files/ch8/ch8_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 8. 2 | -------------------------------------------------------------------------------- /backup/additional_files/ch8/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch8/unnamed-chunk-2.png -------------------------------------------------------------------------------- /backup/additional_files/ch8/unnamed-chunk-36.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch8/unnamed-chunk-36.png -------------------------------------------------------------------------------- /backup/additional_files/ch8/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch8/unnamed-chunk-4.png -------------------------------------------------------------------------------- /backup/additional_files/ch8/unnamed-chunk-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/additional_files/ch8/unnamed-chunk-5.png -------------------------------------------------------------------------------- /backup/book-sections.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book-sections.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/1-introduction-phylogenetic-comparative-method.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/1-introduction-phylogenetic-comparative-method.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/11-general-quantitative-genetic-methods-comparative-biology.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/11-general-quantitative-genetic-methods-comparative-biology.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/12-multimodel-inference-comparative-analyses.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/12-multimodel-inference-comparative-analyses.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/13-simulation-phylogenetic-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/13-simulation-phylogenetic-data.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/14-use-misuse-comparative-methods-study-adaptation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/14-use-misuse-comparative-methods-study-adaptation.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/15-modelling-stabilising-selection-attraction-ornstein-uhlenbeck-models.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/15-modelling-stabilising-selection-attraction-ornstein-uhlenbeck-models.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/16-hidden-markov-models-studying-evolution-binary-morphological-characters.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/16-hidden-markov-models-studying-evolution-binary-morphological-characters.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/17-detecting-phenotypic-selection-approximate-bayesian-computation-abc-phylogenetic-comparative-methods.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/17-detecting-phenotypic-selection-approximate-bayesian-computation-abc-phylogenetic-comparative-methods.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/18-phylogenetic-comparative-methods-studying-clade-wide-convergence.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/18-phylogenetic-comparative-methods-studying-clade-wide-convergence.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/19-metrics-models-community-phylogenetics.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/19-metrics-models-community-phylogenetics.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/2-working-tree-life-comparative-studies-build-tailor-phylogenies-interspecific-datasets.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/2-working-tree-life-comparative-studies-build-tailor-phylogenies-interspecific-datasets.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/20-event-based-cophylogenetic-comparative-analysis.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/20-event-based-cophylogenetic-comparative-analysis.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/21-phylogenetic-prediction-identify-evolutionary-singularities.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/21-phylogenetic-prediction-identify-evolutionary-singularities.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/22-preparing-paleontological-datasets-phylogenetic-comparative-methods.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/22-preparing-paleontological-datasets-phylogenetic-comparative-methods.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/3-introduction-supertree-construction-partitioned-phylogenetic-analyses-view-toward-distinction-gene-trees-species-trees.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/3-introduction-supertree-construction-partitioned-phylogenetic-analyses-view-toward-distinction-gene-trees-species-trees.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/4-graphical-methods-visualizing-comparative-data-phylogenies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/4-graphical-methods-visualizing-comparative-data-phylogenies.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/5-primer-phylogenetic-generalised-least-squares.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/5-primer-phylogenetic-generalised-least-squares.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/6-statistical-issues-assumptions-phylogenetic-generalised-least-squares.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/6-statistical-issues-assumptions-phylogenetic-generalised-least-squares.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/7-uncertainties-due-within-species-variation-comparative-studies-measurement-errors-statistical-weights.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/7-uncertainties-due-within-species-variation-comparative-studies-measurement-errors-statistical-weights.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/8-introduction-phylogenetic-path-analysis.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/8-introduction-phylogenetic-path-analysis.md -------------------------------------------------------------------------------- /backup/book/CHAPTERS/9-phylogenetic-logistic-regression-binary-dependent-variables.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/book/CHAPTERS/9-phylogenetic-logistic-regression-binary-dependent-variables.md -------------------------------------------------------------------------------- /backup/data_files/ch10/Primates.trees: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch10/Primates.trees -------------------------------------------------------------------------------- /backup/data_files/ch10/Primates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch10/Primates.txt -------------------------------------------------------------------------------- /backup/data_files/ch10/ch10_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 10. 2 | -------------------------------------------------------------------------------- /backup/data_files/ch11/ch11_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 11. 2 | -------------------------------------------------------------------------------- /backup/data_files/ch11/data_effect.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch11/data_effect.txt -------------------------------------------------------------------------------- /backup/data_files/ch11/data_pois.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch11/data_pois.txt -------------------------------------------------------------------------------- /backup/data_files/ch11/data_pois_missing.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch11/data_pois_missing.txt -------------------------------------------------------------------------------- /backup/data_files/ch11/data_repeat.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch11/data_repeat.txt -------------------------------------------------------------------------------- /backup/data_files/ch11/data_simple.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch11/data_simple.txt -------------------------------------------------------------------------------- /backup/data_files/ch11/phylo.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch11/phylo.nex -------------------------------------------------------------------------------- /backup/data_files/ch12/10kTrees_Primates.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch12/10kTrees_Primates.nex -------------------------------------------------------------------------------- /backup/data_files/ch12/consensusTre_Primates.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch12/consensusTre_Primates.nex -------------------------------------------------------------------------------- /backup/data_files/ch12/primate_data.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch12/primate_data.txt -------------------------------------------------------------------------------- /backup/data_files/ch12/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch12/primate_spec.txt -------------------------------------------------------------------------------- /backup/data_files/ch12/primate_tree.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch12/primate_tree.nex -------------------------------------------------------------------------------- /backup/data_files/ch17/ABC_PCM.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch17/ABC_PCM.c -------------------------------------------------------------------------------- /backup/data_files/ch19/figures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch19/figures.R -------------------------------------------------------------------------------- /backup/data_files/ch19/functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch19/functions.R -------------------------------------------------------------------------------- /backup/data_files/ch19/metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch19/metrics.R -------------------------------------------------------------------------------- /backup/data_files/ch19/pglmm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch19/pglmm.R -------------------------------------------------------------------------------- /backup/data_files/ch19/tables.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch19/tables.pdf -------------------------------------------------------------------------------- /backup/data_files/ch2/Bird_tree5.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch2/Bird_tree5.nex -------------------------------------------------------------------------------- /backup/data_files/ch2/Bird_tree7.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch2/Bird_tree7.tre -------------------------------------------------------------------------------- /backup/data_files/ch2/bird_trees.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch2/bird_trees.tre -------------------------------------------------------------------------------- /backup/data_files/ch2/ch2_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 2. 2 | -------------------------------------------------------------------------------- /backup/data_files/ch2/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch2/primate_spec.txt -------------------------------------------------------------------------------- /backup/data_files/ch2/primate_tree.phy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch2/primate_tree.phy -------------------------------------------------------------------------------- /backup/data_files/ch21/BayesModelS_v22.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch21/BayesModelS_v22.R -------------------------------------------------------------------------------- /backup/data_files/ch21/e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch21/e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt -------------------------------------------------------------------------------- /backup/data_files/ch21/e.dataIMI_corrected.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch21/e.dataIMI_corrected.csv -------------------------------------------------------------------------------- /backup/data_files/ch4/Centrarchidae.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch4/Centrarchidae.tre -------------------------------------------------------------------------------- /backup/data_files/ch4/anole.data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch4/anole.data.csv -------------------------------------------------------------------------------- /backup/data_files/ch4/ch4_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 4. 2 | -------------------------------------------------------------------------------- /backup/data_files/ch4/elopomorph.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch4/elopomorph.csv -------------------------------------------------------------------------------- /backup/data_files/ch4/elopomorph.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch4/elopomorph.tre -------------------------------------------------------------------------------- /backup/data_files/ch5/ch5_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 5. 2 | -------------------------------------------------------------------------------- /backup/data_files/ch5/vcv2phylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch5/vcv2phylo.R -------------------------------------------------------------------------------- /backup/data_files/ch6/ch6_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 6. 2 | -------------------------------------------------------------------------------- /backup/data_files/ch6/covariates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch6/covariates.txt -------------------------------------------------------------------------------- /backup/data_files/ch6/fict_phylo.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch6/fict_phylo.nex -------------------------------------------------------------------------------- /backup/data_files/ch6/pgls_check_fncs.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch6/pgls_check_fncs.r -------------------------------------------------------------------------------- /backup/data_files/ch7/GLSME.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch7/GLSME.R -------------------------------------------------------------------------------- /backup/data_files/ch7/ch7_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 7. 2 | -------------------------------------------------------------------------------- /backup/data_files/ch7/primate_ind.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch7/primate_ind.txt -------------------------------------------------------------------------------- /backup/data_files/ch7/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch7/primate_spec.txt -------------------------------------------------------------------------------- /backup/data_files/ch7/primate_tree.phy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch7/primate_tree.phy -------------------------------------------------------------------------------- /backup/data_files/ch8/ch8_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 8. 2 | -------------------------------------------------------------------------------- /backup/data_files/ch8/rhino.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch8/rhino.csv -------------------------------------------------------------------------------- /backup/data_files/ch8/rhino.tree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch8/rhino.tree -------------------------------------------------------------------------------- /backup/data_files/ch8/storks.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/data_files/ch8/storks.csv -------------------------------------------------------------------------------- /backup/modern-phylogenetic-comparative-methods-application-evolutionary-biology-concepts-practice.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/modern-phylogenetic-comparative-methods-application-evolutionary-biology-concepts-practice.md -------------------------------------------------------------------------------- /backup/part-ii-handling-phylogenies-different-statistical-designs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/part-ii-handling-phylogenies-different-statistical-designs.md -------------------------------------------------------------------------------- /backup/part-iii-specific-models-studying-evolutionary-mechanisms.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/part-iii-specific-models-studying-evolutionary-mechanisms.md -------------------------------------------------------------------------------- /backup/part-introduction.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/backup/part-introduction.md -------------------------------------------------------------------------------- /online_practical_material/02-chapter.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/02-chapter.md -------------------------------------------------------------------------------- /online_practical_material/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/README.md -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/ch10_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 10. 2 | -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-1.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-10.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-11.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-12.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-4.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-5.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-6.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-7.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-8.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch10/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch10/unnamed-chunk-9.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch11/ch11_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 11. 2 | -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch11/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch11/unnamed-chunk-1.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch11/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch11/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch11/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch11/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch12/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch12/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch12/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch12/unnamed-chunk-4.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch12/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch12/unnamed-chunk-7.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch12/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch12/unnamed-chunk-9.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch13/unnamed-chunk-15.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch13/unnamed-chunk-15.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch13/unnamed-chunk-16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch13/unnamed-chunk-16.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch17/image001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch17/image001.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/ch2_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 2. 2 | -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-10.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-11.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-17.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-17.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-181.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-181.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-182.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-182.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-20.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-221.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-221.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-222.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-222.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-223.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-223.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-41.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-41.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-42.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-42.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-61.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-62.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-63.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-64.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-7.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch2/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch2/unnamed-chunk-9.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch21/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch21/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch21/unnamed-chunk-31.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch21/unnamed-chunk-31.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch21/unnamed-chunk-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch21/unnamed-chunk-32.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch21/unnamed-chunk-33.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch21/unnamed-chunk-33.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch21/unnamed-chunk-34.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch21/unnamed-chunk-34.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch21/unnamed-chunk-35.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch21/unnamed-chunk-35.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-10.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-11.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-13.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-13.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-14.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-14.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-17.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-17.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-181.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-181.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-182.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-182.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-20.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-221.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-221.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-222.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-222.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-223.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-223.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-41.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-41.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-42.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-42.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-6.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-61.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-62.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-63.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-64.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-7.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-8.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch22/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch22/unnamed-chunk-9.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/ch4_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 4. 2 | -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-1.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-10.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-11.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-12.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-4.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-5.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-6.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-7.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-8.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch4/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch4/unnamed-chunk-9.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch5/ch5_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 5. 2 | -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch5/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch5/unnamed-chunk-1.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch5/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch5/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch5/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch5/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch5/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch5/unnamed-chunk-4.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch5/unnamed-chunk-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch5/unnamed-chunk-5.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch5/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch5/unnamed-chunk-6.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/ch6_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 6. 2 | -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-1.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-31.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-31.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-32.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-33.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-33.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-34.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-34.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-35.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-35.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-36.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-36.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-61.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-62.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-63.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch6/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch6/unnamed-chunk-64.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch7/ch7_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 7. 2 | -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch7/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch7/unnamed-chunk-1.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch7/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch7/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch7/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch7/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch7/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch7/unnamed-chunk-4.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch7/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch7/unnamed-chunk-6.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch8/ch8_figures.md: -------------------------------------------------------------------------------- 1 | Figures for Chapter 8. 2 | -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch8/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch8/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch8/unnamed-chunk-36.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch8/unnamed-chunk-36.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch8/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch8/unnamed-chunk-4.png -------------------------------------------------------------------------------- /online_practical_material/additional_files/ch8/unnamed-chunk-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/additional_files/ch8/unnamed-chunk-5.png -------------------------------------------------------------------------------- /online_practical_material/data_files/ch10/Primates.trees: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch10/Primates.trees -------------------------------------------------------------------------------- /online_practical_material/data_files/ch10/Primates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch10/Primates.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch10/ch10_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 10. 2 | -------------------------------------------------------------------------------- /online_practical_material/data_files/ch11/ch11_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 11. 2 | -------------------------------------------------------------------------------- /online_practical_material/data_files/ch11/data_effect.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch11/data_effect.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch11/data_pois.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch11/data_pois.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch11/data_pois_missing.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch11/data_pois_missing.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch11/data_repeat.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch11/data_repeat.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch11/data_simple.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch11/data_simple.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch11/phylo.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch11/phylo.nex -------------------------------------------------------------------------------- /online_practical_material/data_files/ch12/10kTrees_Primates.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch12/10kTrees_Primates.nex -------------------------------------------------------------------------------- /online_practical_material/data_files/ch12/consensusTre_Primates.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch12/consensusTre_Primates.nex -------------------------------------------------------------------------------- /online_practical_material/data_files/ch12/primate_data.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch12/primate_data.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch12/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch12/primate_spec.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch12/primate_tree.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch12/primate_tree.nex -------------------------------------------------------------------------------- /online_practical_material/data_files/ch17/ABC_PCM.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch17/ABC_PCM.c -------------------------------------------------------------------------------- /online_practical_material/data_files/ch19/figures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch19/figures.R -------------------------------------------------------------------------------- /online_practical_material/data_files/ch19/functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch19/functions.R -------------------------------------------------------------------------------- /online_practical_material/data_files/ch19/metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch19/metrics.R -------------------------------------------------------------------------------- /online_practical_material/data_files/ch19/pglmm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch19/pglmm.R -------------------------------------------------------------------------------- /online_practical_material/data_files/ch19/tables.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch19/tables.pdf -------------------------------------------------------------------------------- /online_practical_material/data_files/ch2/Bird_tree5.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch2/Bird_tree5.nex -------------------------------------------------------------------------------- /online_practical_material/data_files/ch2/Bird_tree7.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch2/Bird_tree7.tre -------------------------------------------------------------------------------- /online_practical_material/data_files/ch2/bird_trees.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch2/bird_trees.tre -------------------------------------------------------------------------------- /online_practical_material/data_files/ch2/ch2_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 2. 2 | -------------------------------------------------------------------------------- /online_practical_material/data_files/ch2/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch2/primate_spec.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch2/primate_tree.phy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch2/primate_tree.phy -------------------------------------------------------------------------------- /online_practical_material/data_files/ch21/BayesModelS_v22.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch21/BayesModelS_v22.R -------------------------------------------------------------------------------- /online_practical_material/data_files/ch21/e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch21/e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch21/e.dataIMI_corrected.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch21/e.dataIMI_corrected.csv -------------------------------------------------------------------------------- /online_practical_material/data_files/ch4/Centrarchidae.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch4/Centrarchidae.tre -------------------------------------------------------------------------------- /online_practical_material/data_files/ch4/anole.data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch4/anole.data.csv -------------------------------------------------------------------------------- /online_practical_material/data_files/ch4/ch4_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 4. 2 | -------------------------------------------------------------------------------- /online_practical_material/data_files/ch4/elopomorph.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch4/elopomorph.csv -------------------------------------------------------------------------------- /online_practical_material/data_files/ch4/elopomorph.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch4/elopomorph.tre -------------------------------------------------------------------------------- /online_practical_material/data_files/ch5/ch5_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 5. 2 | -------------------------------------------------------------------------------- /online_practical_material/data_files/ch5/vcv2phylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch5/vcv2phylo.R -------------------------------------------------------------------------------- /online_practical_material/data_files/ch6/ch6_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 6. 2 | -------------------------------------------------------------------------------- /online_practical_material/data_files/ch6/covariates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch6/covariates.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch6/fict_phylo.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch6/fict_phylo.nex -------------------------------------------------------------------------------- /online_practical_material/data_files/ch6/pgls_check_fncs.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch6/pgls_check_fncs.r -------------------------------------------------------------------------------- /online_practical_material/data_files/ch7/GLSME.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch7/GLSME.R -------------------------------------------------------------------------------- /online_practical_material/data_files/ch7/ch7_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 7. 2 | -------------------------------------------------------------------------------- /online_practical_material/data_files/ch7/primate_ind.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch7/primate_ind.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch7/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch7/primate_spec.txt -------------------------------------------------------------------------------- /online_practical_material/data_files/ch7/primate_tree.phy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch7/primate_tree.phy -------------------------------------------------------------------------------- /online_practical_material/data_files/ch8/ch8_data.md: -------------------------------------------------------------------------------- 1 | Data files for Chapter 8. 2 | -------------------------------------------------------------------------------- /online_practical_material/data_files/ch8/rhino.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch8/rhino.csv -------------------------------------------------------------------------------- /online_practical_material/data_files/ch8/rhino.tree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch8/rhino.tree -------------------------------------------------------------------------------- /online_practical_material/data_files/ch8/storks.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/data_files/ch8/storks.csv -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-10-keeping-updated-bayesian-approaches-phylogenetic-comparative-methods-focus-markov-chain-models-discrete-character-evolution.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-11-1-simple-model-mcmcglmm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-11-1-simple-model-mcmcglmm.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-11-2-multiple-measurements-model-mcmcglmm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-11-2-multiple-measurements-model-mcmcglmm.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-11-3-example-meta-analysis-fishers-transformation-r-zr.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-11-3-example-meta-analysis-fishers-transformation-r-zr.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-11-4-example-non-gaussian-trait-using-count-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-11-4-example-non-gaussian-trait-using-count-data.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-11-bibliography.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-11-bibliography.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-11-example-mar-comparative-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-11-example-mar-comparative-data.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-12-1-evolutionary-models-different-combinations-predictors.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-12-1-evolutionary-models-different-combinations-predictors.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-12-2-dealing-phylogenetic-uncertainty-inference-across-models-considering-different-phylogenetic-hypotheses.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-12-2-dealing-phylogenetic-uncertainty-inference-across-models-considering-different-phylogenetic-hypotheses.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-12-3-playing-statistical-weights-adjusting-omega-parameter.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-12-3-playing-statistical-weights-adjusting-omega-parameter.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-12-4-multimodel-inference-exploring-multidimensional-parameter-space-simultaneously-varying-lambda-omega.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-12-4-multimodel-inference-exploring-multidimensional-parameter-space-simultaneously-varying-lambda-omega.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-13-1-trees.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-13-1-trees.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-13-2-traits.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-13-2-traits.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-13-3-trees-traits.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-13-3-trees-traits.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-17-1-brief-description-program-code.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-17-1-brief-description-program-code.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-19-1-calculating-community-phylogenetic-metrics-opm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-19-1-calculating-community-phylogenetic-metrics-opm.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-2-1-exercises-building-manipulating-phylogenetic-trees.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-2-1-exercises-building-manipulating-phylogenetic-trees.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-21-1-exercises-analyses-displaying-results.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-21-1-exercises-analyses-displaying-results.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-22-1-example-time-scaling-using-r-package-paleotree.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-22-1-example-time-scaling-using-r-package-paleotree.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-4-1-codes-used-produce-twelve-figures-chapter.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-4-1-codes-used-produce-twelve-figures-chapter.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-6-1exercises-testing-assumptions-statistical-issues-framework-phylogenetic-generalized-least-squares.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-6-1exercises-testing-assumptions-statistical-issues-framework-phylogenetic-generalized-least-squares.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-7-1-repeatability-opm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-7-1-repeatability-opm.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-7-2-data-opm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-7-2-data-opm.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-7-3-weighted-regr-opm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-7-3-weighted-regr-opm.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-7-4-univariate-opm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-7-4-univariate-opm.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-7-5-bivariate-opm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-7-5-bivariate-opm.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-8-1-baby-delivering-storks-example.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-8-1-baby-delivering-storks-example.md -------------------------------------------------------------------------------- /online_practical_material/exercises_and_tutorials/chapter-8-2-step-step-guide-phylogenetic-path-analysis-using-d-sep-method-rhinograds-example.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/exercises_and_tutorials/chapter-8-2-step-step-guide-phylogenetic-path-analysis-using-d-sep-method-rhinograds-example.md -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter10_OPM/OPM_chap10.doc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter10_OPM/OPM_chap10.doc -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter10_OPM/OPM_chap10.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter10_OPM/OPM_chap10.pdf -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter10_OPM/Primates.trees: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter10_OPM/Primates.trees -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter10_OPM/Primates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter10_OPM/Primates.txt -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/1_simple.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/1_simple.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/2_multi.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/2_multi.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/3_fisher.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/3_fisher.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/4_nongaussian.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/4_nongaussian.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/5_missing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/5_missing.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/VCV.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/VCV.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/biblio.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/biblio.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/data.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/data.zip -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/fixed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/fixed.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/funnel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/funnel.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img1.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img10.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img11.old: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img11.png: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img12.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img13.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img13.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img14.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img14.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img15.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img15.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img16.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img17.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img17.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img2.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img3.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img4.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img5.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img6.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/img7.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img8.old: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img8.png: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img9.old: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/img9.png: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/internals.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/internals.pl -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/labels.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/labels.pl -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/opm.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/opm.css -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter11_OPM/opm.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter11_OPM/opm.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/1_multi_predictors_OUT.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/1_multi_predictors_OUT.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/1_multi_predictors_OUT_corr.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/1_multi_predictors_OUT_corr.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/2_phylo_uncertainity_OUT.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/2_phylo_uncertainity_OUT.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/3_weights_OUT.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/3_weights_OUT.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/4_weight&lambda_OUT.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/4_weight&lambda_OUT.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/download/10kTrees_Primates.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/download/10kTrees_Primates.nex -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/download/consensusTre_Primates.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/download/consensusTre_Primates.nex -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/download/primate_data.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/download/primate_data.txt -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/download/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/download/primate_spec.txt -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/download/primate_tree.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/download/primate_tree.nex -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/figure/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/figure/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/figure/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/figure/unnamed-chunk-4.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/figure/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/figure/unnamed-chunk-7.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter12_OPM/figure/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter12_OPM/figure/unnamed-chunk-9.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter13_OPM/1_Trees.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter13_OPM/1_Trees.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter13_OPM/2_Traits.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter13_OPM/2_Traits.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter13_OPM/3_Trees_and_traits.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter13_OPM/3_Trees_and_traits.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter13_OPM/figure/unnamed-chunk-15.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter13_OPM/figure/unnamed-chunk-15.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter13_OPM/figure/unnamed-chunk-16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter13_OPM/figure/unnamed-chunk-16.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter17_OPM/download/ABC_PCM.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter17_OPM/download/ABC_PCM.c -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter17_OPM/figure/image001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter17_OPM/figure/image001.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter17_OPM/html_frame_chap17.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter17_OPM/html_frame_chap17.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter19_OPM/1_Calculating_community_phylogenetic_metrics_OPM.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter19_OPM/1_Calculating_community_phylogenetic_metrics_OPM.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter19_OPM/download/figures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter19_OPM/download/figures.R -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter19_OPM/download/functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter19_OPM/download/functions.R -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter19_OPM/download/metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter19_OPM/download/metrics.R -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter19_OPM/download/pglmm.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter19_OPM/download/pglmm.R -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter19_OPM/download/tables.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter19_OPM/download/tables.pdf -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/download/BayesModelS_v22.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/download/BayesModelS_v22.R -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/download/e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/download/e.IMI.TreeBlock_10kTrees_Primates_Version3.nex.txt -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/download/e.dataIMI_corrected.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/download/e.dataIMI_corrected.csv -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/Thumbs.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/Thumbs.db -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-31.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-31.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-32.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-33.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-33.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-34.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-34.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-35.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/figures for IMI OPM/unnamed-chunk-35.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter21_OPM/html_frame_chap21.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter21_OPM/html_frame_chap21.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-10.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-11.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-13.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-13.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-14.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-14.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-17.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-17.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-181.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-181.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-182.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-182.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-20.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-221.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-221.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-222.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-222.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-223.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-223.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-41.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-41.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-42.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-42.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-6.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-61.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-62.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-63.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-64.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-7.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-8.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/figure/unnamed-chunk-9.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter22_OPM/html_frame_chap22_OUT.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter22_OPM/html_frame_chap22_OUT.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/download/bird_trees.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/download/bird_trees.tre -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/download/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/download/primate_spec.txt -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/download/primate_tree.phy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/download/primate_tree.phy -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-10.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-11.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-17.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-17.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-181.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-181.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-182.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-182.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-20.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-221.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-221.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-222.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-222.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-223.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-223.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-41.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-41.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-42.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-42.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-61.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-62.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-63.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-64.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-7.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/figure/unnamed-chunk-9.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter2_OPM/html_frame_chap2_OUT.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter2_OPM/html_frame_chap2_OUT.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter4_OPM/Centrarchidae.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter4_OPM/Centrarchidae.tre -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter4_OPM/Revell_Chapter4_OPM_mod1.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter4_OPM/Revell_Chapter4_OPM_mod1.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter4_OPM/anole.data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter4_OPM/anole.data.csv -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter4_OPM/elopomorph.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter4_OPM/elopomorph.csv -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter4_OPM/elopomorph.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter4_OPM/elopomorph.tre -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter5_OPM/OPM_chap5.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter5_OPM/OPM_chap5.pdf -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter5_OPM/download/vcv2phylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter5_OPM/download/vcv2phylo.R -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/download/covariates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/download/covariates.txt -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/download/fict_phylo.nex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/download/fict_phylo.nex -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/download/pgls_check_fncs.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/download/pgls_check_fncs.r -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-1.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-31.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-31.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-32.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-33.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-33.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-34.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-34.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-35.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-35.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-36.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-36.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-61.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-62.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-63.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/figure/unnamed-chunk-64.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter6_OPM/html_frame_chap6.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter6_OPM/html_frame_chap6.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/1_repeatability_OPM.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/1_repeatability_OPM.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/2_data_OPM.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/2_data_OPM.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/3_weighted_regr_OPM.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/3_weighted_regr_OPM.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/4_univariate_OPM.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/4_univariate_OPM.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/5_bivariate_OPM.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/5_bivariate_OPM.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/download/GLSME.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/download/GLSME.R -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/download/primate_ind.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/download/primate_ind.txt -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/download/primate_spec.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/download/primate_spec.txt -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/download/primate_tree.phy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/download/primate_tree.phy -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-1.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-2.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-3.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-4.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter7_OPM/figure/unnamed-chunk-6.png -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter8_OPM/Rhinograds example.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter8_OPM/Rhinograds example.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter8_OPM/Storks example.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter8_OPM/Storks example.html -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter8_OPM/download/rhino.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter8_OPM/download/rhino.csv -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter8_OPM/download/rhino.tree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter8_OPM/download/rhino.tree -------------------------------------------------------------------------------- /online_practical_material/iframe/Chapter8_OPM/download/storks.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/iframe/Chapter8_OPM/download/storks.csv -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-11.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-11.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-12.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-12.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-13.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-13.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-17.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-17.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-19.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-19.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-21.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-21.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-22.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-22.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-4.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-4.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-5.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-5.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-6.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-6.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-7.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-7.md -------------------------------------------------------------------------------- /online_practical_material/online-practical-material-chapter-8.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MPCMEvolution/MPCMArchive/HEAD/online_practical_material/online-practical-material-chapter-8.md --------------------------------------------------------------------------------