├── .hugo_build.lock ├── themes └── hugo-theme-learn │ ├── .gitignore │ ├── layouts │ ├── partials │ │ ├── custom-comments.html │ │ ├── toc.html │ │ ├── custom-header.html │ │ ├── tags.html │ │ ├── menu-footer.html │ │ ├── custom-footer.html │ │ ├── meta.html │ │ └── search.html │ ├── shortcodes │ │ ├── notice.html │ │ ├── mermaid.html │ │ ├── siteparam.html │ │ ├── tab.html │ │ ├── ref.html │ │ ├── relref.html │ │ ├── button.html │ │ ├── expand.html │ │ ├── tabs.html │ │ └── attachments.html │ ├── _default │ │ ├── single.html │ │ └── list.html │ ├── index.json │ └── index.html │ ├── archetypes │ ├── default.md │ └── chapter.md │ ├── static │ ├── fonts │ │ ├── Inconsolata.eot │ │ ├── Inconsolata.ttf │ │ ├── Inconsolata.woff │ │ ├── Work_Sans_200.eot │ │ ├── Work_Sans_200.ttf │ │ ├── Work_Sans_200.woff │ │ ├── Work_Sans_300.eot │ │ ├── Work_Sans_300.ttf │ │ ├── Work_Sans_300.woff │ │ ├── Work_Sans_500.eot │ │ ├── Work_Sans_500.ttf │ │ ├── Work_Sans_500.woff │ │ ├── Work_Sans_200.woff2 │ │ ├── Work_Sans_300.woff2 │ │ ├── Work_Sans_500.woff2 │ │ ├── Novecentosanswide-Normal-webfont.eot │ │ ├── Novecentosanswide-Normal-webfont.ttf │ │ ├── Novecentosanswide-Normal-webfont.woff │ │ ├── Novecentosanswide-Normal-webfont.woff2 │ │ ├── Novecentosanswide-UltraLight-webfont.eot │ │ ├── Novecentosanswide-UltraLight-webfont.ttf │ │ ├── Novecentosanswide-UltraLight-webfont.woff │ │ └── Novecentosanswide-UltraLight-webfont.woff2 │ ├── images │ │ ├── gopher-404.jpg │ │ └── clippy.svg │ ├── webfonts │ │ ├── fa-brands-400.eot │ │ ├── fa-brands-400.ttf │ │ ├── fa-solid-900.eot │ │ ├── fa-solid-900.ttf │ │ ├── fa-solid-900.woff │ │ ├── fa-brands-400.woff │ │ ├── fa-brands-400.woff2 │ │ ├── fa-regular-400.eot │ │ ├── fa-regular-400.ttf │ │ ├── fa-regular-400.woff │ │ ├── fa-regular-400.woff2 │ │ └── fa-solid-900.woff2 │ └── css │ │ ├── tabs.css │ │ ├── auto-complete.css │ │ └── tags.css │ ├── .editorconfig │ ├── i18n │ ├── zh-cn.toml │ ├── ja.toml │ ├── ar.toml │ ├── en.toml │ ├── es.toml │ ├── tr.toml │ ├── pt.toml │ ├── hi.toml │ ├── de.toml │ ├── id.toml │ ├── nl.toml │ ├── ru.toml │ └── fr.toml │ ├── wercker.yml │ ├── .grenrc.yml │ ├── netlify.toml │ ├── theme.toml │ └── LICENSE.md ├── .Rbuildignore ├── layouts ├── partials │ ├── favicon.html │ ├── logo.html │ ├── custom-footer.html │ └── menu-footer.html └── shortcodes │ ├── blogdown │ └── postref.html │ └── ghcontributors.html ├── static ├── images │ ├── favicon.png │ ├── E_C_01-01.png │ ├── showcase │ │ ├── tat.png │ │ ├── tshark_dev.png │ │ └── inteliver_docs.png │ ├── hexsticker_EC.png │ └── hex_sticker.R ├── datasets │ ├── multiband.tif │ ├── Landsat_TIR.tif │ ├── Cairns_Mangroves_30m.tif │ ├── River_pH.csv │ ├── Greenhouse.csv │ ├── Turtles.csv │ ├── Pilot.csv │ ├── Bac.factors.csv │ ├── tree_curtis1998.tre │ ├── Leafshape.csv │ ├── Interaction_plots.csv │ ├── Mink.csv │ ├── ReefFish.csv │ ├── Crabs.csv │ ├── Prawns_MR.csv │ ├── Weather_vars.csv │ ├── Sessile.csv │ ├── Geo_data.csv │ └── Estuaries.csv ├── rmarkdown-libs │ ├── leaflet │ │ └── images │ │ │ ├── layers.png │ │ │ ├── layers-2x.png │ │ │ └── marker-shadow.png │ ├── rstudio_leaflet │ │ ├── images │ │ │ └── 1px.png │ │ └── rstudio_leaflet.css │ ├── leaflet-minimap │ │ ├── images │ │ │ └── toggle.png │ │ └── Control.MiniMap.min.css │ ├── header-attrs │ │ └── header-attrs.js │ ├── leaflet-markercluster │ │ ├── package.json │ │ ├── MarkerCluster.css │ │ ├── MIT-LICENCE.txt │ │ └── MarkerCluster.Default.css │ └── leafletfix │ │ └── leafletfix.css ├── Graphics │ ├── ggplot │ │ ├── _index_files │ │ │ └── figure-html │ │ │ │ └── unnamed-chunk-1-1.png │ │ ├── ggplot-barplot │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ └── unnamed-chunk-4-1.png │ │ ├── ggplot-basics │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ ├── unnamed-chunk-7-1.png │ │ │ │ ├── unnamed-chunk-8-1.png │ │ │ │ ├── unnamed-chunk-9-1.png │ │ │ │ └── unnamed-chunk-9-2.png │ │ ├── ggplot-labels │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-11-1.png │ │ │ │ ├── unnamed-chunk-4-1.png │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ ├── unnamed-chunk-7-1.png │ │ │ │ └── unnamed-chunk-9-1.png │ │ ├── ggplot-appearance │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-7-1.png │ │ │ │ ├── unnamed-chunk-8-1.png │ │ │ │ ├── unnamed-chunk-9-1.png │ │ │ │ ├── unnamed-chunk-10-1.png │ │ │ │ ├── unnamed-chunk-11-1.png │ │ │ │ ├── unnamed-chunk-12-1.png │ │ │ │ ├── unnamed-chunk-13-1.png │ │ │ │ └── unnamed-chunk-14-1.png │ │ └── ggplot-colour-shapes │ │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-14-2.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-15-2.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-16-2.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-18-2.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ └── unnamed-chunk-24-1.png │ ├── basic-plotting │ │ ├── _index_files │ │ │ └── figure-html │ │ │ │ └── unnamed-chunk-1-1.png │ │ ├── one-continuous │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ ├── unnamed-chunk-3-1.png │ │ │ │ ├── unnamed-chunk-4-1.png │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-5-2.png │ │ │ │ └── unnamed-chunk-7-1.png │ │ ├── two-continuous │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ ├── unnamed-chunk-4-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ ├── unnamed-chunk-7-1.png │ │ │ │ └── unnamed-chunk-8-1.png │ │ └── one-continuous-one-factor │ │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── multivariate-vis │ │ ├── _index_files │ │ │ └── figure-html │ │ │ │ └── unnamed-chunk-1-1.png │ │ ├── mds │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-8-1.png │ │ │ │ └── unnamed-chunk-9-1.png │ │ ├── pca │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-7-1.png │ │ │ │ └── unnamed-chunk-9-1.png │ │ ├── heatmaps │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-11-1.png │ │ │ │ ├── unnamed-chunk-12-1.png │ │ │ │ ├── unnamed-chunk-13-1.png │ │ │ │ ├── unnamed-chunk-14-1.png │ │ │ │ ├── unnamed-chunk-17-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ ├── unnamed-chunk-7-1.png │ │ │ │ ├── unnamed-chunk-8-1.png │ │ │ │ └── unnamed-chunk-9-1.png │ │ └── cluster-analysis │ │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ └── spatial-vis │ │ ├── simple-maps │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-8-1.png │ │ └── basic-raster │ │ └── _index_files │ │ └── figure-html │ │ ├── unnamed-chunk-22-1.png │ │ ├── unnamed-chunk-29-1.png │ │ ├── unnamed-chunk-37-1.png │ │ └── unnamed-chunk-38-1.png ├── Statistics │ ├── gams │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ └── unnamed-chunk-6-1.png │ ├── mvabund │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── glms │ │ ├── glm-1 │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-4-1.png │ │ │ │ └── unnamed-chunk-6-1.png │ │ └── glm-2 │ │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── time-series │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── linear-models │ │ ├── _index_files │ │ │ └── figure-html │ │ │ │ └── unnamed-chunk-1-1.png │ │ ├── interactions │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ └── unnamed-chunk-2-1.png │ │ ├── anova │ │ │ ├── anova-nested │ │ │ │ └── _index_files │ │ │ │ │ └── figure-html │ │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ │ ├── unnamed-chunk-2-2.png │ │ │ │ │ └── unnamed-chunk-3-1.png │ │ │ ├── anova-single │ │ │ │ └── _index_files │ │ │ │ │ └── figure-html │ │ │ │ │ ├── unnamed-chunk-9-1.png │ │ │ │ │ ├── unnamed-chunk-10-1.png │ │ │ │ │ └── unnamed-chunk-11-1.png │ │ │ └── anova-factorial │ │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-7-1.png │ │ │ │ ├── unnamed-chunk-8-1.png │ │ │ │ ├── unnamed-chunk-9-1.png │ │ │ │ └── unnamed-chunk-10-1.png │ │ └── linear-regression │ │ │ ├── _index_files │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ └── unnamed-chunk-7-1.png │ │ │ └── interpret-lm-coeffs │ │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── power-analysis │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-7-1.png │ ├── meta-analysis │ │ ├── meta-analysis-1 │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── forest-1.png │ │ │ │ └── forest2-1.png │ │ ├── meta-analysis-2 │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── funnel-1.png │ │ │ │ └── trimfill-1.png │ │ └── meta-analysis-3 │ │ │ └── _index_files │ │ │ └── figure-html │ │ │ └── prep1-1.png │ ├── t-tests │ │ ├── paired-t-test │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ └── unnamed-chunk-6-1.png │ │ ├── one-sample-t-test │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ └── unnamed-chunk-5-2.png │ │ └── two-sample-t-test │ │ │ └── _index_files │ │ │ └── figure-html │ │ │ └── unnamed-chunk-5-1.png │ ├── categorical │ │ ├── goodness-of-fit │ │ │ └── _index_files │ │ │ │ └── figure-html │ │ │ │ └── unnamed-chunk-8-1.png │ │ └── contingency-tables │ │ │ └── _index_files │ │ │ └── figure-html │ │ │ └── unnamed-chunk-10-1.png │ └── mixed-models │ │ ├── mixed-model-1 │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ └── unnamed-chunk-6-1.png │ │ ├── mixed-model-2 │ │ └── _index_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ └── mixed-model-3 │ │ └── _index_files │ │ └── figure-html │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-12-1.png │ │ ├── unnamed-chunk-13-1.png │ │ └── unnamed-chunk-7-1.png ├── Data-Manipulation │ └── summarising-data │ │ └── _index_files │ │ └── figure-html │ │ └── unnamed-chunk-15-1.png └── getting-started-with-r │ └── rstudio-notebooks │ └── _index_files │ └── figure-html │ └── unnamed-chunk-8-1.png ├── content ├── Images │ └── DSC06364.jpg ├── Statistics │ ├── gams │ │ └── Mauna_Loa.jpg │ ├── mvabund │ │ ├── MDS_image.jpg │ │ └── Rick-Astley.jpg │ ├── glms │ │ ├── glm-1 │ │ │ ├── GLM1_binary_image.jpg │ │ │ └── Crabs.csv │ │ ├── glm-2 │ │ │ └── GLM2_counts_image.jpg │ │ ├── interpret-glm-coeffs │ │ │ └── glm_coefficients_image.jpg │ │ ├── _index.rmd │ │ └── _index.html │ ├── time-series │ │ ├── Forecasting_image.jpg │ │ └── Forecasting_image3.jpg │ ├── meta-analysis │ │ ├── images │ │ │ └── 4666102_orig.jpg │ │ ├── meta-analysis-2 │ │ │ ├── Fixed.png │ │ │ └── Random.png │ │ ├── meta-analysis-3 │ │ │ ├── Legend.png │ │ │ ├── Multi.png │ │ │ └── tree_curtis1998.tre │ │ ├── meta-analysis-1 │ │ │ ├── 4666102_orig.jpg │ │ │ └── Linear_regression_image.jpg │ │ ├── _index.rmd │ │ └── _index.html │ ├── mixed-models │ │ ├── Mixed_models_intro_image.jpg │ │ ├── mixed-model-1 │ │ │ └── Mixed_models_1_image.jpg │ │ ├── mixed-model-2 │ │ │ └── Mixed_models_2_image.jpg │ │ ├── mixed-model-3 │ │ │ └── Mixed_models_3_image.jpg │ │ ├── _index.rmd │ │ └── _index.html │ ├── power-analysis │ │ ├── Mixed_models_1_image.jpg │ │ └── Pilot.csv │ ├── t-tests │ │ ├── paired-t-test │ │ │ ├── Paired_t_test_image.jpg │ │ │ └── Greenhouse.csv │ │ ├── one-sample-t-test │ │ │ └── One_sample_t_test_image.png │ │ ├── two-sample-t-test │ │ │ ├── Independent_samples_t_test_image.jpg │ │ │ └── River_pH.csv │ │ ├── _index.rmd │ │ └── _index.html │ ├── linear-models │ │ ├── interactions │ │ │ ├── Interactions_image.jpg │ │ │ └── Interaction_plots.csv │ │ ├── anova │ │ │ ├── anova-factorial │ │ │ │ ├── ANOVA_factorial_image.JPG │ │ │ │ └── Sessile.csv │ │ │ ├── anova-nested │ │ │ │ ├── ANOVA_nested_method_image.png │ │ │ │ └── Mink.csv │ │ │ ├── anova-single │ │ │ │ ├── ANOVA_single_factor_image.png │ │ │ │ └── Turtles.csv │ │ │ ├── _index.rmd │ │ │ └── _index.html │ │ ├── linear-regression │ │ │ ├── Linear_regression_image.jpg │ │ │ └── interpret-lm-coeffs │ │ │ │ └── Linear_regression_image.jpg │ │ ├── _index.html │ │ └── _index.rmd │ └── categorical │ │ ├── fishers-exact │ │ ├── Fishers_exact_test_Q1_image.jpg │ │ └── Fishers_exact_test_Q2_image.jpg │ │ ├── goodness-of-fit │ │ └── Goodness_of_fit_test_image.jpg │ │ ├── contingency-tables │ │ └── Contingency_tables_image.jpg │ │ ├── _index.rmd │ │ └── _index.html ├── Coding-Skills │ ├── Coding_image.jpg │ ├── asking-code-questions │ │ └── stack.png │ ├── loops │ │ └── Subsetting_data_image.jpg │ ├── writing-functions │ │ └── Functions_image.JPG │ ├── version-control │ │ ├── Version_control_Fig1.png │ │ ├── Version_control_Fig3.png │ │ ├── Version_control_Fig4.png │ │ ├── Version_control_Fig5.png │ │ ├── Version_control_Fig1b.png │ │ └── Version_control_Fig31.png │ ├── good-practice │ │ └── Good_script_practice_image.jpg │ ├── _index.Rmd │ └── _index.html ├── Graphics │ ├── images │ │ ├── Oz_grazing.png │ │ └── LavenderGraph.png │ ├── ggplot │ │ ├── ggplot-colour-shapes │ │ │ ├── pch.png │ │ │ ├── RColourBrewer_palette.png │ │ │ └── ggplot1_basics_image.JPG │ │ ├── ggplot-basics │ │ │ └── ggplot1_basics_image.JPG │ │ ├── ggplot-labels │ │ │ └── ggplot1_basics_image.JPG │ │ ├── ggplot-barplot │ │ │ └── ggplot1_basics_image.JPG │ │ └── ggplot-appearance │ │ │ └── ggplot1_basics_image.JPG │ ├── multivariate-vis │ │ ├── mds │ │ │ └── MDS_image.jpg │ │ ├── pca │ │ │ ├── PCA_image.png │ │ │ └── Leafshape.csv │ │ ├── heatmaps │ │ │ ├── Heatmaps_image.png │ │ │ ├── SpeciesDiffs.RData │ │ │ └── Bac.factors.csv │ │ ├── cluster-analysis │ │ │ ├── HS-metals.xlsx │ │ │ ├── Cluster_analysis_image.jpg │ │ │ ├── Cluster_analysis_image2.jpg │ │ │ └── Cluster_analysis_method_image2.png │ │ └── _index.html │ ├── spatial-vis │ │ ├── simple-maps │ │ │ ├── basemap.rds │ │ │ ├── Pres_basemap.rds │ │ │ └── Pub_basemap.rds │ │ ├── basic-raster │ │ │ ├── multiband.tif │ │ │ ├── Landsat_TIR.tif │ │ │ ├── teaser_plot.png │ │ │ ├── SST_feb_2013.img │ │ │ ├── SST_feb_mean.img │ │ │ └── Cairns_Mangroves_30m.tif │ │ ├── images │ │ │ └── Visualising_spatial_data_intro_image.jpg │ │ ├── _index.rmd │ │ └── _index.html │ ├── basic-plotting │ │ ├── two-continuous │ │ │ ├── pch.png │ │ │ └── Two_continuous_variables_image.jpg │ │ ├── one-continuous │ │ │ └── Single_continuous_variable_image.jpg │ │ ├── one-continuous-one-factor │ │ │ ├── Single_continuous_vs_categorical_variable_image.jpg │ │ │ └── Prawns_MR.csv │ │ ├── _index.html │ │ └── _index.rmd │ ├── _index.rmd │ └── _index.html ├── Data-Manipulation │ ├── Data_entry_image.jpg │ ├── making-new-variables │ │ ├── MDS_image.jpg │ │ ├── Unite_image.jpg │ │ ├── Separate_image.jpg │ │ └── Making_new_variables_image.jpg │ ├── reshaping-data │ │ ├── Reshaping_data_image.jpg │ │ └── ReefFish.csv │ ├── subsetting-data │ │ ├── Subsetting_data_image.jpg │ │ ├── Subsetting_data_image1.jpg │ │ └── Subsetting_data_image2.jpg │ ├── combining-datasets │ │ ├── Combining_data_image.jpg │ │ ├── Weather_vars.csv │ │ └── Geo_data.csv │ ├── summarising-data │ │ └── Summarising_data_image.jpg │ └── _index.Rmd ├── getting-started-with-r │ ├── images │ │ └── Sampling.jpg │ ├── rstudio-notebooks │ │ ├── menu.png │ │ ├── Chunk1.png │ │ ├── Chunk2.png │ │ ├── Chunk3.png │ │ ├── Menu1.png │ │ ├── Menu2.png │ │ ├── Menu3.png │ │ ├── Menu4.png │ │ ├── Data_entry_image.jpg │ │ ├── Notebooks_image.jpg │ │ └── E_C_Logo_black_square.png │ ├── data-entry │ │ └── Data_entry_image.jpg │ ├── installing-r-rstudio │ │ ├── index.jpg │ │ ├── blue-125.png │ │ └── Installing_R_and_R_Studio_image.jpg │ ├── project-management │ │ ├── projects_new.png │ │ └── Basic_project_managment_image.jpg │ ├── importing-data │ │ └── Importing_data_image.JPG │ └── 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9 | indent_style = space 10 | trim_trailing_whitespace = true 11 | 12 | [*.js] 13 | insert_final_newline = true 14 | 15 | [*.md] 16 | trim_trailing_whitespace = false 17 | -------------------------------------------------------------------------------- /static/datasets/River_pH.csv: -------------------------------------------------------------------------------- 1 | River_name,pH 2 | A,8.968143 3 | A,9.11974 4 | A,9.413058 5 | A,8.665746 6 | A,9.937042 7 | A,8.280083 8 | A,7.864158 9 | A,7.509577 10 | A,9.181173 11 | A,7.676255 12 | B,6.670441 13 | B,5.828061 14 | B,6.840394 15 | B,6.860779 16 | B,5.892154 17 | B,7.422487 18 | B,6.563322 19 | B,5.993992 20 | B,5.326895 21 | B,6.687078 22 | -------------------------------------------------------------------------------- /static/images/hex_sticker.R: -------------------------------------------------------------------------------- 1 | remotes::install_github("GuangchuangYu/hexSticker") 2 | 3 | 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-------------------------------------------------------------------------------- 1 | River_name,pH 2 | A,8.968143 3 | A,9.11974 4 | A,9.413058 5 | A,8.665746 6 | A,9.937042 7 | A,8.280083 8 | A,7.864158 9 | A,7.509577 10 | A,9.181173 11 | A,7.676255 12 | B,6.670441 13 | B,5.828061 14 | B,6.840394 15 | B,6.860779 16 | B,5.892154 17 | B,7.422487 18 | B,6.563322 19 | B,5.993992 20 | B,5.326895 21 | B,6.687078 22 | -------------------------------------------------------------------------------- /content/Statistics/categorical/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 6 3 | title: "Categorical Data Analyses" 4 | output: html_document 5 | aliases: /categorical-data-analyses/ 6 | --- 7 | 8 | Some commonly used tests for contrasting the counts of observations across categorical variables. 9 | 10 | * [Goodness of fit tests](goodness-of-fit) 11 | * [Contingency tables](contingency-tables) 12 | -------------------------------------------------------------------------------- /static/datasets/Greenhouse.csv: -------------------------------------------------------------------------------- 1 | Treatment,Plant,Performance 2 | Shady,1,0.687 3 | Shady,2,0.651 4 | Shady,3,0.635 5 | Shady,4,0.611 6 | Shady,5,0.673 7 | Shady,6,0.646 8 | Shady,7,0.652 9 | Shady,8,0.668 10 | Shady,9,0.672 11 | Shady,10,0.671 12 | Sunny,1,0.884 13 | Sunny,2,0.871 14 | Sunny,3,0.802 15 | Sunny,4,0.860 16 | Sunny,5,0.836 17 | Sunny,6,0.813 18 | Sunny,7,0.845 19 | Sunny,8,0.882 20 | Sunny,9,0.821 21 | Sunny,10,0.837 22 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/_default/single.html: -------------------------------------------------------------------------------- 1 | {{ partial "header.html" . }} 2 | 3 | {{ .Content }} 4 | 5 | 11 | 12 | {{ partial "footer.html" . }} 13 | -------------------------------------------------------------------------------- /content/Statistics/t-tests/paired-t-test/Greenhouse.csv: -------------------------------------------------------------------------------- 1 | Treatment,Plant,Performance 2 | Shady,1,0.687 3 | Shady,2,0.651 4 | Shady,3,0.635 5 | Shady,4,0.611 6 | Shady,5,0.673 7 | Shady,6,0.646 8 | Shady,7,0.652 9 | Shady,8,0.668 10 | Shady,9,0.672 11 | Shady,10,0.671 12 | Sunny,1,0.884 13 | Sunny,2,0.871 14 | Sunny,3,0.802 15 | Sunny,4,0.860 16 | Sunny,5,0.836 17 | Sunny,6,0.813 18 | Sunny,7,0.845 19 | Sunny,8,0.882 20 | Sunny,9,0.821 21 | Sunny,10,0.837 22 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/shortcodes/tab.html: -------------------------------------------------------------------------------- 1 | {{ if .Parent }} 2 | {{ $name := trim (.Get "name") " " }} 3 | {{ if not (.Parent.Scratch.Get "tabs") }} 4 | {{ .Parent.Scratch.Set "tabs" slice }} 5 | {{ end }} 6 | {{ with .Inner }} 7 | {{ $.Parent.Scratch.Add "tabs" (dict "name" $name "content" . ) }} 8 | {{ end }} 9 | {{ else }} 10 | {{- errorf "[%s] %q: tab shortcode missing its parent" site.Language.Lang .Page.Path -}} 11 | {{ end}} 12 | 13 | -------------------------------------------------------------------------------- /content/Graphics/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Graphics' 3 | weight: 5 4 | output: html_document 5 | --- 6 | 7 | R has a very wide range of functions and packages for visualising data. 8 | 9 | These pages have a brief introduction to: 10 | 11 | * [Basic plotting in R](basic-plotting/) 12 | * [More advanced plotting with ggplot](ggplot/) 13 | * [Visualising multivariate data](multivariate-vis/) 14 | * [Visualising spatial data (incl. mapping)](spatial-vis/) 15 | 16 | 17 | -------------------------------------------------------------------------------- /static/datasets/Turtles.csv: -------------------------------------------------------------------------------- 1 | Temperature,Days 2 | 15,37 3 | 15,43 4 | 15,45 5 | 15,54 6 | 15,56 7 | 15,65 8 | 15,62 9 | 15,73 10 | 15,74 11 | 15,75 12 | 20,30 13 | 20,31 14 | 20,34 15 | 20,35 16 | 20,35 17 | 20,47 18 | 20,53 19 | 20,54 20 | 20,63 21 | 20,64 22 | 25,21 23 | 25,23 24 | 25,48 25 | 25,52 26 | 25,52 27 | 25,54 28 | 25,54 29 | 25,61 30 | 25,62 31 | 25,65 32 | 30,13 33 | 30,16 34 | 30,19 35 | 30,11 36 | 30,12 37 | 30,18 38 | 30,21 39 | 30,23 40 | 30,29 41 | 30,39 42 | -------------------------------------------------------------------------------- /static/datasets/Pilot.csv: -------------------------------------------------------------------------------- 1 | temperature,modification,site,abundance 2 | 0.33477576,1,a,18 3 | 0.95243299,1,a,244 4 | 0.69695788,1,a,91 5 | 0.74767863,1,b,121 6 | 0.18343303,1,b,15 7 | 0.58258472,1,b,67 8 | 0.51131205,2,c,118 9 | 0.96539435,2,c,862 10 | 0.44205297,2,c,98 11 | 0.71647069,2,d,331 12 | 0.27455116,2,d,48 13 | 0.31069592,2,d,68 14 | 0.5341597,3,e,452 15 | 0.4729186,3,e,371 16 | 0.19852921,3,e,125 17 | 0.08954998,3,f,97 18 | 0.46928952,3,f,465 19 | 0.67047484,3,f,1020 20 | -------------------------------------------------------------------------------- /content/Statistics/power-analysis/Pilot.csv: -------------------------------------------------------------------------------- 1 | temperature,modification,site,abundance 2 | 0.33477576,1,a,18 3 | 0.95243299,1,a,244 4 | 0.69695788,1,a,91 5 | 0.74767863,1,b,121 6 | 0.18343303,1,b,15 7 | 0.58258472,1,b,67 8 | 0.51131205,2,c,118 9 | 0.96539435,2,c,862 10 | 0.44205297,2,c,98 11 | 0.71647069,2,d,331 12 | 0.27455116,2,d,48 13 | 0.31069592,2,d,68 14 | 0.5341597,3,e,452 15 | 0.4729186,3,e,371 16 | 0.19852921,3,e,125 17 | 0.08954998,3,f,97 18 | 0.46928952,3,f,465 19 | 0.67047484,3,f,1020 20 | -------------------------------------------------------------------------------- /content/Statistics/linear-models/anova/anova-single/Turtles.csv: -------------------------------------------------------------------------------- 1 | Temperature,Days 2 | 15,37 3 | 15,43 4 | 15,45 5 | 15,54 6 | 15,56 7 | 15,65 8 | 15,62 9 | 15,73 10 | 15,74 11 | 15,75 12 | 20,30 13 | 20,31 14 | 20,34 15 | 20,35 16 | 20,35 17 | 20,47 18 | 20,53 19 | 20,54 20 | 20,63 21 | 20,64 22 | 25,21 23 | 25,23 24 | 25,48 25 | 25,52 26 | 25,52 27 | 25,54 28 | 25,54 29 | 25,61 30 | 25,62 31 | 25,65 32 | 30,13 33 | 30,16 34 | 30,19 35 | 30,11 36 | 30,12 37 | 30,18 38 | 30,21 39 | 30,23 40 | 30,29 41 | 30,39 42 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/index.json: -------------------------------------------------------------------------------- 1 | [{{ range $index, $page := .Site.Pages }} 2 | {{- if ne $page.Type "json" -}} 3 | {{- if and $index (gt $index 0) -}},{{- end }} 4 | { 5 | "uri": "{{ $page.Permalink }}", 6 | "title": "{{ htmlEscape $page.Title}}", 7 | "tags": [{{ range $tindex, $tag := $page.Params.tags }}{{ if $tindex }}, {{ end }}"{{ $tag| htmlEscape }}"{{ end }}], 8 | "description": "{{ htmlEscape .Description}}", 9 | "content": {{$page.Plain | jsonify}} 10 | } 11 | {{- end -}} 12 | {{- end -}}] -------------------------------------------------------------------------------- /content/Graphics/spatial-vis/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Spatial Data' 3 | weight: 5 4 | output: html_document 5 | aliases: /visualising-spatial-data/ 6 | --- 7 | 8 | R has a very wide range of functions and packages for visualising spatial data. This page will link to a series of tutorials for handling spatial data and making maps. 9 | 10 | * [Making simple maps with ggmap](simple-maps/) 11 | * [Making maps from shapefiles] 12 | * More soon... 13 | 14 | ![](images/Visualising_spatial_data_intro_image.jpg) 15 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/zh-cn.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "搜索..." 3 | 4 | [Clear-History] 5 | other = "清理历史记录" 6 | 7 | [Attachments-label] 8 | other = "附件" 9 | 10 | [title-404] 11 | other = "错误" 12 | 13 | [message-404] 14 | other = "哎哟。 看起来这个页面不存在 ¯\\_(ツ)_/¯。" 15 | 16 | [Go-to-homepage] 17 | other = "转到主页" 18 | 19 | [Edit-this-page] 20 | other = "编辑当前页" 21 | 22 | [Shortcuts-Title] 23 | other = "更多" 24 | 25 | [Expand-title] 26 | other = "展开" 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" 30 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/wercker.yml: -------------------------------------------------------------------------------- 1 | box: golang 2 | build: 3 | steps: 4 | # Gets the dependencies 5 | - script: 6 | name: get hugo 7 | code: | 8 | git clone https://github.com/gohugoio/hugo.git && cd hugo && go install 9 | # Sets the go workspace and places you package 10 | # at the right place in the workspace tree 11 | - setup-go-workspace 12 | # Build the project 13 | - script: 14 | name: build site 15 | code: | 16 | cd exampleSite && hugo -------------------------------------------------------------------------------- /content/Statistics/t-tests/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 1 3 | title: "T-tests" 4 | output: html_document 5 | aliases: /t-tests/ 6 | --- 7 | 8 | Some simple hypothesis tests with the t statistic: 9 | 10 | * [One sample t tests](one-sample-t-test) to contrasting a single sample parameter to a population parameter 11 | * [Independent samples](two-sample-t-test) t tests to contrast the means of two samples 12 | * [Paired t-tests](paired-t-test) to contrast two groups of values where each pair is measured from the same object. 13 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/ja.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "検索..." 3 | 4 | [Clear-History] 5 | other = "履歴削除" 6 | 7 | [Attachments-label] 8 | other = "添付" 9 | 10 | [title-404] 11 | other = "エラー" 12 | 13 | [message-404] 14 | other = "おっと。ページが見当たりません。 ¯\\_(ツ)_/¯." 15 | 16 | [Go-to-homepage] 17 | other = "ホームページへ行く" 18 | 19 | [Edit-this-page] 20 | other = "このページを編集" 21 | 22 | [Shortcuts-Title] 23 | other = "更に" 24 | 25 | [Expand-title] 26 | other = "開く..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" 30 | -------------------------------------------------------------------------------- /content/Statistics/categorical/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 6 3 | title: "Categorical Data Analyses" 4 | output: html_document 5 | aliases: /categorical-data-analyses/ 6 | --- 7 | 8 | 9 | 10 | 11 |

Some commonly used tests for contrasting the counts of observations across categorical variables.

12 | 17 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/shortcodes/ref.html: -------------------------------------------------------------------------------- 1 | {{- if in (.Get 0) "/_index.md" -}} 2 | {{- $paths := (split (.Get 0) "_index.md") -}} 3 | {{- $pagepath := index $paths 0 -}} 4 | {{- $anchor := index $paths 1 -}} 5 | {{- with .Site.GetPage "section" (trim $pagepath "/") -}} 6 | {{- ( printf "%s%s" $pagepath $anchor ) | relLangURL -}} 7 | {{- end -}} 8 | {{- else -}} 9 | {{- with .Site.GetPage "section" (.Get 0) }} 10 | {{- .RelPermalink -}} 11 | {{- else -}} 12 | {{- .Get 0 | relref .Page -}} 13 | {{- end -}} 14 | {{- end -}} -------------------------------------------------------------------------------- /themes/hugo-theme-learn/static/images/clippy.svg: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/shortcodes/relref.html: -------------------------------------------------------------------------------- 1 | {{- if in (.Get 0) "/_index.md" -}} 2 | {{- $paths := (split (.Get 0) "_index.md") -}} 3 | {{- $pagepath := index $paths 0 -}} 4 | {{- $anchor := index $paths 1 -}} 5 | {{- with .Site.GetPage "section" (trim $pagepath "/") -}} 6 | {{- ( printf "%s%s" $pagepath $anchor ) | relLangURL -}} 7 | {{- end -}} 8 | {{- else -}} 9 | {{- with .Site.GetPage "section" (.Get 0) }} 10 | {{- .RelPermalink -}} 11 | {{- else -}} 12 | {{- .Get 0 | relref .Page -}} 13 | {{- end -}} 14 | {{- end -}} -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/shortcodes/button.html: -------------------------------------------------------------------------------- 1 | {{ $_hugo_config := `{ "version": 1 }` }} 2 | 3 | {{ $icon := .Get "icon" }} 4 | {{ $iconposition := .Get "icon-position" }} 5 | {{ if ($icon) }} 6 | {{ if or (not ($iconposition)) (eq $iconposition "left") }} 7 | 8 | {{ end }} 9 | {{ end }} 10 | {{ .Inner }} 11 | {{ if and ($icon) (eq $iconposition "right")}} 12 | 13 | {{ end }} 14 | 15 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/ar.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "...البحث" 3 | 4 | [Clear-History] 5 | other = "مسح السجل" 6 | 7 | [Attachments-label] 8 | other = "مرفقات" 9 | 10 | [title-404] 11 | other = "خطأ" 12 | 13 | [message-404] 14 | other = ".¯\\_(ツ)_/¯أوبس. يبدو أن هذه الصفحة غير موجودة" 15 | 16 | [Go-to-homepage] 17 | other = "الذهاب إلى الصفحة الرئيسية" 18 | 19 | [Edit-this-page] 20 | other = "تعديل هذه الصفحة" 21 | 22 | [Shortcuts-Title] 23 | other = "المزيد" 24 | 25 | [Expand-title] 26 | other = "...قم بتوسيع" 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/en.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Search..." 3 | 4 | [Clear-History] 5 | other = "Clear History" 6 | 7 | [Attachments-label] 8 | other = "Attachments" 9 | 10 | [title-404] 11 | other = "Error" 12 | 13 | [message-404] 14 | other = "Woops. Looks like this page doesn't exist ¯\\_(ツ)_/¯." 15 | 16 | [Go-to-homepage] 17 | other = "Go to homepage" 18 | 19 | [Edit-this-page] 20 | other = "Edit this page" 21 | 22 | [Shortcuts-Title] 23 | other = "More" 24 | 25 | [Expand-title] 26 | other = "Expand me..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/es.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Buscar..." 3 | 4 | [Clear-History] 5 | other = "Borrar Historial" 6 | 7 | [Attachments-label] 8 | other = "Adjuntos" 9 | 10 | [title-404] 11 | other = "Error" 12 | 13 | [message-404] 14 | other = "Ups. Parece que la página no existe ¯\\_(ツ)_/¯." 15 | 16 | [Go-to-homepage] 17 | other = "Ir al inicio" 18 | 19 | [Edit-this-page] 20 | other = "Editar esta página" 21 | 22 | [Shortcuts-Title] 23 | other = "Más" 24 | 25 | [Expand-title] 26 | other = "Expandir..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" 30 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/tr.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Ara..." 3 | 4 | [Clear-History] 5 | other = "Geçmişi Temizle" 6 | 7 | [Attachments-label] 8 | other = "Ekler" 9 | 10 | [title-404] 11 | other = "Hata" 12 | 13 | [message-404] 14 | other = "Uups. Görünüşe göre böyle bir sayfa yok ¯\\_(ツ)_/¯" 15 | 16 | [Go-to-homepage] 17 | other = "Anasayfaya dön" 18 | 19 | [Edit-this-page] 20 | other = "Sayfayı düzenle" 21 | 22 | [Shortcuts-Title] 23 | other = "Dahası Var" 24 | 25 | [Expand-title] 26 | other = "Genişlet..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" 30 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/.grenrc.yml: -------------------------------------------------------------------------------- 1 | --- 2 | dataSource: "prs" 3 | prefix: "v" 4 | onlyMilestones: false 5 | changelogFilename: "CHANGELOG.md" 6 | includeMessages: "all" 7 | ignoreIssuesWith: 8 | - "support" 9 | ignoreLabels: 10 | - "duplicate" 11 | - "invalid" 12 | - "wontfix" 13 | groupBy: 14 | New features: 15 | - "feature" 16 | Bug Fixes: 17 | - "bug" 18 | Enhancements: 19 | - "enhancement" 20 | Internationalisation: 21 | - "i18n" 22 | Theme Meta: 23 | - "meta" 24 | Uncategorised: 25 | - "closed" 26 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/pt.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Procurar..." 3 | 4 | [Clear-History] 5 | other = "Limpar Histórico" 6 | 7 | [Attachments-label] 8 | other = "Anexos" 9 | 10 | [title-404] 11 | other = "Erro" 12 | 13 | [message-404] 14 | other = "Ops. Parece que a página não existe ¯\\_(ツ)_/¯." 15 | 16 | [Go-to-homepage] 17 | other = "Ir para o início" 18 | 19 | [Edit-this-page] 20 | other = "Editar esta página" 21 | 22 | [Shortcuts-Title] 23 | other = "Mais" 24 | 25 | [Expand-title] 26 | other = "Expandir..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" 30 | -------------------------------------------------------------------------------- /static/rmarkdown-libs/header-attrs/header-attrs.js: -------------------------------------------------------------------------------- 1 | // Pandoc 2.9 adds attributes on both header and div. We remove the former (to 2 | // be compatible with the behavior of Pandoc < 2.8). 3 | document.addEventListener('DOMContentLoaded', function(e) { 4 | var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); 5 | var i, h, a; 6 | for (i = 0; i < hs.length; i++) { 7 | h = hs[i]; 8 | if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 9 | a = h.attributes; 10 | while (a.length > 0) h.removeAttribute(a[0].name); 11 | } 12 | }); 13 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/hi.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "खोजे..." 3 | 4 | [Clear-History] 5 | other = "इतिहास मिटाएँ" 6 | 7 | [Attachments-label] 8 | other = "संलग्नंक (अटैचमेंट)" 9 | 10 | [title-404] 11 | other = "त्रुटि" 12 | 13 | [message-404] 14 | other = "यह पृष्ठ अभि अनुपलब्ध है!" 15 | 16 | [Go-to-homepage] 17 | other = "मुख्य पृष्ठ पर जाऐ" 18 | 19 | [Edit-this-page] 20 | other = "यह पृष्ठ संपादित करें" 21 | 22 | [Shortcuts-Title] 23 | other = "अधिक सामग्री दिखाएं" 24 | 25 | [Expand-title] 26 | other = "विस्तार करे..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" 30 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/de.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Suchen..." 3 | 4 | [Clear-History] 5 | other = "Verlauf löschen" 6 | 7 | [Attachments-label] 8 | other = "Anhänge" 9 | 10 | [title-404] 11 | other = "Fehler" 12 | 13 | [message-404] 14 | other = "Huch. Diese Seite scheint nicht zu existieren ¯\\_(ツ)_/¯." 15 | 16 | [Go-to-homepage] 17 | other = "Gehe zur Homepage" 18 | 19 | [Edit-this-page] 20 | other = "Bearbeite diese Seite" 21 | 22 | [Shortcuts-Title] 23 | other = "Mehr" 24 | 25 | [Expand-title] 26 | other = "Erweitere mich..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/id.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Telusuri..." 3 | 4 | [Clear-History] 5 | other = "Bersihkan Riwayat" 6 | 7 | [Attachments-label] 8 | other = "Lampiran" 9 | 10 | [title-404] 11 | other = "Kesalahan" 12 | 13 | [message-404] 14 | other = "Oops. Sepertinya halaman ini tidak ada ¯\\_(ツ)_/¯." 15 | 16 | [Go-to-homepage] 17 | other = "Ke halaman depan" 18 | 19 | [Edit-this-page] 20 | other = "Edit halaman ini" 21 | 22 | [Shortcuts-Title] 23 | other = "Lainnya" 24 | 25 | [Expand-title] 26 | other = "Bentangkan..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" 30 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/nl.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Zoeken..." 3 | 4 | [Clear-History] 5 | other = "Wis geschiedenis" 6 | 7 | [Attachments-label] 8 | other = "Bijlagen" 9 | 10 | [title-404] 11 | other = "Error" 12 | 13 | [message-404] 14 | other = "Blijkbaar bestaat deze pagina niet ¯\\_(ツ)_/¯." 15 | 16 | [Go-to-homepage] 17 | other = "Naar startpagina" 18 | 19 | [Edit-this-page] 20 | other = "Deze pagina bewerken" 21 | 22 | [Shortcuts-Title] 23 | other = "Snelkoppelingen" 24 | 25 | [Expand-title] 26 | other = "Lees meer..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "kb" 30 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/ru.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Поиск..." 3 | 4 | [Clear-History] 5 | other = "Очистить историю" 6 | 7 | [Attachments-label] 8 | other = "Присоединенные файлы" 9 | 10 | [title-404] 11 | other = "Ошибка" 12 | 13 | [message-404] 14 | other = "Упс. Выглядит будто такой страницы нет ¯\\_(ツ)_/¯." 15 | 16 | [Go-to-homepage] 17 | other = "Перейти на главную" 18 | 19 | [Edit-this-page] 20 | other = "Редактировать" 21 | 22 | [Shortcuts-Title] 23 | other = "Еще" 24 | 25 | [Expand-title] 26 | other = "Развернуть..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "килобайт" -------------------------------------------------------------------------------- /themes/hugo-theme-learn/i18n/fr.toml: -------------------------------------------------------------------------------- 1 | [Search-placeholder] 2 | other = "Rechercher..." 3 | 4 | [Clear-History] 5 | other = "Supprimer l'historique" 6 | 7 | [Attachments-label] 8 | other = "Pièces jointes" 9 | 10 | [title-404] 11 | other = "Erreur" 12 | 13 | [message-404] 14 | other = "Oups. On dirait que cette page n'existe pas ¯\\_(ツ)_/¯" 15 | 16 | [Go-to-homepage] 17 | other = "Vers la page d'accueil" 18 | 19 | [Edit-this-page] 20 | other = "Modifier la page" 21 | 22 | [Shortcuts-Title] 23 | other = "Aller plus loin" 24 | 25 | [Expand-title] 26 | other = "Déroulez-moi..." 27 | 28 | [BinaryPrefix-kilobyte] 29 | other = "ko" -------------------------------------------------------------------------------- /content/Graphics/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Graphics' 3 | weight: 5 4 | output: html_document 5 | --- 6 | 7 | 8 | 9 | 10 |

R has a very wide range of functions and packages for visualising data.

11 |

These pages have a brief introduction to:

12 | 18 | -------------------------------------------------------------------------------- /static/datasets/Bac.factors.csv: -------------------------------------------------------------------------------- 1 | ,Treatment_ID,Density,Species,pch1,pch2,legend 2 | DC1,DC,Dense,Caulerpa,16,4,U - Unvegetated 3 | DC2,DC,Dense,Caulerpa,16,22,SZ - Sparse Zostera 4 | DC3,DC,Dense,Caulerpa,16,21,SC - Sparse Caulerpa 5 | DS1,DS,Dense,Seagrass,15,15,DS - Dense Zostera 6 | DS2,DS,Dense,Seagrass,15,16,DC - Dense Caulerpa 7 | DS3,DS,Dense,Seagrass,15,NA, 8 | SC1,SC,Sparse,Caulerpa,21,NA, 9 | SC2,SC,Sparse,Caulerpa,21,NA, 10 | SC3,SC,Sparse,Caulerpa,21,NA, 11 | SS1,SS,Sparse,Seagrass,22,NA, 12 | SS2,SS,Sparse,Seagrass,22,NA, 13 | SS3,SS,Sparse,Seagrass,22,NA, 14 | U1,U,Other,Other,4,NA, 15 | U2,U,Other,Other,4,NA, 16 | U3,U,Other,Other,4,NA, 17 | -------------------------------------------------------------------------------- /content/Graphics/spatial-vis/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Spatial Data' 3 | weight: 5 4 | output: html_document 5 | aliases: /visualising-spatial-data/ 6 | --- 7 | 8 | 9 | 10 | 11 |

R has a very wide range of functions and packages for visualising spatial data. This page will link to a series of tutorials for handling spatial data and making maps.

12 | 18 |

19 | -------------------------------------------------------------------------------- /content/Statistics/glms/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 3 3 | title: "Generalised Linear Models (GLMs)" 4 | output: html_document 5 | aliases: /generalised-linear-models/ 6 | --- 7 | Generalised linear models (GLMs) are used when the distribution of data do not conform to the assumptions of linear models, specifically the assumptions of normally distributed residuals and no relationship between the variance and the mean (e.g., presence/absence, count or highly skewed data). 8 | 9 | * [Generalised linear models 1](glm-1): Introduction and binomial data 10 | * [Generalised linear models 2](glm-2): Count data 11 | * [Interpreting coefficients in glms](interpret-glm-coeffs) 12 | -------------------------------------------------------------------------------- /content/Graphics/multivariate-vis/heatmaps/Bac.factors.csv: -------------------------------------------------------------------------------- 1 | ,Treatment_ID,Density,Species,pch1,pch2,legend 2 | DC1,DC,Dense,Caulerpa,16,4,U - Unvegetated 3 | DC2,DC,Dense,Caulerpa,16,22,SZ - Sparse Zostera 4 | DC3,DC,Dense,Caulerpa,16,21,SC - Sparse Caulerpa 5 | DS1,DS,Dense,Seagrass,15,15,DS - Dense Zostera 6 | DS2,DS,Dense,Seagrass,15,16,DC - Dense Caulerpa 7 | DS3,DS,Dense,Seagrass,15,NA, 8 | SC1,SC,Sparse,Caulerpa,21,NA, 9 | SC2,SC,Sparse,Caulerpa,21,NA, 10 | SC3,SC,Sparse,Caulerpa,21,NA, 11 | SS1,SS,Sparse,Seagrass,22,NA, 12 | SS2,SS,Sparse,Seagrass,22,NA, 13 | SS3,SS,Sparse,Seagrass,22,NA, 14 | U1,U,Other,Other,4,NA, 15 | U2,U,Other,Other,4,NA, 16 | U3,U,Other,Other,4,NA, 17 | -------------------------------------------------------------------------------- /static/datasets/tree_curtis1998.tre: -------------------------------------------------------------------------------- 1 | (((Fraxinus_americana,(((Maranthes_corymbosa,(Populus_euramericana,Populus_tremuloides)),(Senna_multijuga,((Fuscospora_fusca,((Castanea_sativa,(Quercus_alba,Quercus_rubra,Quercus_prinus)),(Alnus_rubra,(Betula_pendula,Betula_lenta,Betula_pubescens,Betula_papyrifera,Betula_alleghaniensis,Betula_populifolia)))),(Malus_domestica,(Cecropia_obtusifolia,Myriocarpa_longipes))))),(Trichospermum_mexicanum,Citrus_sinensis)),(Acer_saccharum,Acer_rubrum,Acer_pensylvanicum,Acer_saccharinum)),(Piper_auritum,Liriodendron_tulipifera)),(Pseudotsuga_menziesii,((Pinus_banksiana,(Pinus_ponderosa,(Pinus_echinata,Pinus_radiata))),(Picea_glauca,(Picea_abies,Picea_mariana))))); 2 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/_default/list.html: -------------------------------------------------------------------------------- 1 | {{ partial "header.html" . }} 2 | 3 | {{ if eq .Kind "section" }} 4 | {{ .Content }} 5 | {{end}} 6 | 7 | {{ if or (eq .Kind "taxonomy") (eq .Kind "term") }} 8 | 13 | {{end}} 14 | 15 | 21 | 22 | {{ partial "footer.html" . }} -------------------------------------------------------------------------------- /themes/hugo-theme-learn/netlify.toml: -------------------------------------------------------------------------------- 1 | [build] 2 | publish = "exampleSite/public" 3 | command = "hugo -s exampleSite" 4 | 5 | [build.environment] 6 | HUGO_THEME = "repo" 7 | HUGO_THEMESDIR = "/opt/build" 8 | HUGO_VERSION = "0.72.0" 9 | 10 | [context.production.environment] 11 | HUGO_BASEURL = "https://learn.netlify.app/" 12 | 13 | [context.deploy-preview] 14 | command = "hugo -s exampleSite -b $DEPLOY_PRIME_URL" 15 | 16 | [context.deploy-preview.environment] 17 | HUGO_ENABLEGITINFO = "true" 18 | 19 | [context.branch-deplpy] 20 | command = "hugo -s exampleSite -b $DEPLOY_PRIME_URL" 21 | 22 | [context.branch-deploy.environment] 23 | HUGO_ENABLEGITINFO = "true" 24 | -------------------------------------------------------------------------------- /content/Statistics/t-tests/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 1 3 | title: "T-tests" 4 | output: html_document 5 | aliases: /t-tests/ 6 | --- 7 | 8 | 9 | 10 | 11 |

Some simple hypothesis tests with the t statistic:

12 | 18 | -------------------------------------------------------------------------------- /static/rmarkdown-libs/leaflet-markercluster/package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "leaflet.markercluster", 3 | "repository": "https://github.com/Leaflet/Leaflet.markercluster", 4 | "version": "1.1.0", 5 | "description": "Provides Beautiful Animated Marker Clustering functionality for Leaflet", 6 | "devDependencies": { 7 | "jshint": "~2.1.3", 8 | "mocha": "~1.10.0", 9 | "karma": "~0.8.5", 10 | "uglify-js": "~2.6.0", 11 | "jake": "~0.5.16", 12 | "magic-string": "^0.7.0", 13 | "leaflet": "~1.0.3" 14 | }, 15 | "main": "dist/leaflet.markercluster.js", 16 | "scripts": { 17 | "test": "jake test", 18 | "prepublish": "jake" 19 | }, 20 | "keywords": ["gis", "map"], 21 | "license": "MIT" 22 | } 23 | -------------------------------------------------------------------------------- /static/datasets/Leafshape.csv: -------------------------------------------------------------------------------- 1 | Species,Total_length,Petiole_length,Leaf_length,Width1,Width2 2 | A,2.58,0.9,1.68,1.91,1.32 3 | A,2.31,0.52,1.79,1.57,1.67 4 | A,2.37,0.63,1.74,1.64,1.58 5 | A,2.02,0.5,1.52,1.88,1.78 6 | A,2.29,0.75,1.54,1.71,1.73 7 | A,2.13,0.59,1.55,1.75,1.73 8 | A,2.34,0.51,1.83,1.52,1.65 9 | A,2.23,0.64,1.59,1.81,1.66 10 | A,2.51,0.84,1.67,1.62,1.34 11 | A,2.58,0.86,1.72,1.76,1.75 12 | B,2.36,0.72,1.64,0.19,1.35 13 | B,2.37,0.6,1.77,0.11,1 14 | B,2.81,0.84,1.98,0.07,1.02 15 | B,2.28,0.69,1.59,0.24,1.05 16 | B,2.35,0.73,1.62,0.23,1.33 17 | B,2.74,0.81,1.94,0.29,1.23 18 | B,2.28,0.53,1.75,0.33,1.18 19 | B,2.26,0.53,1.74,0.06,1.06 20 | B,2.44,0.65,1.79,0.02,1.09 21 | B,2.43,0.68,1.68,0.01,1.1 22 | -------------------------------------------------------------------------------- /content/Statistics/meta-analysis/meta-analysis-3/tree_curtis1998.tre: -------------------------------------------------------------------------------- 1 | (((Fraxinus_americana,(((Maranthes_corymbosa,(Populus_euramericana,Populus_tremuloides)),(Senna_multijuga,((Fuscospora_fusca,((Castanea_sativa,(Quercus_alba,Quercus_rubra,Quercus_prinus)),(Alnus_rubra,(Betula_pendula,Betula_lenta,Betula_pubescens,Betula_papyrifera,Betula_alleghaniensis,Betula_populifolia)))),(Malus_domestica,(Cecropia_obtusifolia,Myriocarpa_longipes))))),(Trichospermum_mexicanum,Citrus_sinensis)),(Acer_saccharum,Acer_rubrum,Acer_pensylvanicum,Acer_saccharinum)),(Piper_auritum,Liriodendron_tulipifera)),(Pseudotsuga_menziesii,((Pinus_banksiana,(Pinus_ponderosa,(Pinus_echinata,Pinus_radiata))),(Picea_glauca,(Picea_abies,Picea_mariana))))); 2 | -------------------------------------------------------------------------------- /content/Graphics/multivariate-vis/pca/Leafshape.csv: -------------------------------------------------------------------------------- 1 | Species,Total_length,Petiole_length,Leaf_length,Width1,Width2 2 | A,2.58,0.9,1.68,1.91,1.32 3 | A,2.31,0.52,1.79,1.57,1.67 4 | A,2.37,0.63,1.74,1.64,1.58 5 | A,2.02,0.5,1.52,1.88,1.78 6 | A,2.29,0.75,1.54,1.71,1.73 7 | A,2.13,0.59,1.55,1.75,1.73 8 | A,2.34,0.51,1.83,1.52,1.65 9 | A,2.23,0.64,1.59,1.81,1.66 10 | A,2.51,0.84,1.67,1.62,1.34 11 | A,2.58,0.86,1.72,1.76,1.75 12 | B,2.36,0.72,1.64,0.19,1.35 13 | B,2.37,0.6,1.77,0.11,1 14 | B,2.81,0.84,1.98,0.07,1.02 15 | B,2.28,0.69,1.59,0.24,1.05 16 | B,2.35,0.73,1.62,0.23,1.33 17 | B,2.74,0.81,1.94,0.29,1.23 18 | B,2.28,0.53,1.75,0.33,1.18 19 | B,2.26,0.53,1.74,0.06,1.06 20 | B,2.44,0.65,1.79,0.02,1.09 21 | B,2.43,0.68,1.68,0.01,1.1 22 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/reporting-mistakes.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Reporting mistakes 3 | about: Spot a typo? Broken or missing links? Let us know and so we can fix these errors! 4 | title: 'Mistake found:' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | **Which page(s) do this mistake(s) pertain to?** 11 | Please provide the title(s) and URL of the pages the error is found. 12 | 13 | **Describe the error(s)** 14 | Concisely describe the error you discovered, references to specific lines in the code would be helpful. 15 | 16 | **Describe a potential solution** 17 | Provide a description what you expect if the error was resolved. 18 | 19 | **Additional context** 20 | Feel free to attach any screenshots/screen record of the error. 21 | -------------------------------------------------------------------------------- /content/_index.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: 3 | --- 4 | # Welcome to Environmental Computing 5 | 6 | ### Getting started with R, data manipulation, graphics, and statistics for the environmental sciences 7 | 8 | Students and researchers in the environmental sciences require a wide range of quantitative skills in analytical and data processing software, including R, geographic information systems (GIS) and the processing of remotely sensed data. There is increasingly a need to ensure transparency of data processing supported by statistical analyses to justify conclusions of scientific research and monitoring for management and policy. This site is a brief introduction to techniques for data organisation, graphics and statistical analyses. 9 | 10 | ![](Images/DSC06364.jpg) 11 | -------------------------------------------------------------------------------- /layouts/partials/custom-footer.html: -------------------------------------------------------------------------------- 1 | 11 | 12 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /content/Statistics/meta-analysis/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 10 3 | title: "Meta-Analyses" 4 | output: html_document 5 | aliases: /meta-analysis/ 6 | editor_options: 7 | chunk_output_type: console 8 | --- 9 | 10 | Meta-analyses are increasingly used in ecology, evolution and the environmental sciences to find general patterns among many studies, settle controversies among conflicting studies and to generate new hypotheses. These tutorials provide an introduction to running meta-analyses with the R package [metafor](http://www.metafor-project.org/doku.php). 11 | 12 | * [Meta-analyses 1](meta-analysis-1): Introduction and calculating effect sizes 13 | * [Meta-analyses 2](meta-analysis-2): Fixed effect and random effect models 14 | * [Meta-analyses 3](meta-analysis-3): More complex models 15 | 16 | ![](images/4666102_orig.jpg) 17 | -------------------------------------------------------------------------------- /static/datasets/Interaction_plots.csv: -------------------------------------------------------------------------------- 1 | Figure,Temperature,pH,Growth 2 | NoIntA,control,control,4 3 | NoIntA,control,acid,4 4 | NoIntA,warm,control,2 5 | NoIntA,warm,acid,2 6 | NoIntB,control,control,4 7 | NoIntB,control,acid,2 8 | NoIntB,warm,control,3.9 9 | NoIntB,warm,acid,1.9 10 | NoIntC,control,control,4 11 | NoIntC,control,acid,3 12 | NoIntC,warm,control,2 13 | NoIntC,warm,acid,1 14 | IntD,control,control,4 15 | IntD,control,acid,4 16 | IntD,warm,control,3.9 17 | IntD,warm,acid,1.5 18 | IntE,control,control,4 19 | IntE,control,acid,3 20 | IntE,warm,control,3 21 | IntE,warm,acid,0.2 22 | IntF,control,control,4 23 | IntF,control,acid,2.1 24 | IntF,warm,control,1.8 25 | IntF,warm,acid,3.8 26 | IntG,control,control,4 27 | IntG,control,acid,3.9 28 | IntG,warm,control,3.9 29 | IntG,warm,acid,2.3 30 | IntG,hot,control,3 31 | IntG,hot,acid,0.5 32 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/shortcodes/expand.html: -------------------------------------------------------------------------------- 1 | {{ $_hugo_config := `{ "version": 1 }` }} 2 |
3 |
4 | 5 | 6 | {{$expandMessage := T "Expand-title"}} 7 | {{ if .IsNamedParams }} 8 | {{.Get "default" | default $expandMessage}} 9 | {{else}} 10 | {{.Get 0 | default $expandMessage}} 11 | {{end}} 12 | 13 |
14 | 17 |
-------------------------------------------------------------------------------- /content/Statistics/glms/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 3 3 | title: "Generalised Linear Models (GLMs)" 4 | output: html_document 5 | aliases: /generalised-linear-models/ 6 | --- 7 | 8 | 9 | 10 | 11 |

Generalised linear models (GLMs) are used when the distribution of data do not conform to the assumptions of linear models, specifically the assumptions of normally distributed residuals and no relationship between the variance and the mean (e.g., presence/absence, count or highly skewed data).

12 | 18 | -------------------------------------------------------------------------------- /static/rmarkdown-libs/leafletfix/leafletfix.css: -------------------------------------------------------------------------------- 1 | /* Work around CSS properties introduced on img by bootstrap */ 2 | img.leaflet-tile { 3 | padding: 0; 4 | margin: 0; 5 | border-radius: 0; 6 | border: none; 7 | } 8 | .info { 9 | padding: 6px 8px; 10 | font: 14px/16px Arial, Helvetica, sans-serif; 11 | background: white; 12 | background: rgba(255,255,255,0.8); 13 | box-shadow: 0 0 15px rgba(0,0,0,0.2); 14 | border-radius: 5px; 15 | } 16 | .legend { 17 | line-height: 18px; 18 | color: #555; 19 | } 20 | .legend svg text { 21 | fill: #555; 22 | } 23 | .legend svg line { 24 | stroke: #555; 25 | } 26 | .legend i { 27 | width: 18px; 28 | height: 18px; 29 | margin-right: 4px; 30 | opacity: 0.7; 31 | display: inline-block; 32 | vertical-align: top; 33 | /*For IE 7*/ 34 | zoom: 1; 35 | *display: inline; 36 | } 37 | -------------------------------------------------------------------------------- /layouts/shortcodes/ghcontributors.html: -------------------------------------------------------------------------------- 1 | 22 |
23 | {{ $url := .Get 0 }} 24 | {{ range getJSON $url }} 25 |
26 | 27 | 28 | {{.contributions}} commits 29 |
30 | {{ end }} 31 |
-------------------------------------------------------------------------------- /content/Statistics/linear-models/interactions/Interaction_plots.csv: -------------------------------------------------------------------------------- 1 | Figure,Temperature,pH,Growth 2 | NoIntA,control,control,4 3 | NoIntA,control,acid,4 4 | NoIntA,warm,control,2 5 | NoIntA,warm,acid,2 6 | NoIntB,control,control,4 7 | NoIntB,control,acid,2 8 | NoIntB,warm,control,3.9 9 | NoIntB,warm,acid,1.9 10 | NoIntC,control,control,4 11 | NoIntC,control,acid,3 12 | NoIntC,warm,control,2 13 | NoIntC,warm,acid,1 14 | IntD,control,control,4 15 | IntD,control,acid,4 16 | IntD,warm,control,3.9 17 | IntD,warm,acid,1.5 18 | IntE,control,control,4 19 | IntE,control,acid,3 20 | IntE,warm,control,3 21 | IntE,warm,acid,0.2 22 | IntF,control,control,4 23 | IntF,control,acid,2.1 24 | IntF,warm,control,1.8 25 | IntF,warm,acid,3.8 26 | IntG,control,control,4 27 | IntG,control,acid,3.9 28 | IntG,warm,control,3.9 29 | IntG,warm,acid,2.3 30 | IntG,hot,control,3 31 | IntG,hot,acid,0.5 32 | -------------------------------------------------------------------------------- /content/Graphics/multivariate-vis/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Multivariate Data' 3 | weight: 4 4 | output: html_document 5 | editor_options: 6 | chunk_output_type: console 7 | aliases: /visualising-multivariate-data/ 8 | --- 9 | 10 | 11 | 12 | 13 |

14 |

R has a very wide range of functions and packages for visualising multivariate data. Here is some help for some of the more commonly used techniques:

15 | 22 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/theme.toml: -------------------------------------------------------------------------------- 1 | # theme.toml template for a Hugo theme 2 | # See https://github.com/spf13/hugoThemes#themetoml for an example 3 | 4 | name = "Learn" 5 | license = "MIT" 6 | licenselink = "https://github.com/matcornic/hugo-theme-learn/blob/master/LICENSE.md" 7 | description = "Documentation theme for Hugo, based on Grav Learn theme" 8 | homepage = "https://github.com/matcornic/hugo-theme-learn/" 9 | repo = "https://github.com/matcornic/hugo-theme-learn" 10 | tags = ["documentation", "grav", "learn", "doc", "search"] 11 | features = ["documentation", "menu", "nested sections", "search", "mermaid"] 12 | min_version = 0.25 13 | 14 | [author] 15 | name = "Mathieu Cornic" 16 | homepage = "https://matcornic.github.io/" 17 | 18 | [original] 19 | name = "Grav Learn" 20 | homepage = "https://learn.getgrav.org/" 21 | repo = "https://github.com/getgrav/grav-learn" 22 | -------------------------------------------------------------------------------- /static/datasets/Mink.csv: -------------------------------------------------------------------------------- 1 | Treatment,Area,Voles 2 | Control,area1,8 3 | Control,area1,16 4 | Control,area1,11 5 | Control,area1,15 6 | Control,area1,9 7 | Control,area1,10 8 | Control,area1,11 9 | Control,area1,9 10 | Control,area1,8 11 | Control,area1,14 12 | Control,area2,16 13 | Control,area2,23 14 | Control,area2,11 15 | Control,area2,8 16 | Control,area2,11 17 | Control,area2,8 18 | Control,area2,8 19 | Control,area2,12 20 | Control,area2,9 21 | Control,area2,15 22 | Removal,area3,33 23 | Removal,area3,26 24 | Removal,area3,34 25 | Removal,area3,34 26 | Removal,area3,26 27 | Removal,area3,41 28 | Removal,area3,20 29 | Removal,area3,17 30 | Removal,area3,20 31 | Removal,area3,26 32 | Removal,area4,29 33 | Removal,area4,18 34 | Removal,area4,16 35 | Removal,area4,18 36 | Removal,area4,13 37 | Removal,area4,24 38 | Removal,area4,9 39 | Removal,area4,21 40 | Removal,area4,33 41 | Removal,area4,12 42 | -------------------------------------------------------------------------------- /static/datasets/ReefFish.csv: -------------------------------------------------------------------------------- 1 | Site,Month,Transect,Species,Abundance 2 | Reef1,January,1,RedFish,4 3 | Reef1,January,1,BlueFish,5 4 | Reef1,January,1,BlackFish,10 5 | Reef1,January,2,RedFish,42 6 | Reef1,January,2,BlueFish,13 7 | Reef1,January,3,RedFish,3 8 | Reef1,January,3,BlackFish,8 9 | Reef2,January,1,RedFish,5 10 | Reef2,January,1,BlackFish,72 11 | Reef2,January,2,BlueFish,9 12 | Reef2,January,3,RedFish,24 13 | Reef2,January,3,BlueFish,101 14 | Reef2,January,3,BlackFish,65 15 | Reef1,February,1,RedFish,52 16 | Reef1,February,1,BlueFish,12 17 | Reef1,February,1,BlackFish,47 18 | Reef1,February,2,BlueFish,3 19 | Reef1,February,2,BlackFish,69 20 | Reef1,February,3,RedFish,8 21 | Reef2,February,1,BlackFish,25 22 | Reef2,February,2,RedFish,3 23 | Reef2,February,2,BlueFish,22 24 | Reef2,February,2,BlackFish,10 25 | Reef2,February,3,RedFish,15 26 | Reef2,February,3,BlueFish,84 27 | Reef2,February,3,BlackFish,7 28 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/shortcodes/tabs.html: -------------------------------------------------------------------------------- 1 | {{ with .Inner }}{{/* don't do anything, just call it */}}{{ end }} 2 | {{ $groupId := default "default" (.Get "groupId") }} 3 |
4 |
5 | {{ range $idx, $tab := .Scratch.Get "tabs" }} 6 | 12 | {{ end }} 13 |
14 |
15 | {{ range $idx, $tab := .Scratch.Get "tabs" }} 16 |
17 | {{ .content }} 18 |
19 | {{ end }} 20 |
21 |
22 | -------------------------------------------------------------------------------- /content/Statistics/linear-models/anova/anova-nested/Mink.csv: -------------------------------------------------------------------------------- 1 | Treatment,Area,Voles 2 | Control,area1,8 3 | Control,area1,16 4 | Control,area1,11 5 | Control,area1,15 6 | Control,area1,9 7 | Control,area1,10 8 | Control,area1,11 9 | Control,area1,9 10 | Control,area1,8 11 | Control,area1,14 12 | Control,area2,16 13 | Control,area2,23 14 | Control,area2,11 15 | Control,area2,8 16 | Control,area2,11 17 | Control,area2,8 18 | Control,area2,8 19 | Control,area2,12 20 | Control,area2,9 21 | Control,area2,15 22 | Removal,area3,33 23 | Removal,area3,26 24 | Removal,area3,34 25 | Removal,area3,34 26 | Removal,area3,26 27 | Removal,area3,41 28 | Removal,area3,20 29 | Removal,area3,17 30 | Removal,area3,20 31 | Removal,area3,26 32 | Removal,area4,29 33 | Removal,area4,18 34 | Removal,area4,16 35 | Removal,area4,18 36 | Removal,area4,13 37 | Removal,area4,24 38 | Removal,area4,9 39 | Removal,area4,21 40 | Removal,area4,33 41 | Removal,area4,12 42 | -------------------------------------------------------------------------------- /content/Data-Manipulation/reshaping-data/ReefFish.csv: -------------------------------------------------------------------------------- 1 | Site,Month,Transect,Species,Abundance 2 | Reef1,January,1,RedFish,4 3 | Reef1,January,1,BlueFish,5 4 | Reef1,January,1,BlackFish,10 5 | Reef1,January,2,RedFish,42 6 | Reef1,January,2,BlueFish,13 7 | Reef1,January,3,RedFish,3 8 | Reef1,January,3,BlackFish,8 9 | Reef2,January,1,RedFish,5 10 | Reef2,January,1,BlackFish,72 11 | Reef2,January,2,BlueFish,9 12 | Reef2,January,3,RedFish,24 13 | Reef2,January,3,BlueFish,101 14 | Reef2,January,3,BlackFish,65 15 | Reef1,February,1,RedFish,52 16 | Reef1,February,1,BlueFish,12 17 | Reef1,February,1,BlackFish,47 18 | Reef1,February,2,BlueFish,3 19 | Reef1,February,2,BlackFish,69 20 | Reef1,February,3,RedFish,8 21 | Reef2,February,1,BlackFish,25 22 | Reef2,February,2,RedFish,3 23 | Reef2,February,2,BlueFish,22 24 | Reef2,February,2,BlackFish,10 25 | Reef2,February,3,RedFish,15 26 | Reef2,February,3,BlueFish,84 27 | Reef2,February,3,BlackFish,7 28 | -------------------------------------------------------------------------------- /content/Graphics/basic-plotting/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Basic Plotting in R' 3 | weight: 1 4 | output: html_document 5 | aliases: /basic-plotting-in-r/ 6 | --- 7 | 8 | 9 | 10 | 11 |

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R has a very wide range of functions and packages for visualising data. Here is some help for some very simple plots using the base functions in R for data with:

13 | 20 | -------------------------------------------------------------------------------- /static/rmarkdown-libs/leaflet-markercluster/MarkerCluster.css: -------------------------------------------------------------------------------- 1 | .leaflet-cluster-anim .leaflet-marker-icon, .leaflet-cluster-anim .leaflet-marker-shadow { 2 | -webkit-transition: -webkit-transform 0.3s ease-out, opacity 0.3s ease-in; 3 | -moz-transition: -moz-transform 0.3s ease-out, opacity 0.3s ease-in; 4 | -o-transition: -o-transform 0.3s ease-out, opacity 0.3s ease-in; 5 | transition: transform 0.3s ease-out, opacity 0.3s ease-in; 6 | } 7 | 8 | .leaflet-cluster-spider-leg { 9 | /* stroke-dashoffset (duration and function) should match with leaflet-marker-icon transform in order to track it exactly */ 10 | -webkit-transition: -webkit-stroke-dashoffset 0.3s ease-out, -webkit-stroke-opacity 0.3s ease-in; 11 | -moz-transition: -moz-stroke-dashoffset 0.3s ease-out, -moz-stroke-opacity 0.3s ease-in; 12 | -o-transition: -o-stroke-dashoffset 0.3s ease-out, -o-stroke-opacity 0.3s ease-in; 13 | transition: stroke-dashoffset 0.3s ease-out, stroke-opacity 0.3s ease-in; 14 | } 15 | -------------------------------------------------------------------------------- /static/datasets/Crabs.csv: -------------------------------------------------------------------------------- 1 | "","Dist","Time","CrabPres" 2 | "1",0,5,0 3 | "2",0,5,1 4 | "3",0,5,1 5 | "4",0,5,0 6 | "5",0,5,0 7 | "6",2,5,0 8 | "7",2,5,0 9 | "8",2,5,1 10 | "9",2,5,0 11 | "10",2,5,0 12 | "11",10,5,1 13 | "12",10,5,0 14 | "13",10,5,0 15 | "14",10,5,1 16 | "15",10,5,0 17 | "16",0,10,0 18 | "17",0,10,0 19 | "18",0,10,1 20 | "19",0,10,1 21 | "20",0,10,1 22 | "21",2,10,0 23 | "22",2,10,0 24 | "23",2,10,1 25 | "24",2,10,0 26 | "25",2,10,0 27 | "26",10,10,1 28 | "27",10,10,0 29 | "28",10,10,1 30 | "29",10,10,1 31 | "30",10,10,0 32 | "31",0,5,0 33 | "32",0,5,0 34 | "33",0,5,0 35 | "34",0,5,0 36 | "35",0,5,0 37 | "36",2,5,0 38 | "37",2,5,0 39 | "38",2,5,0 40 | "39",2,5,0 41 | "40",2,5,0 42 | "41",10,5,0 43 | "42",10,5,0 44 | "43",10,5,0 45 | "44",10,5,0 46 | "45",10,5,0 47 | "46",0,10,0 48 | "47",0,10,0 49 | "48",0,10,0 50 | "49",0,10,0 51 | "50",0,10,1 52 | "51",2,10,1 53 | "52",2,10,1 54 | "53",10,10,0 55 | "54",10,10,1 56 | "55",10,10,0 57 | "56",10,10,1 58 | "57",10,10,1 59 | -------------------------------------------------------------------------------- /content/Statistics/glms/glm-1/Crabs.csv: -------------------------------------------------------------------------------- 1 | "","Dist","Time","CrabPres" 2 | "1",0,5,0 3 | "2",0,5,1 4 | "3",0,5,1 5 | "4",0,5,0 6 | "5",0,5,0 7 | "6",2,5,0 8 | "7",2,5,0 9 | "8",2,5,1 10 | "9",2,5,0 11 | "10",2,5,0 12 | "11",10,5,1 13 | "12",10,5,0 14 | "13",10,5,0 15 | "14",10,5,1 16 | "15",10,5,0 17 | "16",0,10,0 18 | "17",0,10,0 19 | "18",0,10,1 20 | "19",0,10,1 21 | "20",0,10,1 22 | "21",2,10,0 23 | "22",2,10,0 24 | "23",2,10,1 25 | "24",2,10,0 26 | "25",2,10,0 27 | "26",10,10,1 28 | "27",10,10,0 29 | "28",10,10,1 30 | "29",10,10,1 31 | "30",10,10,0 32 | "31",0,5,0 33 | "32",0,5,0 34 | "33",0,5,0 35 | "34",0,5,0 36 | "35",0,5,0 37 | "36",2,5,0 38 | "37",2,5,0 39 | "38",2,5,0 40 | "39",2,5,0 41 | "40",2,5,0 42 | "41",10,5,0 43 | "42",10,5,0 44 | "43",10,5,0 45 | "44",10,5,0 46 | "45",10,5,0 47 | "46",0,10,0 48 | "47",0,10,0 49 | "48",0,10,0 50 | "49",0,10,0 51 | "50",0,10,1 52 | "51",2,10,1 53 | "52",2,10,1 54 | "53",10,10,0 55 | "54",10,10,1 56 | "55",10,10,0 57 | "56",10,10,1 58 | "57",10,10,1 59 | -------------------------------------------------------------------------------- /static/rmarkdown-libs/rstudio_leaflet/rstudio_leaflet.css: -------------------------------------------------------------------------------- 1 | .leaflet-tooltip.leaflet-tooltip-text-only, 2 | .leaflet-tooltip.leaflet-tooltip-text-only:before, 3 | .leaflet-tooltip.leaflet-tooltip-text-only:after { 4 | background: none; 5 | border: none; 6 | box-shadow: none; 7 | } 8 | 9 | .leaflet-tooltip.leaflet-tooltip-text-only.leaflet-tooltip-left { 10 | margin-left: 5px; 11 | } 12 | 13 | .leaflet-tooltip.leaflet-tooltip-text-only.leaflet-tooltip-right { 14 | margin-left: -5px; 15 | } 16 | 17 | .leaflet-tooltip:after { 18 | border-right: 6px solid transparent; 19 | /* right: -16px; */ 20 | } 21 | 22 | .leaflet-popup-pane .leaflet-popup-tip-container { 23 | /* when the tooltip container is clicked, it is closed */ 24 | pointer-events: all; 25 | /* tooltips should display the "hand" icon, just like .leaflet-interactive*/ 26 | cursor: pointer; 27 | } 28 | 29 | /* have the widget be displayed in the right 'layer' */ 30 | .leaflet-map-pane { 31 | z-index: auto; 32 | } 33 | -------------------------------------------------------------------------------- /layouts/partials/menu-footer.html: -------------------------------------------------------------------------------- 1 |
2 | 3 | GitHub 4 | 5 | 6 | Star 7 | 8 |

Built with Hugo via blogdown, 9 | using the Learn theme

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12 | 13 | 14 | -------------------------------------------------------------------------------- /config.yaml: -------------------------------------------------------------------------------- 1 | baseURL: https://environmentalcomputing.net/ 2 | languageCode: en-US 3 | defaultContentLanguage: en 4 | title: Environmental Computing 5 | theme: hugo-theme-learn 6 | metaDataFormat: yaml 7 | defaultContentLanguageInSubdir: yes 8 | googleAnalyticsID: G-KVTJFRWP8M 9 | googleAnalytics: UA-77528433-1 10 | params: 11 | author: Fonti Kar, Daniel Falster, and Will Cornwell 12 | customMermaidURL: NA 13 | description: Environmental Computing 14 | disableBreadcrumb: no 15 | disableLandingPageButton: yes 16 | disableMermaid: no 17 | disableNextPrev: no 18 | editURL: https://github.com/nicercode/EnvironmentalComputing/edit/master/content/ 19 | showVisitedLinks: yes 20 | titleSeparator: '::' 21 | themeVariant: 'green' 22 | outputs: 23 | home: 24 | - HTML 25 | - RSS 26 | - JSON 27 | 28 | ignoreFiles: 29 | - \.Rmd$ 30 | - \.Rmarkdown$ 31 | - _cache$ 32 | - \.knit\.md$ 33 | - \.utf8\.md$ 34 | 35 | markup: 36 | goldmark: 37 | renderer: 38 | unsafe: true 39 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/partials/search.html: -------------------------------------------------------------------------------- 1 |
2 | 3 | 4 | 5 |
6 | {{ $assetBusting := not .Site.Params.disableAssetsBusting }} 7 | 8 | 9 | 16 | 17 | -------------------------------------------------------------------------------- /content/Coding-Skills/_index.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Coding Skills' 3 | weight: 4 4 | output: html_document 5 | --- 6 | 7 | You might think having skills in computer coding is just for web site and game developers, but skills in coding are increasing valuable for environmental scientists. Running your data analyses and graphics using code means that your research methods are explicitly saved, reproducible and easily shared with colleagues or supervisors. 8 | 9 | On these pages, we give some advice for writing effective code and some of the very useful coding skills that will save you lots of time. 10 | 11 | * [Good practice for writing scripts](good-practice/) 12 | * [Writing simple functions](writing-functions/) 13 | * [Using loops](loops/) 14 | * Using Lists...coming soon 15 | * Logical control...coming soon 16 | * [Version control](version-control/) 17 | 18 | ![](Coding_image.jpg) 19 | 20 | **Author**: Alistair Poore & Will Cornwell 21 | 22 | **Year:** 2016 23 | 24 | **Last updated:** `r format(Sys.time(), "%b %Y")` 25 | -------------------------------------------------------------------------------- /content/Statistics/meta-analysis/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 10 3 | title: "Meta-Analyses" 4 | output: html_document 5 | aliases: /meta-analysis/ 6 | editor_options: 7 | chunk_output_type: console 8 | --- 9 | 10 | 11 | 12 | 13 |

Meta-analyses are increasingly used in ecology, evolution and the environmental sciences to find general patterns among many studies, settle controversies among conflicting studies and to generate new hypotheses. These tutorials provide an introduction to running meta-analyses with the R package metafor.

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22 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/static/css/tabs.css: -------------------------------------------------------------------------------- 1 | #body .tab-nav-button { 2 | border-width: 1px 1px 1px 1px !important; 3 | border-color: #ccc !important; 4 | border-radius: 4px 4px 0 0 !important; 5 | background-color: #ddd !important; 6 | float: left; 7 | display: block; 8 | position: relative; 9 | margin-left: 4px; 10 | bottom: -1px; 11 | } 12 | #body .tab-nav-button:first-child { 13 | margin-left: 0px; 14 | } 15 | #body .tab-nav-button.active { 16 | background-color: #fff !important; 17 | border-bottom-color: #fff !important; 18 | } 19 | 20 | #body .tab-panel { 21 | margin-top: 32px; 22 | margin-bottom: 32px; 23 | } 24 | #body .tab-content { 25 | display: block; 26 | clear: both; 27 | padding: 8px; 28 | border-width: 1px; 29 | border-style: solid; 30 | border-color: #ccc; 31 | } 32 | #body .tab-content .tab-item{ 33 | display: none; 34 | } 35 | 36 | #body .tab-content .tab-item.active{ 37 | display: block; 38 | } 39 | 40 | #body .tab-item pre{ 41 | margin-bottom: 0; 42 | margin-top: 0; 43 | } 44 | -------------------------------------------------------------------------------- /.Rprofile: -------------------------------------------------------------------------------- 1 | # REMEMBER to restart R after you modify and save this file! 2 | 3 | # First, execute the global .Rprofile if it exists. You may configure blogdown 4 | # options there, too, so they apply to any blogdown projects. Feel free to 5 | # ignore this part if it sounds too complicated to you. 6 | if (file.exists("~/.Rprofile")) { 7 | base::sys.source("~/.Rprofile", envir = environment()) 8 | } 9 | 10 | # Now set options to customize the behavior of blogdown for this project. Below 11 | # are a few sample options; for more options, see 12 | # https://bookdown.org/yihui/blogdown/global-options.html 13 | options( 14 | # to automatically serve the site on RStudio startup, set this option to TRUE 15 | blogdown.serve_site.startup = FALSE, 16 | # to disable knitting Rmd files on save, set this option to FALSE 17 | blogdown.knit.on_save = TRUE, 18 | # build .Rmd to .html (via Pandoc); to build to Markdown, set this option to 'markdown' 19 | blogdown.method = 'html', 20 | blogdown.server.verbose = TRUE 21 | ) 22 | 23 | # fix Hugo version 24 | options(blogdown.hugo.version = "0.91.2") 25 | -------------------------------------------------------------------------------- /content/Statistics/mixed-models/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 4 3 | title: "Mixed Models" 4 | output: html_document 5 | aliases: /mixed-models/ 6 | --- 7 | Mixed models are those with a mixture of fixed and random effects. Random effects are categorical factors where the levels have been selected from many possible levels and the investigator would like to make inferences beyond just the levels chosen. Tricky concept, but imagine contrasting two habitat types (forest and grassland) by sampling five sites within each, and five replicate measures within each site. Habitat type is a fixed factor with the researcher only interested in those two levels of habitat type. If the five sites were chosen from a larger collection of possible sites, then site is considered a random effect with 10 levels. 8 | 9 | * [Mixed models 1](mixed-model-1): Linear mixed models with one random effect 10 | * [Mixed models 2](mixed-model-2): Linear mixed models with several random effects 11 | * [Mixed models 3](mixed-model-3): Generalised linear mixed models 12 | 13 | ![](Mixed_models_intro_image.jpg) 14 | Photo: N. Murray 15 | -------------------------------------------------------------------------------- /static/datasets/Prawns_MR.csv: -------------------------------------------------------------------------------- 1 | "Species","Metabolic_rate" 2 | "A",0.369385900685492 3 | "A",0.606495165268205 4 | "A",0.565637540205046 5 | "A",0.418352219947038 6 | "A",0.572821857515413 7 | "A",0.330236588738936 8 | "A",0.604916067253415 9 | "A",0.533671328992217 10 | "A",0.45777262208129 11 | "A",0.526674455317587 12 | "A",0.529980602715604 13 | "A",0.409163735284848 14 | "A",0.456311608683266 15 | "A",0.465257903111991 16 | "A",0.692887256243914 17 | "A",0.539754872265383 18 | "A",0.659755755935955 19 | "A",0.56317030007795 20 | "A",0.464631779112357 21 | "A",0.57657952505784 22 | "B",0.711328292118508 23 | "B",0.625150374550374 24 | "B",0.67499326675106 25 | "B",0.681993702473118 26 | "B",0.788056490233949 27 | "B",0.730649053204385 28 | "B",0.867433768967066 29 | "B",0.853334344836263 30 | "B",1.0035757872879 31 | "B",0.632714500891573 32 | "B",0.751755669060109 33 | "B",0.681863702821682 34 | "B",0.863086759973589 35 | "B",0.909126352015289 36 | "B",0.769505621085088 37 | "B",0.724809594948497 38 | "B",0.758077924099366 39 | "B",0.765498847739066 40 | "B",0.743745353998118 41 | "B",0.667288078482038 42 | -------------------------------------------------------------------------------- /content/Statistics/linear-models/anova/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 3 3 | title: "ANOVA" 4 | output: html_document 5 | aliases: /analysis-variance/ 6 | --- 7 | 8 | Analysis of variance (ANOVA) is one of the most frequently used techniques in the biological and environmental sciences. ANOVA is used to contrast a continuous dependent variable *y* across levels of one or more categorical independent variables *x*. The independent variables are termed the factor or treatment, and the various categories within that treatment are termed the levels. In this module, we will start with the simplest design - those with a single factor. 9 | 10 | Where an independent samples *t*-test would be used for comparison of group means across two levels, ANOVA is used for the comparison of >2 group means, or when there are more than two or more predictor variables (see [ANOVA: factorial](/statistics/linear-models/anova/anova-factorial)). The logic of this test is essentially the same as the *t*-test - it compares variation between groups to variation within groups to determine whether the observed differences are due to chance or not. 11 | -------------------------------------------------------------------------------- /content/Graphics/basic-plotting/one-continuous-one-factor/Prawns_MR.csv: -------------------------------------------------------------------------------- 1 | "Species","Metabolic_rate" 2 | "A",0.369385900685492 3 | "A",0.606495165268205 4 | "A",0.565637540205046 5 | "A",0.418352219947038 6 | "A",0.572821857515413 7 | "A",0.330236588738936 8 | "A",0.604916067253415 9 | "A",0.533671328992217 10 | "A",0.45777262208129 11 | "A",0.526674455317587 12 | "A",0.529980602715604 13 | "A",0.409163735284848 14 | "A",0.456311608683266 15 | "A",0.465257903111991 16 | "A",0.692887256243914 17 | "A",0.539754872265383 18 | "A",0.659755755935955 19 | "A",0.56317030007795 20 | "A",0.464631779112357 21 | "A",0.57657952505784 22 | "B",0.711328292118508 23 | "B",0.625150374550374 24 | "B",0.67499326675106 25 | "B",0.681993702473118 26 | "B",0.788056490233949 27 | "B",0.730649053204385 28 | "B",0.867433768967066 29 | "B",0.853334344836263 30 | "B",1.0035757872879 31 | "B",0.632714500891573 32 | "B",0.751755669060109 33 | "B",0.681863702821682 34 | "B",0.863086759973589 35 | "B",0.909126352015289 36 | "B",0.769505621085088 37 | "B",0.724809594948497 38 | "B",0.758077924099366 39 | "B",0.765498847739066 40 | "B",0.743745353998118 41 | "B",0.667288078482038 42 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/static/css/auto-complete.css: -------------------------------------------------------------------------------- 1 | .autocomplete-suggestions { 2 | text-align: left; 3 | cursor: default; 4 | border: 1px solid #ccc; 5 | border-top: 0; 6 | background: #fff; 7 | box-shadow: -1px 1px 3px rgba(0,0,0,.1); 8 | 9 | /* core styles should not be changed */ 10 | position: absolute; 11 | display: none; 12 | z-index: 9999; 13 | max-height: 254px; 14 | overflow: hidden; 15 | overflow-y: auto; 16 | box-sizing: border-box; 17 | 18 | } 19 | .autocomplete-suggestion { 20 | position: relative; 21 | cursor: pointer; 22 | padding: 7px; 23 | line-height: 23px; 24 | white-space: nowrap; 25 | overflow: hidden; 26 | text-overflow: ellipsis; 27 | color: #333; 28 | } 29 | 30 | .autocomplete-suggestion b { 31 | font-weight: normal; 32 | color: #1f8dd6; 33 | } 34 | 35 | .autocomplete-suggestion.selected { 36 | background: #333; 37 | color: #fff; 38 | } 39 | 40 | .autocomplete-suggestion:hover { 41 | background: #444; 42 | color: #fff; 43 | } 44 | 45 | .autocomplete-suggestion > .context { 46 | font-size: 12px; 47 | } 48 | -------------------------------------------------------------------------------- /static/rmarkdown-libs/leaflet-markercluster/MIT-LICENCE.txt: -------------------------------------------------------------------------------- 1 | Copyright 2012 David Leaver 2 | 3 | Permission is hereby granted, free of charge, to any person obtaining 4 | a copy of this software and associated documentation files (the 5 | "Software"), to deal in the Software without restriction, including 6 | without limitation the rights to use, copy, modify, merge, publish, 7 | distribute, sublicense, and/or sell copies of the Software, and to 8 | permit persons to whom the Software is furnished to do so, subject to 9 | the following conditions: 10 | 11 | The above copyright notice and this permission notice shall be 12 | included in all copies or substantial portions of the Software. 13 | 14 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 15 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 16 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 17 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE 18 | LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION 19 | OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION 20 | WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 21 | -------------------------------------------------------------------------------- /static/datasets/Weather_vars.csv: -------------------------------------------------------------------------------- 1 | Date,Mean_temperature,Mean_humidity 2 | 11/12/2012,26.8375,34.125 3 | 12/12/2012,29.312,28.16 4 | 13/12/2012,25.42083333,55.5 5 | 14/12/2012,23.242,64.94 6 | 15/12/2012,19.112,52.56 7 | 16/12/2012,18.35625,38.08333333 8 | 17/12/2012,21.60416667,35.52083333 9 | 18/12/2012,29.58,25 10 | 19/12/2012,21.04791667,44.33333333 11 | 20/12/2012,22.05,35 12 | 21/12/2012,24.62083333,29.27083333 13 | 22/12/2012,30.46041667,24.5 14 | 23/12/2012,27.37586207,35.98275862 15 | 24/12/2012,20.138,39.1 16 | 25/12/2012,21.09375,39.1875 17 | 26/12/2012,25.44489796,30.91836735 18 | 27/12/2012,21.91694915,37.77966102 19 | 28/12/2012,21.29803922,41.62745098 20 | 29/12/2012,21.60208333,32.1875 21 | 30/12/2012,23.05208333,25.70833333 22 | 31/12/2012,26.28269231,24.25 23 | 1/01/2013,22.564,34.1 24 | 2/01/2013,26.51458333,26.91666667 25 | 3/01/2013,32.95714286,21.89795918 26 | 4/01/2013,35.98979592,19.42857143 27 | 5/01/2013,29.21041667,31.47916667 28 | 6/01/2013,32.60625,29.5625 29 | 7/01/2013,30.62280702,21.31578947 30 | 8/01/2013,18.76727273,35.12727273 31 | 9/01/2013,21.36041667,31 32 | 10/01/2013,29.84375,16.10416667 33 | 11/01/2013,23.27916667,38.29166667 34 | 12/01/2013,16.202,70.54 35 | -------------------------------------------------------------------------------- /content/Data-Manipulation/combining-datasets/Weather_vars.csv: -------------------------------------------------------------------------------- 1 | Date,Mean_temperature,Mean_humidity 2 | 11/12/2012,26.8375,34.125 3 | 12/12/2012,29.312,28.16 4 | 13/12/2012,25.42083333,55.5 5 | 14/12/2012,23.242,64.94 6 | 15/12/2012,19.112,52.56 7 | 16/12/2012,18.35625,38.08333333 8 | 17/12/2012,21.60416667,35.52083333 9 | 18/12/2012,29.58,25 10 | 19/12/2012,21.04791667,44.33333333 11 | 20/12/2012,22.05,35 12 | 21/12/2012,24.62083333,29.27083333 13 | 22/12/2012,30.46041667,24.5 14 | 23/12/2012,27.37586207,35.98275862 15 | 24/12/2012,20.138,39.1 16 | 25/12/2012,21.09375,39.1875 17 | 26/12/2012,25.44489796,30.91836735 18 | 27/12/2012,21.91694915,37.77966102 19 | 28/12/2012,21.29803922,41.62745098 20 | 29/12/2012,21.60208333,32.1875 21 | 30/12/2012,23.05208333,25.70833333 22 | 31/12/2012,26.28269231,24.25 23 | 1/01/2013,22.564,34.1 24 | 2/01/2013,26.51458333,26.91666667 25 | 3/01/2013,32.95714286,21.89795918 26 | 4/01/2013,35.98979592,19.42857143 27 | 5/01/2013,29.21041667,31.47916667 28 | 6/01/2013,32.60625,29.5625 29 | 7/01/2013,30.62280702,21.31578947 30 | 8/01/2013,18.76727273,35.12727273 31 | 9/01/2013,21.36041667,31 32 | 10/01/2013,29.84375,16.10416667 33 | 11/01/2013,23.27916667,38.29166667 34 | 12/01/2013,16.202,70.54 35 | -------------------------------------------------------------------------------- /content/Statistics/linear-models/anova/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 3 3 | title: "ANOVA" 4 | output: html_document 5 | aliases: /analysis-variance/ 6 | --- 7 | 8 | 9 | 10 | 11 |

Analysis of variance (ANOVA) is one of the most frequently used techniques in the biological and environmental sciences. ANOVA is used to contrast a continuous dependent variable y across levels of one or more categorical independent variables x. The independent variables are termed the factor or treatment, and the various categories within that treatment are termed the levels. In this module, we will start with the simplest design - those with a single factor.

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Where an independent samples t-test would be used for comparison of group means across two levels, ANOVA is used for the comparison of >2 group means, or when there are more than two or more predictor variables (see ANOVA: factorial). The logic of this test is essentially the same as the t-test - it compares variation between groups to variation within groups to determine whether the observed differences are due to chance or not.

13 | -------------------------------------------------------------------------------- /content/Coding-Skills/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Coding Skills' 3 | weight: 4 4 | output: html_document 5 | --- 6 | 7 | 8 | 9 | 10 |

You might think having skills in computer coding is just for web site and game developers, but skills in coding are increasing valuable for environmental scientists. Running your data analyses and graphics using code means that your research methods are explicitly saved, reproducible and easily shared with colleagues or supervisors.

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On these pages, we give some advice for writing effective code and some of the very useful coding skills that will save you lots of time.

12 | 21 |

22 |

Author: Alistair Poore & Will Cornwell

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Year: 2016

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Last updated: Feb 2022

25 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/LICENSE.md: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2014 Grav 4 | Copyright (c) 2016 MATHIEU CORNIC 5 | Copyright (c) 2017 Valere JEANTET 6 | 7 | Permission is hereby granted, free of charge, to any person obtaining a copy of 8 | this software and associated documentation files (the "Software"), to deal in 9 | the Software without restriction, including without limitation the rights to 10 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of 11 | the Software, and to permit persons to whom the Software is furnished to do so, 12 | subject to the following conditions: 13 | 14 | The above copyright notice and this permission notice shall be included in all 15 | copies or substantial portions of the Software. 16 | 17 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 18 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS 19 | FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR 20 | COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER 21 | IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN 22 | CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 23 | -------------------------------------------------------------------------------- /content/Graphics/basic-plotting/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Basic Plotting in R' 3 | weight: 1 4 | output: html_document 5 | aliases: /basic-plotting-in-r/ 6 | --- 7 | 8 | ```{r,echo=F,fig.width=6, fig.height=2.5} 9 | Plant_height <- read.csv(file = "data/Plant_Height.csv", header = TRUE) 10 | 11 | par(mfrow = c(1, 3)) 12 | 13 | hist(Plant_height$height, main = NULL, xlab = "Plant heigth (cm)", col = "red") 14 | 15 | model <- lm(loght ~ temp, data = Plant_height) 16 | plot(loght ~ temp, data = Plant_height, xlab = "Temperature (C)", ylab = "log(Plant height)", pch = 16, col = "darkgreen") 17 | abline(model, col = "red") 18 | 19 | boxplot(loght ~ hemisphere, data = Plant_height, ylab = "log(Plant height)", xlab = "Hemisphere", names = c("South", "North"), col = "lightblue") 20 | ``` 21 | 22 | R has a very wide range of functions and packages for visualising data. Here is some help for some very simple plots using the base functions in R for data with: 23 | 24 | * [one continuous variable](/graphics/basic-plotting/one-continuous/) - histograms and box plots 25 | * [two continuous variables](/graphics/basic-plotting/two-continuous/) - scatter plots 26 | * [one continuous vs categorical variables](/graphics/basic-plotting/one-continuous-one-factor/) - box plots and bar plots 27 | 28 | -------------------------------------------------------------------------------- /content/Statistics/mixed-models/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 4 3 | title: "Mixed Models" 4 | output: html_document 5 | aliases: /mixed-models/ 6 | --- 7 | 8 | 9 | 10 | 11 |

Mixed models are those with a mixture of fixed and random effects. Random effects are categorical factors where the levels have been selected from many possible levels and the investigator would like to make inferences beyond just the levels chosen. Tricky concept, but imagine contrasting two habitat types (forest and grassland) by sampling five sites within each, and five replicate measures within each site. Habitat type is a fixed factor with the researcher only interested in those two levels of habitat type. If the five sites were chosen from a larger collection of possible sites, then site is considered a random effect with 10 levels.

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20 | Photo: N. Murray

21 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/static/css/tags.css: -------------------------------------------------------------------------------- 1 | /* Tags */ 2 | 3 | #head-tags{ 4 | margin-left:1em; 5 | margin-top:1em; 6 | } 7 | 8 | #body .tags a.tag-link { 9 | display: inline-block; 10 | line-height: 2em; 11 | font-size: 0.8em; 12 | position: relative; 13 | margin: 0 16px 8px 0; 14 | padding: 0 10px 0 12px; 15 | background: #8451a1; 16 | 17 | -webkit-border-bottom-right-radius: 3px; 18 | border-bottom-right-radius: 3px; 19 | -webkit-border-top-right-radius: 3px; 20 | border-top-right-radius: 3px; 21 | 22 | -webkit-box-shadow: 0 1px 2px rgba(0,0,0,0.2); 23 | box-shadow: 0 1px 2px rgba(0,0,0,0.2); 24 | color: #fff; 25 | } 26 | 27 | #body .tags a.tag-link:before { 28 | content: ""; 29 | position: absolute; 30 | top:0; 31 | left: -1em; 32 | width: 0; 33 | height: 0; 34 | border-color: transparent #8451a1 transparent transparent; 35 | border-style: solid; 36 | border-width: 1em 1em 1em 0; 37 | } 38 | 39 | #body .tags a.tag-link:after { 40 | content: ""; 41 | position: absolute; 42 | top: 10px; 43 | left: 1px; 44 | width: 5px; 45 | height: 5px; 46 | -webkit-border-radius: 50%; 47 | border-radius: 100%; 48 | background: #fff; 49 | } 50 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/request-for-new-tutorial.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Request for new tutorial 3 | about: Didn't find the tutorial you were looking for? Did an exisiting tutorial need 4 | further explanation? Let us know and we can see what we can do! 5 | title: 'Tutorial Request:' 6 | labels: '' 7 | assignees: '' 8 | 9 | --- 10 | 11 | **Is your request related to an exisiting tutorial page. Please describe.** 12 | If so, please supply us with a clear and concise description of what you changes would improve the page. 13 | E.g. I would like more explanation on [...] 14 | Please provide a URL or title of the existing tutorial would be super helpful! 15 | 16 | **Which submenu would this new tutorial belong?** 17 | Can you categorise the new tutorial under any of the submenus? E.g. Graphics, Statistics, Data Manipulation, Coding Skills. 18 | 19 | **Describe the new tutorial you'd like** 20 | Concisely describe the goal of the requested tutorial. Please provide links to a package or specific functions the tutorial will likely use 21 | E.g. The tutorial would teach readers how to [...]. 22 | 23 | **Additional context** 24 | Are there other existing tutorials from the internet that is similar to the requested tutorial? If so, please supply us with a link. Stack Overflow posts, Github issues and alike are welcomed! 25 | -------------------------------------------------------------------------------- /content/Statistics/linear-models/_index.html: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 2 3 | title: "Linear Models" 4 | output: html_document 5 | aliases: /linear-models/ 6 | --- 7 | 8 | 9 | 10 | 11 |

These pages have some introductions to commonly used linear models that test the response of a continuous dependent variable against one or more predictor variables that may be continuous or categorical. Note that these are only named as different techniques (e.g., regression vs ANOVA) due to common usage in the literature that you will encounter - they all involve the same linear modelling framework.

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Author: Alistair Poore

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Year: 2016

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Last updated: Feb 2022

24 | -------------------------------------------------------------------------------- /content/Statistics/linear-models/_index.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | weight: 2 3 | title: "Linear Models" 4 | output: html_document 5 | aliases: /linear-models/ 6 | --- 7 | 8 | These pages have some introductions to commonly used linear models that test the response of a continuous dependent variable against one or more predictor variables that may be continuous or categorical. Note that these are only named as different techniques (e.g., regression vs ANOVA) due to common usage in the literature that you will encounter - they all involve the same linear modelling framework. 9 | 10 | 11 | ```{r,echo=F} 12 | Plant_height <- read.csv(file = "data/Plant_Height.csv", header = TRUE) 13 | model <- lm(loght ~ temp, data = Plant_height) 14 | plot(loght ~ temp, data = Plant_height, col = "darkgreen", xlab = "Temperature (C)", ylab = "log(Plant height)", pch = 16) 15 | abline(model, col = "red") 16 | ``` 17 | 18 | * [Linear regression](linear-regression/) 19 | * [Analysis of variance: single factor](anova/anova-single/) 20 | * [Analysis of variance: factorial](anova/anova-factorial/) 21 | * [Understanding interactions](interactions) 22 | * [Interpreting coefficients in linear models](../glms/interpret-glm-coeffs/) 23 | 24 | 25 | 26 | **Author**: Alistair Poore 27 | 28 | **Year:** 2016 29 | 30 | **Last updated:** `r format(Sys.time(), "%b %Y")` 31 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/shortcodes/attachments.html: -------------------------------------------------------------------------------- 1 | {{ $_hugo_config := `{ "version": 1 }` }} 2 |
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On these pages, we give some guidance for manipulating data in ways that can save a lot of time when it comes to analysing data and making effective figures. 9 | 10 | ![](Data_entry_image.jpg) 11 | 12 | Data manipulation using the packages [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html), [tidyr](https://blog.rstudio.org/2014/07/22/introducing-tidyr/) and [reshape2](https://cran.r-project.org/web/packages/reshape2/). 13 | 14 | * [Making new variables](making-new-variables/) 15 | * [Subsetting data](subsetting-data/) - selecting rows and columns 16 | * [Summarising data](summarising-data/) - extracting summary statistics 17 | * [Combining data sets](combining-datasets/) - joining entire data sets, or parts by matching rows 18 | * [Reshaping data](reshaping-data/) between wide and long formats 19 | 20 | 21 | ### Further help 22 | 23 | The British Ecological Society's [Guide to Data Management in Ecology and Evolution](http://www.britishecologicalsociety.org/wp-content/uploads/Publ_Data-Management-Booklet.pdf) 24 | 25 | 26 | **Author**: Alistair Poore 27 | 28 | **Year:** 2016 29 | 30 | **Last updated:** `r format(Sys.time(), "%b %Y")` 31 | -------------------------------------------------------------------------------- /content/Statistics/linear-models/anova/anova-factorial/Sessile.csv: -------------------------------------------------------------------------------- 1 | Richness,Copper,Orientation 2 | 68,None,vertical 3 | 64,None,vertical 4 | 64,None,vertical 5 | 63,None,vertical 6 | 69,None,vertical 7 | 63,None,vertical 8 | 70,None,vertical 9 | 68,None,vertical 10 | 68,None,vertical 11 | 62,None,vertical 12 | 70,None,Horizontal 13 | 71,None,Horizontal 14 | 81,None,Horizontal 15 | 67,None,Horizontal 16 | 71,None,Horizontal 17 | 65,None,Horizontal 18 | 65,None,Horizontal 19 | 67,None,Horizontal 20 | 74,None,Horizontal 21 | 65,None,Horizontal 22 | 60,Low,vertical 23 | 58,Low,vertical 24 | 57,Low,vertical 25 | 62,Low,vertical 26 | 60,Low,vertical 27 | 59,Low,vertical 28 | 58,Low,vertical 29 | 58,Low,vertical 30 | 59,Low,vertical 31 | 61,Low,vertical 32 | 57,Low,Horizontal 33 | 54,Low,Horizontal 34 | 54,Low,Horizontal 35 | 57,Low,Horizontal 36 | 54,Low,Horizontal 37 | 57,Low,Horizontal 38 | 56,Low,Horizontal 39 | 56,Low,Horizontal 40 | 57,Low,Horizontal 41 | 56,Low,Horizontal 42 | 39,High,vertical 43 | 42,High,vertical 44 | 41,High,vertical 45 | 47,High,vertical 46 | 48,High,vertical 47 | 46,High,vertical 48 | 46,High,vertical 49 | 44,High,vertical 50 | 46,High,vertical 51 | 38,High,vertical 52 | 56,High,Horizontal 53 | 53,High,Horizontal 54 | 56,High,Horizontal 55 | 56,High,Horizontal 56 | 56,High,Horizontal 57 | 56,High,Horizontal 58 | 54,High,Horizontal 59 | 56,High,Horizontal 60 | 56,High,Horizontal 61 | 55,High,Horizontal 62 | -------------------------------------------------------------------------------- /themes/hugo-theme-learn/layouts/index.html: -------------------------------------------------------------------------------- 1 | {{ partial "header.html" . }} 2 | 3 | navigation 4 | 5 | 6 | {{if .Site.Home.Content }} 7 | {{.Site.Home.Content}} 8 | {{else}} 9 | {{if eq .Site.Language.Lang "fr"}} 10 |

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