├── .gitignore ├── 2d_convolution.ipynb ├── Makefile ├── Peeves.pdf ├── Rmisc ├── CLMM_example.R ├── RTMB_mnom.R ├── analemma.R ├── annotation.R ├── brackets.Rmd ├── comp_pkg_versions.R ├── cran_pkg_scrape.R ├── dirich.R ├── distrib_lme4.R ├── extremecold.R ├── find_identity.R ├── fitting.qmd ├── ggpies.Rmd ├── glm_scrape.R ├── gscrape.RData ├── het_lmm.R ├── investigate.R ├── jacobian.Rmd ├── lme4_hvar.R ├── noncent.R ├── ordinal_RTMB.R ├── powexp_prior.R ├── prior_shiny.R ├── rtmb_glmm.qmd ├── rtmb_mle.rmd ├── seo_table1.R ├── seo_table1.csv ├── sonify_pendulum.R ├── spline_quantiles.R ├── wei_fig.png ├── wei_tab.csv ├── wei_tab.png └── wei_tab_to_fig.R ├── ad_in_R.qmd ├── apa.csl ├── aristotle.md ├── bayes ├── .gitignore ├── Makefile ├── README.md ├── TODO.md ├── bayes.bib ├── examples.rmd ├── examples1.rda ├── intro.rmd ├── outputs │ └── quantiles.Rout.pdf ├── pix │ ├── cc-attrib-nc.png │ ├── parlett.png │ └── workflow.png ├── priors.rmd ├── quantiles.R ├── reading.rmd ├── run_examples.R └── setup.rmd ├── beta_df.rmd ├── brant.bib ├── brant_survive.csv ├── brant_survive.rmd ├── carrigan.qmd ├── cc.png ├── celebrate ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R │ ├── funs.R │ └── pkgname.R ├── README.md ├── cat_big_x.wav ├── cat_fight.wav ├── cat_growl.wav ├── cat_kitten.wav ├── cat_meow2.wav ├── cat_meow_x.wav ├── cat_y.wav ├── inst │ ├── .DS_Store │ ├── 146960__zabuhailo__cathisses.wav │ ├── 213889__counter-gamer__the-cat-s-meow.wav │ ├── 322012__abolla__cat-purr.wav │ ├── cat_purr.wav │ └── sounds │ │ ├── 175409__kirbydx__wah-wah-sad-trombone.wav │ │ ├── 78822__primordiality__fanfare-1.wav │ │ └── README.md └── man │ ├── celebrate.Rd │ └── load_sounds.Rd ├── contrasts.bib ├── corr_bootstrap.bib ├── corr_bootstrap.qmd ├── distrib.bib ├── distrib.html ├── distrib.rmd ├── docs ├── aristotle.html ├── bayes │ ├── README.md │ ├── bayes.bib │ ├── examples.html │ ├── intro.html │ ├── priors.html │ ├── reading.html │ └── setup.html ├── beta_df.html ├── brant_survive.html ├── by-sa.png ├── carrigan.html ├── corr_bootstrap.html ├── elliptope.html ├── federated.html ├── ggpies.html ├── graphics_formats.html ├── hundredflowers.html ├── mgreen_contrasts.html ├── mmd_mixedeffects.html ├── nonlin_timevar.html ├── nonlin_timevar_files │ ├── figure-revealjs │ │ └── procobs_plot-1.png │ └── libs │ │ ├── clipboard │ │ └── clipboard.min.js │ │ ├── quarto-html │ │ ├── light-border.css │ │ ├── popper.min.js │ │ ├── quarto-html.min.css │ │ ├── quarto-syntax-highlighting.css │ │ ├── tabby.min.js │ │ ├── tippy.css │ │ └── tippy.umd.min.js │ │ └── revealjs │ │ ├── dist │ │ ├── reset.css │ │ ├── reveal.css │ │ ├── reveal.esm.js │ │ ├── reveal.esm.js.map │ │ ├── reveal.js │ │ ├── reveal.js.map │ │ └── theme │ │ │ ├── fonts │ │ │ ├── league-gothic │ │ │ │ ├── LICENSE │ │ │ │ ├── league-gothic.css │ │ │ │ ├── league-gothic.eot │ │ │ │ ├── league-gothic.ttf │ │ │ │ └── league-gothic.woff │ │ │ └── source-sans-pro │ │ │ │ ├── LICENSE │ │ │ │ ├── source-sans-pro-italic.eot │ │ │ │ ├── source-sans-pro-italic.ttf │ │ │ │ ├── source-sans-pro-italic.woff │ │ │ │ ├── source-sans-pro-regular.eot │ │ │ │ ├── source-sans-pro-regular.ttf │ │ │ │ ├── source-sans-pro-regular.woff │ │ │ │ ├── source-sans-pro-semibold.eot │ │ │ │ ├── source-sans-pro-semibold.ttf │ │ │ │ ├── source-sans-pro-semibold.woff │ │ │ │ ├── source-sans-pro-semibolditalic.eot │ │ │ │ ├── source-sans-pro-semibolditalic.ttf │ │ │ │ ├── source-sans-pro-semibolditalic.woff │ │ │ │ └── source-sans-pro.css │ │ │ └── quarto.css │ │ └── plugin │ │ ├── highlight │ │ ├── highlight.esm.js │ │ ├── highlight.js │ │ ├── monokai.css │ │ ├── plugin.js │ │ └── zenburn.css │ │ ├── markdown │ │ ├── markdown.esm.js │ │ ├── markdown.js │ │ └── plugin.js │ │ ├── math │ │ ├── katex.js │ │ ├── math.esm.js │ │ ├── math.js │ │ ├── mathjax2.js │ │ ├── mathjax3.js │ │ └── plugin.js │ │ ├── notes │ │ ├── notes.esm.js │ │ ├── notes.js │ │ ├── plugin.js │ │ └── speaker-view.html │ │ ├── pdf-export │ │ ├── pdfexport.js │ │ └── plugin.yml │ │ ├── quarto-line-highlight │ │ ├── line-highlight.css │ │ ├── line-highlight.js │ │ └── plugin.yml │ │ ├── quarto-support │ │ ├── footer.css │ │ ├── plugin.yml │ │ └── support.js │ │ ├── reveal-menu │ │ ├── menu.css │ │ ├── menu.js │ │ ├── plugin.yml │ │ ├── quarto-menu.css │ │ └── quarto-menu.js │ │ ├── search │ │ ├── plugin.js │ │ ├── search.esm.js │ │ └── search.js │ │ └── zoom │ │ ├── plugin.js │ │ ├── zoom.esm.js │ │ └── zoom.js ├── ode_braindump.html ├── peeves.html ├── pix │ ├── 400Behandlung_der_Syphilis.jpg │ ├── George_C._Williams.jpg │ ├── HIV_dur.rds │ ├── HIV_progression.jpg │ ├── Rabbit_with_Myxomatosis_1(RLH).jpg │ ├── addsides │ ├── beaumont_abc.png │ ├── berngruber0.png │ ├── berngruber0_A.png │ ├── berngruber0_B.png │ ├── bolker.jpg │ ├── bolker_sm.jpg │ ├── citation_advantage.jpg │ ├── darwin2_small.jpg │ ├── dynam-DAG.png │ ├── fig1.pdf │ ├── fig1.png │ ├── forking_paths.jpg │ ├── gelmanhill.jpg │ ├── gh_sm.jpg │ ├── harrell.jpg │ ├── harrell_sm.jpg │ ├── hilborn_mangel.jpg │ ├── hilborn_mangel_sm.jpg │ ├── miller_2021.jpg │ ├── particle.png │ ├── raberg_tol.png │ ├── royall.jpg │ ├── royall_sm.jpg │ ├── sci_hell.png │ ├── sci_hellB.png │ ├── scicit.jpg │ ├── scream.jpeg │ ├── stackoverflow.png │ ├── stackoverflowB.png │ ├── student_kurtosis.png │ ├── tmp.jpg │ ├── vines_data.png │ ├── yellowstone_browse.png │ ├── yellowstone_browse2.png │ ├── zuur.jpg │ └── zuur_sm.jpg ├── poscor3d.html ├── posfun.html ├── r_parallel_hpc.html ├── r_performance.html ├── rtmb_glmm.html ├── rtmb_intro.html ├── sim_sesoi.html ├── stats_poetry.html ├── thesis_notes.html └── thesis_stats.html ├── duodec_7th.txt ├── elliptope.bib ├── elliptope.qmd ├── equity.bib ├── equity.md ├── equity.pdf ├── equity2.md ├── federated.qmd ├── github_actions.md ├── graphics_formats.qmd ├── guelph-reefqual.pdf ├── hundredflowers.bib ├── hundredflowers.png ├── hundredflowers.qmd ├── logexp ├── logexp.rmd ├── nestsurv.bib └── shaffer_sas_2004.txt ├── mail_generic.R ├── make_sched.R ├── mathsounds.qmd ├── mcmc.bib ├── mcmc.html ├── mcmc.md ├── mcmc_epidemic.bib ├── mcmc_epidemic.md ├── mgreen_contrasts.Rmd ├── misc_stats ├── RatioMods.R ├── cd_df.rds ├── ordinal_probpredCI.rmd └── priors.rmd ├── nestpred_scrape.md ├── ode_braindump.bib ├── ode_braindump.qmd ├── ode_tools.csv ├── peak_I.rmd ├── peak_I_simple.rmd ├── peeves.md ├── penguins ├── lots_of_penguins.R ├── penguin_traits.pdf └── penguin_traits.rds ├── posfun.Rmd ├── posfun.bib ├── posfun.pdf ├── posfun_ex.cpp ├── qq ├── README.md ├── qq.bib ├── qq_analysis.Rmd ├── qq_responses.csv └── qqsurvey.R ├── r_parallel_hpc.rmd ├── reflist2.csl ├── respec.rmd ├── rouss_elliptope.png ├── rstudio_beamer ├── README.md ├── phd052810s.png ├── repro.bib ├── rstudio_beamer.Rnw └── rstudio_beamer.pdf ├── sensitivity ├── sensitivity.bib ├── sensitivity.pdf └── sensitivity.tex ├── shaffer_chat_nest.txt ├── shiny_sicklecell ├── server.R └── ui.R ├── sim_sesoi ├── TODO.md ├── clarityFuns.R ├── claritySims.R ├── jd_notes.md ├── sesoi.bib ├── sesoi_shiny.R ├── sim_sesoi.R ├── sim_sesoi.qmd ├── sim_sesoi │ └── app.R ├── sim_sesoi_batch1.R ├── sim_sesoi_batch2.R ├── sim_sesoi_funs.R └── simfun2_test.R ├── simulation_notes.md ├── solve-beta.Rnw ├── solve-beta.bib ├── spacetime_splines.qmd ├── stats_poetry.md ├── stochsim ├── erlangseir-funs.R └── gillesp.R ├── tab_to_fig ├── tab.csv ├── tab.png └── tab_to_fig.R ├── talks ├── Makefile ├── apa.csl ├── auto.dta ├── blank_pvals.png ├── by-sa.png ├── contraceptionTimings.rda ├── csee_2017 │ ├── Makefile │ ├── TODO.md │ ├── bolker_jsdm.html │ ├── bolker_jsdm.rmd │ ├── csee.bib │ ├── pix │ │ ├── USA.pdf │ │ ├── abutilon.png │ │ ├── acaena.png │ │ ├── aspen.png │ │ ├── bakeoff_cartoon.png │ │ ├── bakeoff_cartoon1A.png │ │ ├── bakeoff_cartoon2.png │ │ ├── bakeoff_cartoon2B.png │ │ ├── bakeoff_res1.png │ │ ├── bakeoff_sampling_2.png │ │ ├── bakeoff_sum_all_Ac.png │ │ ├── bakeoff_sum_all_Bc.png │ │ ├── bakeoff_sum_coverage.png │ │ ├── bakeoff_sum_deviance.png │ │ ├── bakeoff_sum_deviance_A.png │ │ ├── bakeoff_sum_deviance_Ac.png │ │ ├── bakeoff_sum_deviance_B.png │ │ ├── bakeoff_sum_deviance_Bc.png │ │ ├── bakeoff_sum_sprichMSE.png │ │ ├── bakeoff_sum_sprichMSE_A.png │ │ ├── bakeoff_sum_sprichMSE_Ac.png │ │ ├── bakeoff_sum_sprichMSE_B.png │ │ ├── bakeoff_sum_sprichMSE_Bc.png │ │ ├── bakeoff_sum_tjur.png │ │ ├── bakeoff_sum_tjur_A.png │ │ ├── bakeoff_sum_tjur_Ac.png │ │ ├── bakeoff_sum_tjur_B.png │ │ ├── bakeoff_sum_tjur_Bc.png │ │ ├── bakeoff_summ_P1-6.png │ │ ├── bakeoff_summ_all.png │ │ ├── bakeoff_summ_all_A.png │ │ ├── bakeoff_summ_all_B.png │ │ ├── black_spruce.png │ │ ├── breiman.png │ │ ├── butterfly1.png │ │ ├── butterfly2.png │ │ ├── butterfly3.png │ │ ├── butterfly_sites.png │ │ ├── cratoneuropsis.png │ │ ├── dawsonia.png │ │ ├── diatom_sites.png │ │ ├── diatoms.png │ │ ├── epilobium.png │ │ ├── fungus1.png │ │ ├── fungus2.png │ │ ├── fungus_sites.png │ │ ├── larch.png │ │ ├── lodge_pole.png │ │ ├── peters.jpg │ │ ├── peters2.png │ │ ├── sclerodontium.png │ │ ├── timings.png │ │ ├── usa.png │ │ ├── victoria.png │ │ └── white_spruce.png │ ├── reflist2.csl │ ├── timings.R │ └── timings.txt ├── eco_models.bib ├── eco_models.pdf ├── eco_models.rmd ├── ewald_cholera.csv ├── ewald_cholera.jpg ├── excel_ex.png ├── nonlin.bib ├── nonlin_timevar.qmd ├── oa.bib ├── open_pub.html ├── open_pub.rmd ├── pix │ ├── 400Behandlung_der_Syphilis.jpg │ ├── George_C._Williams.jpg │ ├── HIV_dur.rds │ ├── HIV_progression.jpg │ ├── Rabbit_with_Myxomatosis_1(RLH).jpg │ ├── TMB.png │ ├── addsides │ ├── beaumont_abc.png │ ├── berngruber0.png │ ├── berngruber0_A.png │ ├── berngruber0_B.png │ ├── better_computer.png │ ├── bolker.jpg │ ├── bolker_sm.jpg │ ├── citation_advantage.jpg │ ├── darwin2_small.jpg │ ├── data_table_bench.png │ ├── dynam-DAG.png │ ├── fig1.pdf │ ├── fig1.png │ ├── forking_paths.jpg │ ├── gelmanhill.jpg │ ├── gh_sm.jpg │ ├── harrell.jpg │ ├── harrell_sm.jpg │ ├── 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