This repository includes R scripts to simulate datasets, fit models (LMMs and PLMMs), and plot the results. It also includes R functions to do bootstrapping on PLMMs and examples about how to use it.
Theses scripts are under MIT license and come with no guaranntees. Please cite the paper if you use the code elsewhere.
All questions should be directed to Daijiang Li (firstname.lastname@example.org).
Rcodefolder: all R codes used in the main text.
simulation.R: simulates datasets, fits models (LMMs and PLMMs), and saves results.
plot.R: plot the results, reproduce all figures from the paper.
bootstrap_plmm_mc.R: do bootstrapping on PLMMs, with multiple cores as an option.
rdsfolder: model fitting results from LMMs and PLMMs with varing number of species (i.e. Type I errors).
rds2folder: model fitting results from LMMs and PLMMs with varing true parameters (i.e. Type II errors).
rds_bootstrapfolder: results of bootstrapping on PLMMs.
appendixS1folder: R code and data to show that they way to simulate the phylogeny does not affect our results and conclusions. The R codes are mostly the same as those in the main text, with their ways to simulate phylogeny changed.
`sessionInfo()` R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.2 locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  viridis_0.3.4 cowplot_0.6.2 ggplot2_2.2.0 tidyr_0.6.0 dplyr_0.5.0 plyr_1.8.4 loaded via a namespace (and not attached):  Rcpp_0.12.8 digest_0.6.10 assertthat_0.1 MASS_7.3-45 grid_3.3.2 R6_2.2.0 gtable_0.2.0 DBI_0.5 magrittr_1.5  scales_0.4.1 stringi_1.1.1 reshape2_1.4.1 lazyeval_0.2.0 labeling_0.3 tools_3.3.2 stringr_1.1.0 munsell_0.4.3 colorspace_1.2-6  gridExtra_2.2.1 tibble_1.2
Copyright (c)  [Daijiang Li]
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