Benjamin Wong Blonder
28 November 2022
Blonder et al., Navigation between initial and desired community states using shortcuts.
Code used to generate the 'outputs' folder, as well as explanation of file structure, is in: https://github.com/michaelhlim/CoexistenceControl.jl
To replicate all analyses in R:
- source('1 prep datasets.R'), which generates the 'outputs' subfolder.
- Then source('2 analysis.R'), which creates figures and tables in the 'figures' subfolder.
- Figure 1 is created separately and appears in the 'figure 1' subfolder.
R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.6.1
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] caret_6.0-93 lattice_0.20-45 forcats_0.5.2 stringr_1.4.1 purrr_0.3.4 readr_2.1.2 tibble_3.1.8
[8] tidyverse_1.3.2 pdp_0.8.1 ranger_0.14.1 colorRamps_2.3.1 igraph_1.3.4 data.table_1.14.2 ggpubr_0.4.0
[15] ggplot2_3.3.6 tidyr_1.2.1 dplyr_1.0.10
loaded via a namespace (and not attached):
[1] nlme_3.1-159 fs_1.5.2 lubridate_1.8.0 RColorBrewer_1.1-3 httr_1.4.4 tools_4.2.0
[7] backports_1.4.1 utf8_1.2.2 R6_2.5.1 rpart_4.1.16 DBI_1.1.3 colorspace_2.0-3
[13] nnet_7.3-17 withr_2.5.0 tidyselect_1.1.2 compiler_4.2.0 cli_3.4.0 rvest_1.0.3
[19] xml2_1.3.3 scales_1.2.1 proxy_0.4-27 digest_0.6.29 pkgconfig_2.0.3 parallelly_1.32.1
[25] dbplyr_2.2.1 rlang_1.0.5 readxl_1.4.1 rstudioapi_0.14 generics_0.1.3 jsonlite_1.8.0
[31] ModelMetrics_1.2.2.2 car_3.1-0 googlesheets4_1.0.1 magrittr_2.0.3 Matrix_1.5-1 Rcpp_1.0.9
[37] munsell_0.5.0 fansi_1.0.3 abind_1.4-5 lifecycle_1.0.2 stringi_1.7.8 pROC_1.18.0
[43] carData_3.0-5 MASS_7.3-58.1 plyr_1.8.7 recipes_1.0.1 grid_4.2.0 parallel_4.2.0
[49] listenv_0.8.0 crayon_1.5.1 haven_2.5.1 splines_4.2.0 hms_1.1.2 pillar_1.8.1
[55] ggsignif_0.6.3 future.apply_1.9.1 reshape2_1.4.4 codetools_0.2-18 stats4_4.2.0 reprex_2.0.2
[61] glue_1.6.2 modelr_0.1.9 vctrs_0.4.1 tzdb_0.3.0 foreach_1.5.2 cellranger_1.1.0
[67] gtable_0.3.1 future_1.28.0 assertthat_0.2.1 gower_1.0.0 prodlim_2019.11.13 broom_1.0.1
[73] e1071_1.7-11 rstatix_0.7.0 class_7.3-20 survival_3.4-0 googledrive_2.0.0 gargle_1.2.1
[79] timeDate_4021.104 iterators_1.0.14 hardhat_1.2.0 lava_1.6.10 globals_0.16.1 ellipsis_0.3.2
[85] ipred_0.9-13