Appendix B Software versions

This book was rendered from the source code on Jun 21, 2023 at 07:15:19 PM with the following R package versions.

R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
[6] methods   base     

other attached packages:
 [1] scales_1.2.1     ggrepel_0.9.3    kableExtra_1.3.4
 [4] phangorn_2.11.1  Matrix_1.5-1     lubridate_1.9.2 
 [7] forcats_1.0.0    dplyr_1.1.0      purrr_1.0.1     
[10] readr_2.1.4      tidyr_1.3.0      tibble_3.2.0    
[13] ggplot2_3.4.1    tidyverse_2.0.0  stringr_1.5.0   
[16] phytools_1.5-1   maps_3.4.1       magrittr_2.0.3  
[19] gridExtra_2.3    geiger_2.0.10    ape_5.7-1       
[22] ggtree_3.6.2     treeio_1.22.0    bookdown_0.33   

loaded via a namespace (and not attached):
 [1] subplex_1.8             nlme_3.1-160           
 [3] webshot_0.5.4           doParallel_1.0.17      
 [5] httr_1.4.5              numDeriv_2016.8-1.1    
 [7] tools_4.2.2             bslib_0.4.2            
 [9] utf8_1.2.3              R6_2.5.1               
[11] mgcv_1.8-41             lazyeval_0.2.2         
[13] colorspace_2.1-0        withr_2.5.0            
[15] tidyselect_1.2.0        mnormt_2.1.1           
[17] compiler_4.2.2          cli_3.6.0              
[19] rvest_1.0.3             expm_0.999-7           
[21] xml2_1.3.3              labeling_0.4.2         
[23] sass_0.4.5              mvtnorm_1.1-3          
[25] quadprog_1.5-8          systemfonts_1.0.4      
[27] digest_0.6.31           yulab.utils_0.0.6      
[29] rmarkdown_2.20          svglite_2.1.1          
[31] pkgconfig_2.0.3         htmltools_0.5.4        
[33] plotrix_3.8-2           highr_0.10             
[35] fastmap_1.1.1           rlang_1.0.6            
[37] rstudioapi_0.14         optimParallel_1.0-2    
[39] farver_2.1.1            gridGraphics_0.5-1     
[41] jquerylib_0.1.4         generics_0.1.3         
[43] combinat_0.0-8          jsonlite_1.8.4         
[45] ggplotify_0.1.0         patchwork_1.1.2        
[47] Rcpp_1.0.10             munsell_0.5.0          
[49] fansi_1.0.4             lifecycle_1.0.3        
[51] scatterplot3d_0.3-42    stringi_1.7.12         
[53] yaml_2.3.7              clusterGeneration_1.3.7
[55] MASS_7.3-58.1           grid_4.2.2             
[57] parallel_4.2.2          lattice_0.20-45        
[59] splines_4.2.2           hms_1.1.2              
[61] magick_2.7.4            knitr_1.42             
[63] pillar_1.8.1            igraph_1.4.1           
[65] codetools_0.2-18        fastmatch_1.1-3        
[67] glue_1.6.2              evaluate_0.20          
[69] ggimage_0.3.1           ggfun_0.0.9            
[71] deSolve_1.35            png_0.1-8              
[73] vctrs_0.5.2             tzdb_0.3.0             
[75] foreach_1.5.2           gtable_0.3.1           
[77] cachem_1.0.7            xfun_0.37              
[79] tidytree_0.4.2          coda_0.19-4            
[81] viridisLite_0.4.1       iterators_1.0.14       
[83] aplot_0.1.10            timechange_0.2.0       
[85] ellipsis_0.3.2