Appendix B Software versions

This book, version 1.0.0, was rendered from the source code on Aug 07, 2026 at 02:46:01 PM, at git commit a25c6a5 (2026-08-04), with the following R package versions.

R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.s
o.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenbl
asp-r0.3.26.so;  LAPACK version 3.12.0

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       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] nlme_3.1-168     scales_1.4.0     ggrepel_0.9.6   
 [4] kableExtra_1.4.0 phangorn_2.12.1  Matrix_1.7-3    
 [7] lubridate_1.9.4  forcats_1.0.1    dplyr_1.1.4     
[10] purrr_1.1.0      readr_2.1.5      tidyr_1.3.1     
[13] tibble_3.3.0     ggplot2_4.0.0    tidyverse_2.0.0 
[16] stringr_1.5.2    magrittr_2.0.4   gridExtra_2.3   
[19] geiger_2.0.11    phytools_2.5-2   maps_3.4.3      
[22] ape_5.8-1        ggtree_4.0.5     treeio_1.34.0   
[25] renv_1.1.8       bookdown_0.45   

loaded via a namespace (and not attached):
 [1] mnormt_2.1.1            rlang_1.1.6            
 [3] compiler_4.5.1          mgcv_1.9-3             
 [5] png_0.1-8               systemfonts_1.3.1      
 [7] vctrs_0.6.5             combinat_0.0-8         
 [9] quadprog_1.5-8          crayon_1.5.3           
[11] pkgconfig_2.0.3         fastmap_1.2.0          
[13] magick_2.9.1            labeling_0.4.3         
[15] subplex_1.9             deSolve_1.40           
[17] rmarkdown_2.30          tzdb_0.5.0             
[19] bit_4.6.0               tinytex_0.57           
[21] xfun_0.53               cachem_1.1.0           
[23] aplot_0.2.9             clusterGeneration_1.3.8
[25] jsonlite_2.0.0          parallel_4.5.1         
[27] R6_2.6.1                bslib_0.9.0            
[29] stringi_1.8.7           RColorBrewer_1.1-3     
[31] jquerylib_0.1.4         numDeriv_2016.8-1.1    
[33] Rcpp_1.1.0              iterators_1.0.14       
[35] knitr_1.50              optimParallel_1.0-2    
[37] splines_4.5.1           igraph_2.2.1           
[39] timechange_0.3.0        tidyselect_1.2.1       
[41] rstudioapi_0.17.1       yaml_2.3.10            
[43] doParallel_1.0.17       codetools_0.2-20       
[45] lattice_0.22-7          withr_3.0.2            
[47] S7_0.2.0                coda_0.19-4.1          
[49] evaluate_1.0.5          ggimage_0.3.5          
[51] gridGraphics_0.5-1      xml2_1.4.1             
[53] pillar_1.11.1           foreach_1.5.2          
[55] ggfun_0.2.0             generics_0.1.4         
[57] vroom_1.6.6             hms_1.1.4              
[59] tidytree_0.4.6          glue_1.8.0             
[61] gdtools_0.4.4           scatterplot3d_0.3-44   
[63] lazyeval_0.2.2          tools_4.5.1            
[65] ggiraph_0.9.2           fs_1.6.6               
[67] mvtnorm_1.3-3           fastmatch_1.1-6        
[69] grid_4.5.1              patchwork_1.3.2        
[71] cli_3.6.5               rappdirs_0.3.3         
[73] DEoptim_2.2-8           textshaping_1.0.4      
[75] fontBitstreamVera_0.1.1 expm_1.0-0             
[77] viridisLite_0.4.2       svglite_2.2.2          
[79] gtable_0.3.6            yulab.utils_0.2.1      
[81] sass_0.4.10             digest_0.6.37          
[83] fontquiver_0.2.1        ggplotify_0.1.3        
[85] htmlwidgets_1.6.4       farver_2.1.2           
[87] htmltools_0.5.8.1       lifecycle_1.0.4        
[89] fontLiberation_0.1.0    bit64_4.6.0-1          
[91] MASS_7.3-65