Appendix B Software versions

This book, version 1.1.0, was rendered from the source code on Aug 24, 2026 at 11:42:31 AM, at git commit f36b616 (2026-08-24), 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      

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] systemfonts_1.3.1       vctrs_0.6.5            
 [7] combinat_0.0-8          quadprog_1.5-8         
 [9] crayon_1.5.3            pkgconfig_2.0.3        
[11] fastmap_1.2.0           magick_2.9.1           
[13] labeling_0.4.3          subplex_1.9            
[15] deSolve_1.40            rmarkdown_2.30         
[17] tzdb_0.5.0              bit_4.6.0              
[19] xfun_0.53               cachem_1.1.0           
[21] aplot_0.2.9             clusterGeneration_1.3.8
[23] jsonlite_2.0.0          parallel_4.5.1         
[25] R6_2.6.1                bslib_0.9.0            
[27] stringi_1.8.7           RColorBrewer_1.1-3     
[29] jquerylib_0.1.4         numDeriv_2016.8-1.1    
[31] Rcpp_1.1.0              bookdown_0.45          
[33] iterators_1.0.14        knitr_1.50             
[35] optimParallel_1.0-2     splines_4.5.1          
[37] igraph_2.2.1            timechange_0.3.0       
[39] tidyselect_1.2.1        rstudioapi_0.17.1      
[41] yaml_2.3.10             doParallel_1.0.17      
[43] codetools_0.2-20        lattice_0.22-7         
[45] withr_3.0.2             S7_0.2.0               
[47] coda_0.19-4.1           evaluate_1.0.5         
[49] ggimage_0.3.5           gridGraphics_0.5-1     
[51] xml2_1.4.1              pillar_1.11.1          
[53] foreach_1.5.2           ggfun_0.2.0            
[55] generics_0.1.4          vroom_1.6.6            
[57] hms_1.1.4               tidytree_0.4.6         
[59] glue_1.8.0              gdtools_0.4.4          
[61] scatterplot3d_0.3-44    lazyeval_0.2.2         
[63] tools_4.5.1             ggiraph_0.9.2          
[65] fs_1.6.6                mvtnorm_1.3-3          
[67] fastmatch_1.1-6         grid_4.5.1             
[69] patchwork_1.3.2         cli_3.6.5              
[71] rappdirs_0.3.3          DEoptim_2.2-8          
[73] textshaping_1.0.4       fontBitstreamVera_0.1.1
[75] expm_1.0-0              viridisLite_0.4.2      
[77] svglite_2.2.2           gtable_0.3.6           
[79] yulab.utils_0.2.1       sass_0.4.10            
[81] digest_0.6.37           fontquiver_0.2.1       
[83] ggplotify_0.1.3         htmlwidgets_1.6.4      
[85] farver_2.1.2            htmltools_0.5.8.1      
[87] lifecycle_1.0.4         fontLiberation_0.1.0   
[89] bit64_4.6.0-1           MASS_7.3-65