Appendix B Software versions

This book was rendered from the source code on Oct 07, 2025 at 03:34:23 PM 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.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-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] scales_1.4.0     ggrepel_0.9.6    kableExtra_1.4.0
 [4] phangorn_2.12.1  Matrix_1.7-3     lubridate_1.9.4 
 [7] forcats_1.0.1    dplyr_1.1.4      purrr_1.1.0     
[10] readr_2.1.5      tidyr_1.3.1      tibble_3.3.0    
[13] ggplot2_4.0.0    tidyverse_2.0.0  stringr_1.5.2   
[16] magrittr_2.0.4   gridExtra_2.3    geiger_2.0.11   
[19] phytools_2.5-2   maps_3.4.3       ape_5.8-1       
[22] ggtree_3.16.3    treeio_1.32.0    bookdown_0.44   

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_2.9.0            labeling_0.4.3         
[15] subplex_1.9             deSolve_1.40           
[17] rmarkdown_2.30          tzdb_0.5.0             
[19] bit_4.6.0               xfun_0.53              
[21] cachem_1.1.0            aplot_0.2.9            
[23] clusterGeneration_1.3.8 jsonlite_2.0.0         
[25] uuid_1.2-1              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_2.1.4           
[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_0.3.4          
[51] gridGraphics_0.5-1      xml2_1.4.0             
[53] pillar_1.11.1           rsconnect_1.5.1        
[55] foreach_1.5.2           ggfun_0.2.0            
[57] generics_0.1.4          vroom_1.6.6            
[59] hms_1.1.3               tidytree_0.4.6         
[61] glue_1.8.0              scatterplot3d_0.3-44   
[63] lazyeval_0.2.2          tools_4.5.1            
[65] ggiraph_0.9.1           fs_1.6.6               
[67] mvtnorm_1.3-3           fastmatch_1.1-6        
[69] grid_4.5.1              nlme_3.1-168           
[71] patchwork_1.3.2         cli_3.6.5              
[73] rappdirs_0.3.3          DEoptim_2.2-8          
[75] textshaping_1.0.3       expm_1.0-0             
[77] viridisLite_0.4.2       svglite_2.2.1          
[79] gtable_0.3.6            yulab.utils_0.2.1      
[81] sass_0.4.10             digest_0.6.37          
[83] ggplotify_0.1.3         htmlwidgets_1.6.4      
[85] farver_2.1.2            htmltools_0.5.8.1      
[87] lifecycle_1.0.4         bit64_4.6.0-1          
[89] MASS_7.3-65