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