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