Appendix B Software versions

This book was rendered from the source code on Oct 28, 2024 at 02:36:39 AM with the following R package versions.

R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 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/liblapack.so.3

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_1.1.1     ggrepel_0.9.1    kableExtra_1.3.4
 [4] phangorn_2.8.1   Matrix_1.4-0     forcats_0.5.1   
 [7] dplyr_1.0.8      purrr_0.3.4      readr_2.1.2     
[10] tidyr_1.2.0      tibble_3.1.6     ggplot2_3.3.5   
[13] tidyverse_1.3.1  stringr_1.4.0    phytools_1.0-1  
[16] maps_3.4.0       magrittr_2.0.3   gridExtra_2.3   
[19] geiger_2.0.7     ape_5.6-2        ggtree_3.2.1    
[22] treeio_1.18.1    bookdown_0.25   

loaded via a namespace (and not attached):
 [1] colorspace_2.0-3        ellipsis_0.3.2         
 [3] fs_1.5.2                aplot_0.1.2            
 [5] rstudioapi_0.13         farver_2.1.0           
 [7] bit64_4.0.5             fansi_1.0.3            
 [9] mvtnorm_1.1-3           lubridate_1.8.0        
[11] xml2_1.3.3              splines_4.1.3          
[13] codetools_0.2-18        mnormt_2.0.2           
[15] knitr_1.38              jsonlite_1.8.0         
[17] broom_0.7.12            dbplyr_2.1.1           
[19] png_0.1-7               compiler_4.1.3         
[21] httr_1.4.2              backports_1.4.1        
[23] assertthat_0.2.1        fastmap_1.1.0          
[25] lazyeval_0.2.2          cli_3.2.0              
[27] htmltools_0.5.2         tools_4.1.3            
[29] igraph_1.2.11           coda_0.19-4            
[31] gtable_0.3.0            glue_1.6.2             
[33] clusterGeneration_1.3.7 fastmatch_1.1-3        
[35] Rcpp_1.0.8.3            cellranger_1.1.0       
[37] jquerylib_0.1.4         vctrs_0.4.0            
[39] svglite_2.1.0           nlme_3.1-155           
[41] xfun_0.30               rvest_1.0.2            
[43] ggimage_0.3.0           lifecycle_1.0.1        
[45] MASS_7.3-55             subplex_1.7            
[47] vroom_1.5.7             hms_1.1.1              
[49] parallel_4.1.3          expm_0.999-6           
[51] yaml_2.3.5              ggfun_0.0.5            
[53] yulab.utils_0.0.4       sass_0.4.1             
[55] stringi_1.7.6           highr_0.9              
[57] plotrix_3.8-2           tidytree_0.3.9         
[59] rlang_1.0.2             pkgconfig_2.0.3        
[61] systemfonts_1.0.4       evaluate_0.15          
[63] lattice_0.20-45         patchwork_1.1.1        
[65] labeling_0.4.2          bit_4.0.4              
[67] tidyselect_1.1.2        deSolve_1.31           
[69] R6_2.5.1                magick_2.7.3           
[71] generics_0.1.2          combinat_0.0-8         
[73] DBI_1.1.2               mgcv_1.8-39            
[75] pillar_1.7.0            haven_2.4.3            
[77] withr_2.5.0             scatterplot3d_0.3-41   
[79] modelr_0.1.8            crayon_1.5.1           
[81] utf8_1.2.2              tmvnsim_1.0-2          
[83] tzdb_0.3.0              rmarkdown_2.13         
[85] grid_4.1.3              readxl_1.4.0           
[87] reprex_2.0.1            digest_0.6.29          
[89] webshot_0.5.2           numDeriv_2016.8-1.1    
[91] gridGraphics_0.5-1      munsell_0.5.0          
[93] viridisLite_0.4.0       ggplotify_0.1.0        
[95] bslib_0.3.1             quadprog_1.5-8