I Session Info
The book was written using R Markdown and was compiled by bookdown package. Here is the session information on the system on which this thesis was compiled:
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Arch Linux
##
## 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] stats4 parallel stats graphics grDevices
## [6] utils datasets methods base
##
## other attached packages:
## [1] ggstar_0.0.9 ggtreeExtra_0.99.12
## [3] ggplotify_0.0.5 devout_0.2.7
## [5] data.tree_1.0.0 comicR_0.2
## [7] gridSVG_1.7-2 XML_3.99-0.5
## [9] htmltools_0.5.0 rotl_3.0.10
## [11] ggrepel_0.9.0 gggenes_0.4.0
## [13] tibble_3.0.3 reshape2_1.4.4
## [15] ggstance_0.3.4 ggridges_0.5.2
## [17] scales_1.1.1 phyloseq_1.32.0
## [19] ade4_1.7-15 aplot_0.0.5
## [21] ggnewscale_0.4.2 ggimage_0.2.8
## [23] jsonlite_1.7.0 phangorn_2.5.5
## [25] stringr_1.4.0 phytools_0.7-47
## [27] maps_3.3.0 tidyr_1.1.1
## [29] knitr_1.29 ggtree_2.3.4
## [31] treeio_1.13.1 tidytree_0.3.3.991
## [33] kableExtra_1.1.0 dplyr_1.0.1
## [35] ggplot2_3.3.2 cowplot_1.0.0
## [37] emojifont_0.5.3 phylobase_0.8.10
## [39] igraph_1.2.5 Biostrings_2.56.0
## [41] XVector_0.28.0 IRanges_2.22.2
## [43] S4Vectors_0.26.1 BiocGenerics_0.34.0
## [45] ape_5.4-1 conflicted_1.0.4
## [47] bookdown_0.20
##
## loaded via a namespace (and not attached):
## [1] uuid_0.1-4 fastmatch_1.1-0
## [3] plyr_1.8.6 lazyeval_0.2.2
## [5] splines_4.0.2 rncl_0.8.4
## [7] digest_0.6.25 foreach_1.5.0
## [9] magick_2.4.0 magrittr_1.5
## [11] memoise_1.1.0 cluster_2.1.0
## [13] readr_1.3.1 ggfittext_0.9.0
## [15] sysfonts_0.8.1 prettyunits_1.1.1
## [17] colorspace_1.4-1 rvest_0.3.6
## [19] xfun_0.16 crayon_1.3.4
## [21] dlstats_0.1.3 survival_3.2-3
## [23] iterators_1.0.12 glue_1.4.1
## [25] gtable_0.3.0 zlibbioc_1.34.0
## [27] webshot_0.5.2 Rhdf5lib_1.10.1
## [29] rentrez_1.2.2 Rcpp_1.0.5
## [31] showtextdb_3.0 plotrix_3.7-8
## [33] viridisLite_0.3.0 progress_1.2.2
## [35] tmvnsim_1.0-2 gridGraphics_0.5-0
## [37] animation_2.6 htmlwidgets_1.5.1
## [39] httr_1.4.2 badger_0.0.8
## [41] RColorBrewer_1.1-2 ellipsis_0.3.1
## [43] farver_2.0.3 pkgconfig_2.0.3
## [45] labeling_0.3 tidyselect_1.1.0
## [47] rlang_0.4.7 munsell_0.5.0
## [49] tools_4.0.2 generics_0.0.2
## [51] evaluate_0.14 biomformat_1.16.0
## [53] yaml_2.2.1 purrr_0.3.4
## [55] showtext_0.9 nlme_3.1-148
## [57] xml2_1.3.2 compiler_4.0.2
## [59] rstudioapi_0.11 clusterGeneration_1.3.4
## [61] RNeXML_2.4.5 stringi_1.4.6
## [63] highr_0.8 lattice_0.20-41
## [65] Matrix_1.2-18 vegan_2.5-6
## [67] permute_0.9-5 multtest_2.44.0
## [69] vctrs_0.3.2 pillar_1.4.6
## [71] lifecycle_0.2.0 BiocManager_1.30.10
## [73] combinat_0.0-8 data.table_1.13.0
## [75] patchwork_1.0.1 R6_2.4.1
## [77] gridExtra_2.3 codetools_0.2-16
## [79] MASS_7.3-51.6 gtools_3.8.2
## [81] assertthat_0.2.1 rhdf5_2.32.2
## [83] proto_1.0.0 withr_2.2.0
## [85] mnormt_2.0.1 mgcv_1.8-31
## [87] expm_0.999-5 hms_0.5.3
## [89] quadprog_1.5-8 grid_4.0.2
## [91] coda_0.19-3 rmarkdown_2.3
## [93] rvcheck_0.1.8 numDeriv_2016.8-1.1
## [95] scatterplot3d_0.3-41 Biobase_2.48.0