D 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 4.0.3 (2020-10-10) 
##  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] gdtools_0.2.2           magrittr_2.0.1          
##   [3] rvcheck_0.1.8           wget_0.0.1              
##   [5] rmarkdown_2.5           devout_0.2.7            
##   [7] data.tree_1.0.0         comicR_0.2              
##   [9] gridSVG_1.7-2           XML_3.99-0.5            
##  [11] htmltools_0.5.0.9002    rotl_3.0.11             
##  [13] ggrepel_0.9.0           gggenes_0.4.0           
##  [15] tibble_3.0.4            ggplotify_0.0.5.993     
##  [17] reshape2_1.4.4          ggstance_0.3.4          
##  [19] ggnetworx_0.99.0        MicrobiotaProcess_1.3.3 
##  [21] ggstar_0.0.9            ggtreeExtra_1.0.0       
##  [23] ggridges_0.5.2          scales_1.1.1            
##  [25] phyloseq_1.34.0         ade4_1.7-16             
##  [27] aplot_0.0.6             ggnewscale_0.4.3        
##  [29] ggimage_0.2.8           jsonlite_1.7.1          
##  [31] shadowtext_0.0.7        phangorn_2.5.5          
##  [33] stringr_1.4.0           phytools_0.7-70         
##  [35] maps_3.3.0              tidyr_1.1.2             
##  [37] knitr_1.30              ggtree_2.5.0.992        
##  [39] treeio_1.14.3           tidytree_0.3.4          
##  [41] kableExtra_1.3.1        dplyr_1.0.2             
##  [43] ggplot2_3.3.2           cowplot_1.1.0           
##  [45] emojifont_0.5.3         phylobase_0.8.10        
##  [47] igraph_1.2.6            Biostrings_2.58.0       
##  [49] XVector_0.30.0          IRanges_2.24.0          
##  [51] S4Vectors_0.28.0        BiocGenerics_0.36.0     
##  [53] ape_5.4-1               conflicted_1.0.4        
##  [55] bookdown_0.21.3         
##   
##  loaded via a namespace (and not attached): 
##    [1] proto_1.0.0             tidyselect_1.1.0        
##    [3] RSQLite_2.2.1           htmlwidgets_1.5.2       
##    [5] grid_4.0.3              combinat_0.0-8          
##    [7] RNeXML_2.4.5            munsell_0.5.0           
##    [9] codetools_0.2-18        rentrez_1.2.3           
##   [11] withr_2.3.0             colorspace_2.0-0        
##   [13] Biobase_2.50.0          highr_0.8               
##   [15] uuid_0.1-4              rstudioapi_0.13         
##   [17] ggsignif_0.6.0          labeling_0.4.2          
##   [19] mnormt_2.0.2            farver_2.0.3            
##   [21] bit64_4.0.5             rhdf5_2.34.0            
##   [23] coda_0.19-4             vctrs_0.3.5             
##   [25] generics_0.1.0          TH.data_1.0-10          
##   [27] clusterGeneration_1.3.6 xfun_0.19               
##   [29] randomForest_4.6-14     R6_2.5.0                
##   [31] bootstraplib_0.2.1.9000 rhdf5filters_1.2.0      
##   [33] reshape_0.8.8           gridGraphics_0.5-0      
##   [35] assertthat_0.2.1        showtext_0.9-1          
##   [37] multcomp_1.4-15         gtable_0.3.0            
##   [39] downlit_0.2.1           sandwich_3.0-0          
##   [41] rlang_0.4.8             systemfonts_0.3.2       
##   [43] scatterplot3d_0.3-41    Rmisc_1.5               
##   [45] splines_4.0.3           lazyeval_0.2.2          
##   [47] BiocManager_1.30.10     yaml_2.2.1              
##   [49] tools_4.0.3             ellipsis_0.3.1          
##   [51] jquerylib_0.1.2         biomformat_1.18.0       
##   [53] RColorBrewer_1.1-2      Rcpp_1.0.5              
##   [55] plyr_1.8.6              progress_1.2.2          
##   [57] zlibbioc_1.36.0         purrr_0.3.4             
##   [59] prettyunits_1.1.1       zoo_1.8-8               
##   [61] cluster_2.1.0           fs_1.5.0                
##   [63] DECIPHER_2.18.1         data.table_1.13.2       
##   [65] magick_2.5.2            tmvnsim_1.0-2           
##   [67] mvtnorm_1.1-1           matrixStats_0.57.0      
##   [69] hms_0.5.3               patchwork_1.1.0         
##   [71] evaluate_0.14           gridExtra_2.3           
##   [73] compiler_4.0.3          crayon_1.3.4            
##   [75] mgcv_1.8-33             libcoin_1.0-6           
##   [77] expm_0.999-5            DBI_1.1.0               
##   [79] MASS_7.3-53             rappdirs_0.3.1          
##   [81] dlstats_0.1.3           Matrix_1.2-18           
##   [83] badger_0.0.8            permute_0.9-5           
##   [85] quadprog_1.5-8          pkgconfig_2.0.3         
##   [87] rncl_0.8.4              numDeriv_2016.8-1.1     
##   [89] coin_1.3-1              xml2_1.3.2              
##   [91] foreach_1.5.1           multtest_2.46.0         
##   [93] webshot_0.5.2           rvest_0.3.6             
##   [95] digest_0.6.27           vegan_2.5-6             
##   [97] showtextdb_3.0          fastmatch_1.1-0         
##   [99] gtools_3.8.2            modeltools_0.2-23       
##  [101] icon_0.1.0              lifecycle_0.2.0         
##  [103] nlme_3.1-150            Rhdf5lib_1.12.0         
##  [105] viridisLite_0.3.0       pillar_1.4.7            
##  [107] lattice_0.20-41         httr_1.4.2              
##  [109] plotrix_3.7-8           survival_3.2-7          
##  [111] glue_1.4.2              iterators_1.0.13        
##  [113] bit_4.0.4               stringi_1.5.3           
##  [115] sass_0.2.0.9005         blob_1.2.1              
##  [117] ggfittext_0.9.0         memoise_1.1.0           
##  [119] sysfonts_0.8.2