H 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 3.6.1 (2019-07-05) 
##  Platform: x86_64-pc-linux-gnu (64-bit) 
##  Running under: Anarchy 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] ggtree_2.1.1         treeio_1.10.0        
##   [3] tidytree_0.3.0       kableExtra_1.1.0     
##   [5] dplyr_0.8.3          cowplot_1.0.0        
##   [7] phylobase_0.8.6      igraph_1.2.4.1       
##   [9] OutbreakTools_0.1-16 knitr_1.25           
##  [11] network_1.15         ggplot2_3.2.1        
##  [13] Biostrings_2.54.0    XVector_0.26.0       
##  [15] IRanges_2.20.0       S4Vectors_0.24.0     
##  [17] BiocGenerics_0.32.0  ape_5.3              
##  [19] conflicted_1.0.4     bookdown_0.14        
##   
##  loaded via a namespace (and not attached): 
##   [1] httr_1.4.1            tidyr_1.0.0           
##   [3] jsonlite_1.6          viridisLite_0.3.0     
##   [5] assertthat_0.2.1      BiocManager_1.30.9    
##   [7] rvcheck_0.1.6         yaml_2.2.0            
##   [9] progress_1.2.2        pillar_1.4.2          
##  [11] backports_1.1.5       lattice_0.20-38       
##  [13] glue_1.3.1            uuid_0.1-2            
##  [15] digest_0.6.22         RColorBrewer_1.1-2    
##  [17] rvest_0.3.4           colorspace_1.4-1      
##  [19] htmltools_0.4.0       plyr_1.8.4            
##  [21] XML_3.98-1.20         pkgconfig_2.0.3       
##  [23] rncl_0.8.3            zlibbioc_1.32.0       
##  [25] purrr_0.3.3           webshot_0.5.1         
##  [27] scales_1.0.0          sna_2.4               
##  [29] jpeg_0.1-8.1          ggmap_3.0.0           
##  [31] tibble_2.1.3          withr_2.1.2           
##  [33] lazyeval_0.2.2        networkDynamic_0.10.0 
##  [35] magrittr_1.5          crayon_1.3.4          
##  [37] statnet.common_4.3.0  memoise_1.1.0         
##  [39] evaluate_0.14         nlme_3.1-140          
##  [41] MASS_7.3-51.4         xml2_1.2.2            
##  [43] tools_3.6.1           prettyunits_1.0.2     
##  [45] hms_0.5.2             RgoogleMaps_1.4.4     
##  [47] lifecycle_0.1.0       stringr_1.4.0         
##  [49] munsell_0.5.0         ade4_1.7-13           
##  [51] compiler_3.6.1        RNeXML_2.3.0          
##  [53] rlang_0.4.1           grid_3.6.1            
##  [55] RCurl_1.95-4.12       rstudioapi_0.10       
##  [57] rjson_0.2.20          bitops_1.0-6          
##  [59] rmarkdown_1.16        gtable_0.3.0          
##  [61] reshape2_1.4.3        R6_2.4.0              
##  [63] zeallot_0.1.0         readr_1.3.1           
##  [65] stringi_1.4.3         Rcpp_1.0.2            
##  [67] vctrs_0.2.0           png_0.1-7             
##  [69] tidyselect_0.2.5      xfun_0.10             
##  [71] coda_0.19-3