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:

## ─ Session info ───────────────────────────────────────────
##  setting  value                       
##  version  R version 4.0.3 (2020-10-10)
##  os       Arch Linux                  
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Asia/Chongqing              
##  date     2021-02-24                  
## 
## ─ Packages ───────────────────────────────────────────────
##  package           * version    date       lib
##  ade4              * 1.7-16     2020-10-28 [1]
##  ape               * 5.4-2      2020-12-31 [1]
##  aplot             * 0.0.6      2020-09-02 [1]
##  assertthat          0.2.1      2019-03-21 [1]
##  badger              0.0.9      2020-12-05 [1]
##  Biobase             2.50.0     2020-10-27 [1]
##  BiocGenerics      * 0.36.0     2020-10-27 [1]
##  BiocManager         1.30.10    2019-11-16 [1]
##  biomformat          1.18.0     2020-10-27 [1]
##  Biostrings        * 2.58.0     2020-10-27 [1]
##  bit                 4.0.4      2020-08-04 [1]
##  bit64               4.0.5      2020-08-30 [1]
##  blob                1.2.1      2020-01-20 [1]
##  bookdown          * 0.21.3     2020-11-04 [1]
##  bootstraplib        0.2.1.9000 2020-11-04 [1]
##  callr               3.5.1      2020-10-13 [1]
##  cli                 2.2.0      2020-11-20 [1]
##  cluster             2.1.0      2019-06-19 [1]
##  clusterGeneration   1.3.7      2020-12-15 [1]
##  coda                0.19-4     2020-09-30 [1]
##  codetools           0.2-18     2020-11-04 [1]
##  coin                1.3-1      2019-08-28 [1]
##  colorspace          2.0-0      2020-11-11 [1]
##  combinat            0.0-8      2012-10-29 [1]
##  comicR            * 0.2        2020-04-29 [1]
##  conflicted        * 1.0.4      2019-06-21 [1]
##  cowplot           * 1.1.1      2020-12-30 [1]
##  crayon              1.3.4      2017-09-16 [1]
##  data.table          1.13.6     2020-12-30 [1]
##  data.tree         * 1.0.0      2020-08-03 [1]
##  DBI                 1.1.0      2019-12-15 [1]
##  DECIPHER            2.18.1     2020-10-29 [1]
##  desc                1.2.0      2018-05-01 [1]
##  devout            * 0.2.7      2020-04-26 [1]
##  devtools            2.3.2      2020-09-18 [1]
##  digest              0.6.27     2020-10-24 [1]
##  dlstats             0.1.3      2019-11-14 [1]
##  downlit             0.2.1      2020-11-04 [1]
##  dplyr             * 1.0.2      2020-08-18 [1]
##  ellipsis            0.3.1      2020-05-15 [1]
##  emojifont         * 0.5.3      2019-12-12 [1]
##  evaluate            0.14       2019-05-28 [1]
##  expm                0.999-5    2020-07-20 [1]
##  fansi               0.4.1      2020-01-08 [1]
##  farver              2.0.3      2020-01-16 [1]
##  fastmatch           1.1-0      2017-01-28 [1]
##  foreach             1.5.1      2020-10-15 [1]
##  fs                  1.5.0      2020-07-31 [1]
##  generics            0.1.0      2020-10-31 [1]
##  ggfittext           0.9.0      2020-06-14 [1]
##  gggenes           * 0.4.1      2020-12-10 [1]
##  ggimage           * 0.2.8      2020-04-02 [1]
##  ggnetworx         * 0.99.0     2020-09-18 [1]
##  ggnewscale        * 0.4.5      2021-01-11 [1]
##  ggplot2           * 3.3.3      2020-12-30 [1]
##  ggplotify         * 0.0.5.993  2020-08-30 [1]
##  ggrepel           * 0.9.0      2020-08-06 [1]
##  ggridges          * 0.5.3      2021-01-08 [1]
##  ggsignif            0.6.0      2019-08-08 [1]
##  ggstance          * 0.3.5      2020-12-17 [1]
##  ggstar            * 0.0.9      2020-07-10 [1]
##  ggtree            * 2.5.0.993  2021-01-08 [1]
##  ggtreeExtra       * 1.0.0      2020-10-27 [1]
##  glue                1.4.2      2020-08-27 [1]
##  gridExtra           2.3        2017-09-09 [1]
##  gridGraphics        0.5-1      2020-12-13 [1]
##  gridSVG           * 1.7-2      2020-04-28 [1]
##  gtable              0.3.0      2019-03-25 [1]
##  gtools              3.8.2      2020-03-31 [1]
##  highr               0.8        2019-03-20 [1]
##  hms                 0.5.3      2020-01-08 [1]
##  htmltools         * 0.5.0.9002 2020-11-04 [1]
##  htmlwidgets         1.5.3      2020-12-10 [1]
##  httr                1.4.2      2020-07-20 [1]
##  icon                0.1.0      2020-09-21 [1]
##  igraph            * 1.2.6      2020-10-06 [1]
##  IRanges           * 2.24.1     2020-12-12 [1]
##  iterators           1.0.13     2020-10-15 [1]
##  jquerylib           0.1.3      2020-12-17 [1]
##  jsonlite          * 1.7.2      2020-12-09 [1]
##  kableExtra        * 1.3.1      2020-10-22 [1]
##  knitr             * 1.30       2020-09-22 [1]
##  labeling            0.4.2      2020-10-20 [1]
##  lattice             0.20-41    2020-04-02 [1]
##  lazyeval            0.2.2      2019-03-15 [1]
##  libcoin             1.0-6      2020-08-14 [1]
##  lifecycle           0.2.0      2020-03-06 [1]
##  magick              2.5.2      2020-11-10 [1]
##  magrittr            2.0.1      2020-11-17 [1]
##  maps              * 3.3.0      2018-04-03 [1]
##  MASS                7.3-53     2020-09-09 [1]
##  Matrix              1.3-2      2021-01-06 [1]
##  matrixStats         0.57.0     2020-09-25 [1]
##  memoise             1.1.0      2017-04-21 [1]
##  mgcv                1.8-33     2020-08-27 [1]
##  MicrobiotaProcess * 1.3.3      2020-11-23 [1]
##  mnormt              2.0.2      2020-09-01 [1]
##  modeltools          0.2-23     2020-03-05 [1]
##  multcomp            1.4-15     2020-11-14 [1]
##  multtest            2.46.0     2020-10-27 [1]
##  munsell             0.5.0      2018-06-12 [1]
##  mvtnorm             1.1-1      2020-06-09 [1]
##  nlme                3.1-151    2020-12-10 [1]
##  numDeriv            2016.8-1.1 2019-06-06 [1]
##  patchwork           1.1.1      2020-12-17 [1]
##  permute             0.9-5      2019-03-12 [1]
##  phangorn          * 2.5.5      2019-06-19 [1]
##  phylobase         * 0.8.10     2020-03-01 [1]
##  phyloseq          * 1.34.0     2020-10-27 [1]
##  phytools          * 0.7-70     2020-09-19 [1]
##  pillar              1.4.7      2020-11-20 [1]
##  pkgbuild            1.2.0      2020-12-15 [1]
##  pkgconfig           2.0.3      2019-09-22 [1]
##  pkgload             1.1.0      2020-05-29 [1]
##  plotrix             3.7-8      2020-04-16 [1]
##  plyr                1.8.6      2020-03-03 [1]
##  prettyunits         1.1.1      2020-01-24 [1]
##  processx            3.4.5      2020-11-30 [1]
##  progress            1.2.2      2019-05-16 [1]
##  proto               1.0.0      2016-10-29 [1]
##  ps                  1.5.0      2020-12-05 [1]
##  purrr               0.3.4      2020-04-17 [1]
##  quadprog            1.5-8      2019-11-20 [1]
##  R6                  2.5.0      2020-10-28 [1]
##  randomForest        4.6-14     2018-03-25 [1]
##  rappdirs            0.3.1      2016-03-28 [1]
##  RColorBrewer        1.1-2      2014-12-07 [1]
##  Rcpp                1.0.5      2020-07-06 [1]
##  remotes             2.2.0      2020-07-21 [1]
##  rentrez             1.2.3      2020-11-10 [1]
##  reshape             0.8.8      2018-10-23 [1]
##  reshape2          * 1.4.4      2020-04-09 [1]
##  rhdf5               2.34.0     2020-10-27 [1]
##  rhdf5filters        1.2.0      2020-10-27 [1]
##  Rhdf5lib            1.12.0     2020-10-27 [1]
##  rlang               0.4.10     2020-12-30 [1]
##  rmarkdown           2.6        2020-12-14 [1]
##  Rmisc               1.5        2013-10-22 [1]
##  rncl                0.8.4      2020-02-10 [1]
##  RNeXML              2.4.5      2020-06-18 [1]
##  rotl              * 3.0.11     2020-10-22 [1]
##  rprojroot           2.0.2      2020-11-15 [1]
##  RSQLite             2.2.2      2021-01-08 [1]
##  rstudioapi          0.13       2020-11-12 [1]
##  rvcheck             0.1.8      2020-04-26 [1]
##  rvest               0.3.6      2020-07-25 [1]
##  S4Vectors         * 0.28.1     2020-12-09 [1]
##  sandwich            3.0-0      2020-10-02 [1]
##  sass                0.2.0.9005 2020-11-04 [1]
##  scales            * 1.1.1      2020-05-11 [1]
##  scatterplot3d       0.3-41     2018-03-14 [1]
##  sessioninfo         1.1.1      2018-11-05 [1]
##  shadowtext        * 0.0.7      2019-11-06 [1]
##  showtext            0.9-2      2021-01-10 [1]
##  showtextdb          3.0        2020-06-04 [1]
##  stringi             1.5.3      2020-09-09 [1]
##  stringr           * 1.4.0      2019-02-10 [1]
##  survival            3.2-7      2020-09-28 [1]
##  sysfonts            0.8.3      2021-01-10 [1]
##  testthat            3.0.1      2020-12-17 [1]
##  TH.data             1.0-10     2019-01-21 [1]
##  tibble            * 3.0.4      2020-10-12 [1]
##  tidyr             * 1.1.2      2020-08-27 [1]
##  tidyselect          1.1.0      2020-05-11 [1]
##  tidytree          * 0.3.4      2020-10-22 [1]
##  tmvnsim             1.0-2      2016-12-15 [1]
##  treeio            * 1.15.2     2021-01-11 [1]
##  usethis             2.0.0      2020-12-10 [1]
##  uuid                0.1-4      2020-02-26 [1]
##  vctrs               0.3.6      2020-12-17 [1]
##  vegan               2.5-7      2020-11-28 [1]
##  viridisLite         0.3.0      2018-02-01 [1]
##  webshot             0.5.2      2019-11-22 [1]
##  withr               2.3.0      2020-09-22 [1]
##  xfun                0.20       2021-01-06 [1]
##  XML               * 3.99-0.5   2020-07-23 [1]
##  xml2                1.3.2      2020-04-23 [1]
##  XVector           * 0.30.0     2020-10-27 [1]
##  yaml                2.2.1      2020-02-01 [1]
##  zlibbioc            1.36.0     2020-10-27 [1]
##  zoo                 1.8-8      2020-05-02 [1]
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## [1] /home/ygc/R/library
## [2] /usr/lib/R/library