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