rstudio_notes.rmdGet started with the package usethis and the function use_vignette:
To render the vignette to pdf, you’ll need rmarkdown and run from R:
The following function displays packages that are loaded in the R environment.
## [1] "bats" "abind" "ade4" "anicon" "animation"
## [6] "ape" "askpass" "assertthat" "backports" "base"## [1] "bats" "abind" "ade4"
## [4] "anicon" "animation" "ape"
## [7] "askpass" "assertthat" "backports"
## [10] "base" "base64enc" "base64url"
## [13] "BH" "bibtex" "BiocGenerics"
## [16] "BiocManager" "BiocVersion" "Biostrings"
## [19] "bit" "bit64" "bitops"
## [22] "blob" "blogdown" "bold"
## [25] "bookdown" "boot" "brew"
## [28] "brranching" "callr" "caTools"
## [31] "checkpoint" "citr" "class"
## [34] "cli" "clipr" "clisymbols"
## [37] "cluster" "clusterGeneration" "coda"
## [40] "codetools" "colorspace" "combinat"
## [43] "commonmark" "compare" "compiler"
## [46] "conditionz" "covr" "crancache"
## [49] "cranlike" "crayon" "crosstalk"
## [52] "crul" "curl" "data.table"
## [55] "datasets" "datelife" "DBI"
## [58] "debugme" "deeptime" "desc"
## [61] "deSolve" "devtools" "diffobj"
## [64] "digest" "dplyr" "drake"
## [67] "DT" "ellipsis" "emo"
## [70] "evaluate" "expm" "fansi"
## [73] "farver" "fastmap" "fastmatch"
## [76] "foreach" "foreign" "fs"
## [79] "gargle" "gdata" "geiger"
## [82] "generics" "geoaxe" "geoscale"
## [85] "ggforce" "ggnewscale" "ggplot2"
## [88] "ggraph" "ggrepel" "ggtree"
## [91] "gh" "git2r" "glue"
## [94] "gmailr" "GoogleScholarScrapeR" "gplots"
## [97] "graphics" "graphlayouts" "grDevices"
## [100] "grid" "gridExtra" "gtable"
## [103] "gtools" "highlight" "highr"
## [106] "hms" "htmltools" "htmlwidgets"
## [109] "httpcode" "httpuv" "httr"
## [112] "hunspell" "icon" "igraph"
## [115] "ini" "ips" "IRanges"
## [118] "IRdisplay" "IRkernel" "iterators"
## [121] "jsonlite" "kableExtra" "KernSmooth"
## [124] "knitcitations" "knitr" "koRpus"
## [127] "koRpus.lang.en" "labeling" "later"
## [130] "latexpdf" "lattice" "lazyeval"
## [133] "leaflet" "lifecycle" "lubridate"
## [136] "magick" "magrittr" "maps"
## [139] "markdown" "MASS" "Matrix"
## [142] "memoise" "methods" "mgcv"
## [145] "microbenchmark" "mime" "miniUI"
## [148] "mnormt" "msa" "munsell"
## [151] "mvtnorm" "natserv" "ncbit"
## [154] "NCmisc" "nlme" "nnet"
## [157] "numDeriv" "oai" "officer"
## [160] "openssl" "paleotree" "parallel"
## [163] "parsedate" "pbdZMQ" "permute"
## [166] "phangorn" "phylobase" "phyloch"
## [169] "phylocomr" "physcraperex" "phytools"
## [172] "picante" "pillar" "pixmap"
## [175] "pkgbuild" "pkgconfig" "pkgdown"
## [178] "pkgload" "plogr" "plotrix"
## [181] "plyr" "png" "polyclip"
## [184] "praise" "prettyunits" "processx"
## [187] "proftools" "progress" "promises"
## [190] "ps" "purrr" "quadprog"
## [193] "R.cache" "R.methodsS3" "R.oo"
## [196] "R.utils" "R6" "rappdirs"
## [199] "raster" "rcartocolor" "rcmdcheck"
## [202] "RColorBrewer" "Rcpp" "RcppArmadillo"
## [205] "RcppEigen" "RCurl" "reader"
## [208] "readr" "redoc" "RefManageR"
## [211] "rematch" "rematch2" "remotes"
## [214] "rentrez" "reports" "repr"
## [217] "requirements" "reshape" "reshape2"
## [220] "revdepcheck" "rex" "rgbif"
## [223] "rgeos" "rhub" "rinat"
## [226] "ritis" "rlang" "rmarkdown"
## [229] "rncl" "RNeXML" "rotl"
## [232] "roxygen2" "rpart" "rphylotastic"
## [235] "rprojroot" "rredlist" "RSQLite"
## [238] "rstudioapi" "rticles" "rvcheck"
## [241] "rversions" "rvest" "S4Vectors"
## [244] "scales" "scatterplot3d" "scholar"
## [247] "segmented" "selectr" "seqinr"
## [250] "servr" "sessioninfo" "shiny"
## [253] "shinycustomloader" "shinyjs" "solrium"
## [256] "sourcetools" "sp" "spatial"
## [259] "spelling" "splines" "stats"
## [262] "stats4" "storr" "strap"
## [265] "stringi" "stringr" "subplex"
## [268] "survival" "sylly" "sylly.en"
## [271] "sys" "taxize" "tcltk"
## [274] "testit" "testthat" "tibble"
## [277] "tidygraph" "tidyr" "tidyselect"
## [280] "tidytree" "tinytex" "tools"
## [283] "treebase" "treeio" "triebeard"
## [286] "tweenr" "urltools" "usethis"
## [289] "utf8" "utils" "uuid"
## [292] "vctrs" "vegan" "viridis"
## [295] "viridisLite" "webshot" "whisker"
## [298] "whoami" "wicket" "WikidataR"
## [301] "WikipediR" "wikitaxa" "withr"
## [304] "wordcountaddin" "worrms" "xaringan"
## [307] "xaringanthemer" "xfun" "XML"
## [310] "xml2" "xopen" "xtable"
## [313] "XVector" "yaml" "zeallot"
## [316] "zip" "zlibbioc" "zoo"To install phyloch we will use the package devtools.
Then we can install phyloch from Github.
We will use an R package called pkgdown for this.
We took the following instructions from https://pkgdown.r-lib.org/:
Get started with use_pkgdown. Run it once to configure your package to use pkgdown
Use build_site to update your website:
Now, your website will be built in the docs folder. Make sure that the folder is not in .gitignore. Otherwise, it will not be uplodaded to GitHub and the website will not be available publicly!