Update install.R

install.R

-# From SDD bookdowns
-install.packages(c("anytime", "assertthat", "backports", "base64enc", "bit",
-  "bit64", "blob", "bookdown", "cli", "crayon", "curl", "data.table", "DBI",
-  "devtools", "digest", "evaluate", "fansi", "fastmap", "glue", "htmltools",
-  "htmlwidgets", "httpuv", "httr", "jsonlite", "knitr", "later", "lattice",
-  "learnr", "lintr", "magrittr", "markdown", "memoise", "microbenchmark",
-  "mime", "mongolite", "nanotime", "odbc", "palmerpenguins", "PKI", "promises",
-  "R6", "Rcpp", "RcppCCTZ", "remotes", "rlang", "rmarkdown", "rprojroot",
-  "RSQLite", "sessioninfo", "shiny", "stringi", "stringr", "SuppDists", "vctrs",
-  "withr", "xfun", "xtable", "yaml", "zoo"))
+# From SDD bookdowns, BioDataScienceX & r.snippets (except ggvis & directlabels)
+# (search for 'library(', 'require(', 'package =' and ::)
+install.packages(c("ade4", "anytime", "ape", "assertthat", "automap",
+  "available", "backports", "base64enc", "bit", "bit64", "blob", "bookdown",
+  "broom", "ca", "car", "cartography", "circular", "cli", "corrplot", "crayon",
+  "curl", "data.table", "DBI", "dbplyr", "devtools", "DiagrammeR", "digest",
+  "DT", "evaluate", "factoextra", "FactoMineR", "fansi", "faraway",
+  "fastcluster", "fastmap", "flashClust", "fortunes", "flipdownr", "GGally",
+  "gganimate", "ggdendro", "ggfortify", "ggpubr", "ggrepel", "ggridges", "ggsn",
+  "ggsom", "glue", "gridExtra", "gstat", "here", "htmltools", "htmlwidgets",
+  "httpuv", "httr", "ipred", "iterators", "janitor", "jsonlite", "knitr",
+  "kohonen", "later", "lattice", "lintr", "lobstr", "lme4", "lmerTest",
+  "lubridate", "magrittr", "mapedit", "mapview", "markdown", "memoise",
+  "microbenchmark", "mime", "miniUI", "mlbench", "modelr", "mongolite",
+  "mosaic", "multcomp", "naniar", "nanotime", "nparcomp", "odbc",
+  "palmerpenguins", "pander", "PKI", "plotly", "pROC", "promises", "pryr",
+  "purrr", "pwr", "R6", "raster", "RColorBrewer", "Rcpp", "RcppCCTZ", "readxl",
+  "rgl", "remotes", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSQLite", "sf",
+  "sessioninfo", "shiny", "shinyjs", "shinytest", "skimr", "spData", "stars",
+  "stringi", "stringr", "SuppDists", "tidyr", "tmap", "tmaptools", "TSA",
+  "UsingR", "vctrs", "vegan", "vembedr", "viridis", "visdat", "withr", "xfun",
+  "xtable", "yaml", "zoo"))
 
 # SciViews::R
 #remotes::install_github("SciViews/svMisc")
@@ -28,5 +40,44 @@ remotes::install_url("https://filedn.com/lzGVgfOGxb6mHFQcRn9ueUb/svbox2021/mlear
 remotes::install_url("https://filedn.com/lzGVgfOGxb6mHFQcRn9ueUb/svbox2021/pastecs_1.4.0.tar.gz", upgrade = "never")
 #remotes::install_github("phgrosjean/aurelhy")
 remotes::install_url("https://filedn.com/lzGVgfOGxb6mHFQcRn9ueUb/svbox2021/aurelhy_1.0.8.tar.gz", upgrade = "never")
+#remotes::install_github("phgrosjean/learnitdown")
+remotes::install_url("https://filedn.com/lzGVgfOGxb6mHFQcRn9ueUb/svbox2021/learnitdown_1.3.1.tar.gz", upgrade = "never")
 
-# More R packages ... BioDataScience|1|2|3, learnitdown, gradethis, ...
+remotes::install_github("rstudio/learnr@64cbd2d", upgrade = "never")
+remotes::install_github("rstudio/gradethis@e9b10ae", upgrade = "never")
+
+# More R Markdown formats
+install.packages(c("distill", "flexdashboard", "pagedown", "posterdown",
+  "rticles", "xaringan"))
+
+# More RStudio Addins
+install.packages(c("blogdown", "citr", "convertr", "compareWith", "covr",
+  "esquisse", "ggExtra", "golem", "pins", "pkgdown", "questionr", "reprex",
+  "styler", "todor"))
+
+# More useful package not used in the courses
+install.packages(c("abind", "agricolae", "akima", "archivit", "archivit.github",
+  "arkdb", "babynames", "bench", "BEST", "bmp", "callr", "captioner", "corrr",
+  "datapackage.r", "datasauRus", "digest", "ditsr6", "dtplyr", "e1071", "egg",
+  "emayili", "ensurer", "exams", "fastai", "fauxpas", "fda", "feasts",
+  "filehash", "filehashSQLite", "flashlight", "flextable", "fs", "fst",
+  "ftExtra", "future", "future.apply", "future.callr", "generics", "gert",
+  "ggconf", "ggcorrplot", "ggdist", "ggfocus", "ggforce", "ggimage", "ggiraph",
+  "gglm", "ggmisc", "ggmosaic", "ggRandomForests", "ggsignif", "ggTimeSeries",
+  "ggtext", "ggVennDiagram", "ggwordcloud", "gistr", "gitcreds", "goodpractice",
+  "googlesheets4", "gt", "haven", "hexSticker", "hms", "import", "infer",
+  "inline", "ipred", "ivred", "jpeg", "jsonlite", "kableExtra", "knitcitations",
+  "latex2exp", "leafem", "leaflet", "leaps", "lifecycle", "listcomp", "logger",
+  "modelsummary", "moderndive", "needs", "nortest", "nycflights13",
+  "officedown", "officer", "opencpu", "pagedown", "patchwork", "piggyback",
+  "plumber", "png", "prettyunits", "printr", "quantreg", "R62S3", "ranger",
+  "RANN", "RcppExamples", "Rd2roxygen", "recipes", "renv", "reticulate",
+  "rpart.plot", "rvest", "rvg", "seasonal", "shinybusy", "shinydashboard",
+  "shinylogs", "shinytoastr", "smotefamily", "spelling", "startgazer",
+  "stlplus", "survminer", "svDialogs", "svGUI", "svSweave", "sys", "tab",
+  "tables", "tableschema.r", "tactile", "targets", "tester", "texreg", "tiff",
+  "titanic", "varSelRF", "vip", "vroom", "writexl", "xgboost", "xts",
+  "zeallot", "zip", "ztable"))
+
+# BioDataScience|1|2|3 are installed in the template post installation
+# (in post-init.R) to make sure we got latest versions