R code#
Usage#
SEPAL instances run on focal Ubuntu machines, providing a fully functional R 4.1.2 environment that is accessible in RStudio, Jupyterlab or the terminal.
Description#
The SEPAL R environment is not empty; there are numerous embedded packages.
#!/bin/bash
set -e
echo
echo "*****************************"
echo "*** Installing R packages ***"
echo "*****************************"
export JAVA_HOME=/usr/local/lib/sdkman/candidates/java/current
export JAVA_CPPFLAGS="-I${JAVA_HOME}/include -I${JAVA_HOME}/include/linux"
export JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/server:${JAVA_HOME}/lib
R CMD javareconf
# Install CRAN packages via r-proxy
R -e "install.packages('rgdal', version = '1.3-9', dependencies = TRUE, repos = 'http://r-proxy:8180/', upgrade = 'never')"
R -e "install.packages(c(\
'abind',\
'askpass',\
'assertthat',\
'backports',\
'base64enc',\
'BH',\
'BiodiversityR',\
'BIOMASS',\
'bit',\
'bit64',\
'blob',\
'brew',\
'broom',\
'callr',\
'car',\
'caret',\
'cellranger',\
'chron',\
'classInt',\
'cli',\
'clipr',\
'collapsibleTree',\
'colorspace',\
'colourpicker',\
'corrplot',\
'countrycode',\
'crayon',\
'curl',\
'data.table',\
'DBI',\
'DBItest',\
'dbplyr',\
'desc',\
'devtools',\
'DiagrammeR',\
'dichromat',\
'digest',\
'dismo',\
'doMC',\
'doParallel',\
'downloader',\
'dplyr',\
'DT',\
'e1071',\
'ellipsis',\
'evaluate',\
'evir',\
'expss',\
'fansi',\
'fasterize',\
'feather',\
'filehash',\
'forcats',\
'foreach',\
'forecast',\
'foreign',\
'formatR',\
'formattable',\
'Formula',\
'fs',\
'future',\
'generics',\
'geoR',\
'geosphere',\
'ggalluvial',\
'ggExtra',\
'ggfortify',\
'ggmap',\
'ggplot2',\
'ggrepel',\
'ggthemes',\
'ggthemr',\
'GISTools',\
'glmnet',\
'globals',\
'glue',\
'googleVis',\
'gpclib',\
'grid',\
'gridExtra',\
'gsubfn',\
'gtable',\
'haven',\
'hexbin',\
'highr',\
'Hmisc',\
'hms',\
'htmltools',\
'htmlwidgets',\
'httpuv',\
'httr',\
'igraph',\
'influenceR',\
'iterators',\
'jpeg',\
'jsonlite',\
'kableExtra',\
'keras',\
'knitr',\
'labeling',\
'later',\
'lattice',\
'latticeExtra',\
'lazyeval',\
'leafem',\
'leaflet',\
'leaflet.extras',\
'lifecycle',\
'listenv',\
'littler',\
'lme4',\
'lmfor',\
'lubridate',\
'magick',\
'magrittr',\
'manipulate',\
'mapproj',\
'maps',\
'maptools',\
'mapview',\
'markdown',\
'MASS',\
'memoise',\
'mgcv',\
'mime',\
'miniUI',\
'missForest',\
'mockery',\
'mockr',\
'modelr',\
'moments',\
'multcomp',\
'multicore',\
'munsell',\
'ncdf4',\
'networkD3',\
'nlme',\
'nlstools',\
'openssl',\
'outliers',\
'pacman',\
'parallel',\
'party',\
'permutate',\
'pillar',\
'pkgconfig',\
'pkgdown',\
'pkgKitten',\
'plotly',\
'plyr',\
'png',\
'PracTools',\
'praise',\
'prettycode',\
'prettyunits',\
'processx',\
'progress',\
'promises',\
'proto',\
'ps',\
'purrr',\
'quantmod',\
'R6',\
'ragg',\
'random',\
'randomForest',\
'raster',\
'rasterVis',\
'rclipboard',\
'RColorBrewer',\
'Rcpp',\
'RcppArmadillo',\
'RcppEigen',\
'RCurl',\
'readr',\
'readxl',\
'rematch',\
'rematch2',\
'rentrez',\
'reprex',\
'reshape',\
'reshape2',\
'reticulate',\
'rgbif',\
'rgeos',\
'rgexf',\
'RgoogleMaps',\
'rhandsontable',\
'rJava',\
'rknn',\
'rlang',\
'rmarkdown',\
'Rmpi',\
'Rook',\
'rpart',\
'rpart.plot',\
'RPostgreSQL',\
'rprojroot',\
'rsconnect',\
'RSQLite',\
'RStoolbox',\
'rstudioapi',\
'rticles',\
'RUnit',\
'rvest',\
'Rweka',\
'rworldmap',\
'samplingbook',\
'scales',\
'selectr',\
'sf',\
'shiny',\
'shinyBS',\
'shinycssloaders',\
'shinydashboard',\
'shinyFiles',\
'shinyjs',\
'skimr',\
'snow',\
'sourcetools',\
'sp',\
'spatial',\
'splines',\
'sqldf',\
'stats',\
'stats4',\
'stringi',\
'stringr',\
'styler',\
'summarytools',\
'survival',\
'sys',\
'taxize',\
'Taxonstand',\
'testit',\
'testthat',\
'textclean',\
'textshaping',\
'tibble',\
'tictoc',\
'tidyr',\
'tidyselect',\
'tidyverse',\
'tigris',\
'tikzDevice',\
'tint',\
'tinytex',\
'tools',\
'treemap',\
'tufte',\
'units',\
'UpSetR',\
'urltools',\
'utf8',\
'utils',\
'vcd',\
'vctrs',\
'vegan',\
'viridis',\
'viridisLite',\
'visNetwork',\
'vtree',\
'webshot',\
'whisker',\
'withr',\
'WorldFlora',\
'writexl',\
'xfun',\
'XLConnect',\
'xlsx',\
'xlsxjars',\
'XML',\
'xml2',\
'xtable',\
'xts',\
'yaml',\
'zeallot',\
'zoo'
), repos='http://r-proxy:8180/', upgrade = 'never')"
# Install GitHub packages via r-proxy
R -e "install.packages('remotes', dependencies=TRUE, repos='http://r-proxy:8180/', upgrade = 'never')"
R -e "remotes::install_url(c(\
'http://r-proxy:8180/github/r-barnes/dggridR/archive/refs/heads/master.tar.gz',\
'http://r-proxy:8180/github/bfast2/bfast/archive/refs/heads/master.tar.gz',\
'http://r-proxy:8180/github/azvoleff/gfcanalysis/archive/refs/heads/master.tar.gz',\
'http://r-proxy:8180/github/loicdtx/bfastSpatial/archive/refs/heads/master.tar.gz',\
'http://r-proxy:8180/github/jreiche/bayts/archive/refs/heads/master.tar.gz',\
'http://r-proxy:8180/github/cran/gdalUtils/archive/refs/heads/master.tar.gz'
), repos='http://r-proxy:8180/', build = FALSE, upgrade = 'never')"
To check the availability of a specific package:
Open RStudio.
Go to Help > R Help (from the menu above).
You will see the Help panel opened.
Select
Reference>Packages
Customization#
The SEPAL environment can be customized to user needs by utilizing third-party packages and CRAN in RStudio.
install.packages("vioplot")
Note
If you face compatibility issues when customizing your SEPAL environment, contact the SEPAL team in the Github issue tracker.