Install R Packages

Index

Install R on Windows

Install RTools for Windows with a version corresponding to the R version
Install MiKTeX on Windows for Latex, change on MikTex console setting to “Always”
Install tabu package from MikTex console

tlb <- installed.packages()
tlb

library(devtools)

install.packages("rlang")
install.packages("lifecycle")


install.packages("data.table")
install.packages("rmarkdown")
install.packages("tinytex")
install.packages("knitr")
install.packages("kableExtra")
install.packages("ggplot2")

Basic R Packages

sessionInfo()
install.packages("recipes")
install.packages("usethis")
install.packages("stringr")
install.packages("knitr")
install.packages("tidyr")
install.packages("rmdformats")
install.packages("devtools", repository="https://cran.r-project.org/")
install.packages("pacman", repository="https://cran.r-project.org/")
library(pacman)




package_list <- c(
    "R6"
  , "roxygen2"
  , "scales"
  , "usethis"
  , "recipes"
  , "stringr"
  , "devtools"
  , "pacman"
  , "tidyr"
  , "pkgload"
  , "desc"
  , "covr"
  , "rmdformats"
  , "lazyeval"
  , "lattice"
  , "devtools"
  , "rms"
  , "scales"
  , "covr"
  , "DT"
  , "magrittr"
  , "testthat"
  , "rematch2"
  , "stringr"
  , "dplyr"
  , "dtplyr"
  , "tibble"
  , "KernSmooth"
  , "cli"
  , "viridis"
  , "munsell"
  , "crayon"
  , "pillar"
  , "survival"
  , "knitr"
  , "lattice"
  , "mgcv"
  , "ggplot2"
  , "plotly"
  , "purrr"
  , "rgl"
  , "rmarkdown"
  , "knitr"
  , "zoo"
  , "htmlTable"
  , "rstan"
  , "assertthat"
  , "pkgbuild"
  , "xts"
  , "dygraphs"
  , "sf"
  , "memoise"
  , "spatstat"
  , "classInt"
  , "Hmisc"
  , "rmsb"
  , "KernSmooth"
  , "ks"
  , "KernSmooth"
  , "JuliaCall"
  , "rmarkdown"
  , "ragg"
  , "textshaping"
  , "lattice"
  , "scales"
  , "ggplot2"
  , "munsell"
  , "tibble"
  , "magrittr"
  , "tibble"
  , "crayon"
  , "base64enc"
  , "latticeExtra"
  , "RColorBrewer"
  , "assertthat"
  , "desc"
  , "rprojroot"
  , "sessioninfo"
  , "rmarkdown"
  , "rgl"
  , "rgeos"
  , "gridExtra"
  , "purrr"
  , "lazyeval"
  , "covr"
  , "testthat"
  , "knitr"
  , "rmarkdown"
  , "gifski"
  , "zoo"
  , "sandwich"
  , "MatrixModels"
  , "np"
  , "quantreg"
  , "AER"
  , "rugarch"
  , "ROCR"
  , "ks"
  , "maxLik"
  , "truncreg"
  , "sampleSelection"
  , "mlogit"
  , "plm"
  , "rgl"
  , "viridisLite"
  , "mgcv"
  , "Hmisc"
  , "rms"
  , "htmlTable"
  , "multcomp"
  , "TH.data"
  , "data.table"
  , "askpass"
  , "openssl"
  , "labeling"
  , "rmdformats"
  , "visNetwork"
  , "kableExtra"
  , "digest"
  , "lme4"
  , "sjPlot"
  , "survminer"
  , "coxme"
  , "ordinal"
  , "tidyverse"
  , "BART"
  , "pkgload"
  , "Hmisc"
  , "rms"
  , "caret"
  , "conquer"
  , "recipes"
  , "labelled"
  , "munsell"
  , "gridExtra"
  , "quantreg"
  , "rms"
  , "Hmisc"
)
package_list <- unique(package_list)
length(package_list)

new.packages <- package_list[!(package_list %in% installed.packages()[,"Package"])]
length(new.packages)
print(new.packages)

if(length(package_list)) install.packages(package_list,  repository="https://cran.r-project.org/")


devtools::install_github("ghowoo/Wu", force = TRUE)
install.packages("ordinal", repository="https://cran.r-project.org/")
install.packages("openssl", repository="https://cran.r-project.org/")




install.packages("rms")
install.packages("ggplot2")
install.packages("scales")
install.packages("munsell")
install.packages("gridExtra")
install.packages("quantreg")

install.packages("pacman")
library(pacman)
update.packages()
update.packages(ask=FALSE)
p_load(package_list, install=TRUE, update=TRUE)

pacman Package

print(1:3)
sessionInfo()
## install.packages("devtools", repository="https://cran.r-project.org/")
## install.packages("pacman", repository="https://cran.r-project.org/")
library(pacman)

package_list <- c(
    "R6"
  , "roxygen2"
  , "pkgload"
  , "desc"
  , "covr"
  , "lazyeval"
  , "lattice"
  , "devtools"
  , "rms"
  , "scales"
  , "covr"
  , "DT"
  , "magrittr"
  , "testthat"
  , "rematch2"
  , "stringr"
  , "dplyr"
  , "dtplyr"
  , "tibble"
  , "KernSmooth"
  , "cli"
  , "viridis"
  , "munsell"
  , "crayon"
  , "pillar"
  , "survival"
  , "knitr"
  , "lattice"
  , "mgcv"
  , "ggplot2"
  , "plotly"
  , "purrr"
  , "rgl"
  , "rmarkdown"
  , "knitr"
  , "zoo"
  , "htmlTable"
  , "rstan"
  , "assertthat"
  , "pkgbuild"
  , "xts"
  , "dygraphs"
  , "sf"
  , "memoise"
  , "spatstat"
  , "classInt"
  , "Hmisc"
  , "rmsb"
  , "KernSmooth"
  , "ks"
  , "KernSmooth"
  , "JuliaCall"
  , "rmarkdown"
  , "ragg"
  , "textshaping"
  , "lattice"
  , "scales"
  , "ggplot2"
  , "munsell"
  , "tibble"
  , "magrittr"
  , "tibble"
  , "crayon"
  , "base64enc"
  , "latticeExtra"
  , "RColorBrewer"
  , "assertthat"
  , "desc"
  , "rprojroot"
  , "sessioninfo"
  , "rmarkdown"
  , "rgl"
  , "rgeos"
  , "gridExtra"
  , "purrr"
  , "lazyeval"
  , "covr"
  , "testthat"
  , "knitr"
  , "rmarkdown"
  , "gifski"
  , "zoo"
  , "sandwich"
  , "MatrixModels"
  , "np"
  , "quantreg"
  , "AER"
  , "rugarch"
  , "ROCR"
  , "ks"
  , "maxLik"
  , "truncreg"
  , "sampleSelection"
  , "mlogit"
  , "plm"
  , "rgl"
  , "viridisLite"
  , "mgcv"
  , "Hmisc"
  , "rms"
  , "htmlTable"
  , "multcomp"
  , "TH.data"
  , "data.table"
  , "askpass"
  , "openssl"
  , "labeling"
  , "rmdformats"
  , "visNetwork"
  , "kableExtra"
  , "digest"
  , "lme4"
  , "sjPlot"
  , "survminer"
  , "coxme"
  , "ordinal"
  , "tidyverse"
  , "BART"
)





package_list <- unique(package_list)
new.packages <- package_list[!(package_list %in% installed.packages()[,"Package"])]
length(new.packages)
print(new.packages)

if(length(new.packages)) install.packages(new.packages,  repository="https://cran.r-project.org/")

devtools::install_github("ghowoo/Wu", force = TRUE)
install.packages("ordinal", repository="https://cran.r-project.org/")
install.packages("openssl", repository="https://cran.r-project.org/")


update.packages()



p_load(package_list, install=TRUE, update=TRUE)









### ??????????????
devtools::install_github("r-spatial/sf")
devtools::install_github("cran/rgdal")
devtools::install_github("CRAN/rgdal")


install.packages("digest", repository="https://cran.r-project.org/")

install.packages("sf", repository="https://cran.r-project.org/")
install.packages("rgdal", repository="https://cran.r-project.org/")
devtools::install_version("rgdal", version = "1.3-9")



install.packages("lwgeom", repository="https://cran.r-project.org/")

Install R on Ubuntu

## source
https://cran.r-project.org/bin/linux/ubuntu/README.html


## add CRAN GPG key
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9



## add repository to APT repository
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'


## update to incolude package manifests from new repository
sudo apt update
sudo apt upgrade

## install R
sudo apt install r-base

## check R version
R --version


## need to compile R package
sudo apt-get install r-base-dev


## list all PPA
apt policy

## remove PPA
sudo add-apt-repository --remove ppa:videolan/master-daily

## autoclean and auto remove apt
sudo apt-get autoclean
sudo apt-get autoremove


## install ppa remover
sudo apt-get install ppa-purge
## remove ppa by url
sudo ppa-purge ppa-url


## edit sources.list file, remove or comment (#) entries;
sudo gedit /etc/apt/sources.list

##
apt-get upgrade will not change what is installed (only versions),
apt-get dist-upgrade will install or remove packages as necessary to complete the upgrade,
apt upgrade will automatically install but not remove packages.
apt full-upgrade performs the same function as apt-get dist-upgrade.


##
update.packages()

## install libfrididi-dev
sudo apt-get update -y
sudo apt-get install -y libfribidi-dev


## for sf package
sudo apt install -y libudunits2-0 libudunits2-dev
sudo apt install libgdal-dev
sudo apt-get install libxmu-dev libxmu-headers freeglut3-dev libxext-dev libxi-dev
sudo apt install libgdal-dev
sudo apt-get install libgcc1 lib32gcc1 libx32gcc1
sudo apt-get update
sudo apt-get install gdal-bin
sudo apt-get install libgdal-dev
sudo apt-get install libgeos-dev

sudo apt-get update
sudo apt-get install libgdal-dev libproj-dev
sudo apt install libgeos++dev
sudo apt install gdal-bin libgdal-dev libproj-dev

sudo apt-get install libgdal1-dev libproj-dev


sudo add-apt-repository ppa:ubuntugis/ppa
ogrinfo --version

sudo add-apt-repository ppa:ubuntugis/ppa && sudo apt-get update
sudo add-apt-repository ppa:ubuntugis/ppa


sudo dpkg -i libgdal1-dev_1.11.3+dfsg-3build2_all.deb

## search for current lib name
apt-cache search libgdal
## libgdal-dev is already the newest version (2.4.2+dfsg-1~bionic0).

## for install R rgdal package
sudo apt-get install gdal-bin proj-bin libgdal-dev libproj-dev

## install gcc g++ c++ complier
sudo apt install g++

## sudo apt remove pckage

    sudo apt remove package


## check if installed
dpkg -l packag


apt-cache policy will only show the repos after you have run apt-get update. If you just added a repo with add-apt-repository, it will not show up with apt-cache policy until you run apt-get update

## list all sources
sudo ls /etc/apt/sources.list.d

## remove
sudo rm -i /etc/apt/sources.list.d/PPA_Name.list

sudo gedit /etc/apt/sources.list


apt-cache policy emacs26-common emacs25-common

sudo apt upgrade package - name;

## remove;
sudo rm -f /usr/local/bin/gdal-config

sudo apt-get --purge remove gimp


## remove onld link cache
sudo ldconfig


sudo apt-get install libwebp5