UpdateR and (re-)Install Packages

This script is to be run whenever you want to update R and/or install your required packages. Whenever you install a new package, try to remember to add it to this file. This way, whenver you update, you can just run this script and will then have all your required packages ready to go. Newer versions of RStudio automatically check for missing packages when opening a script, so forgetting to install CRAN packages will be less detrimental to your workflow.

Check for R update: `updateR`

Do you need to update R? If using a Mac, you can do this by using the updateR package (some steps found here):

# install devtools if you don't have it already
install.packages("devtools")

# install updateR
devtools::install_github('andreacirilloac/updateR')

# run; you will be prompted for admin password
updateR::updateR()

updateR macOS compatibility

As of mid-2023, updateR() spits out an error after entering your password:

Updated ~/.Rprofile
Password:Error in if (!compactible) stop(sprintf(e, status$latest, macOS), call. = FALSE) : 
  argument is of length zero

This seems to have something to do with the newest Mac OS (see: discussion on the package GitHub). For now, manual update only directly from CRAN.

Check for R update on Windows: `installR`

The installR package also has an updateR() function which only works on Windows. You will need to run the function in directly in R, not RStudio!

# install installr
install.packages("installr")

# run; you will be prompted for admin password
installr::updateR()

Global options

My preferred global options (RStudio > Tools > Global options):

General > Basic
- R Sessions
  - uncheck ‘Restore previously open source documents at startup’
- Workspace (for reproducibile workflow!!!)
  - uncheck ‘Restore .RData into workshapce at startup’
  - Save workspace to .RData on exit: Never
Code > Display
- General
  - Show whitespace characters
  - Allow scroll past end of document
  - highlight selected line
Appearance
- Editor theme: Cobalt

Install packages

Packages can be available on CRAN or through developer versions.

CRAN packages

First make a list of your packages available on CRAN.

# CRAN packages ####

# run THIS chunk after updating R/RStudio
# from 'install_packages_if_missing.R'; roughly alphabetical
required_packages <- c("binom", "bookdown", "broman", "citr", "dplyr", "doBy",
                       "beepr", # to play sounds
                       "emmeans", "EMAtools", "grid", 
                       "ggplot2", "ggdark", "ggstatplot",
                       "ggpp", # grammar extension of ggplot2
                       "ggpubr",
                       "ggrain",
                       "formatR", "janitor",
                       "here", "knitr", "kableExtra",  "lme4", "lmerTest",
                       "png", "pryr", "papaja", "performance",
                       "tidyverse", "Rmpfr", "rmarkdown", "rotations",
                       "quarto",
"starpolishr", "stargazer", "simr",
                       "xtable")

Then, run this list through a for-loop that checks whether you’ve got these packages installed already. If not, the package will be installed.

for (package in required_packages) {
  print(paste0("checking for install of ", package))
  if (!requireNamespace(package)) install.packages(package, repos = "http://cran.rstudio.com")
}

Install dev packages: `devtools` and `remotes`

Now install the packages that aren’t on CRAN. First, install devtools and remotes if you don’t already have them installed.

# Install remotes package if necessary
if(!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")

# Install remotes package if necessary
if(!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")

`ggrain` package

For raincloud plots geom

if (!require(remotes)) {
    install.packages("remotes")
}
remotes::install_github('jorvlan/raincloudplots')

library(raincloudplots)

`papaja` package

APA formatted templates

# download developer papaja (code https://github.com/crsh/papaja)

# Install the stable development version from GitHub
remotes::install_github("crsh/papaja")

# Install the latest development snapshot from GitHub
remotes::install_github("crsh/papaja@devel")

`rbbt` package

integrates Zotero with RStudio

# Install rbbt Addin from GitHub to use Zotero
remotes::install_github("paleolimbot/rbbt")

To set-up a citation entry shortcut: RStudio > Tools > Modify Keyboard Shortcuts > enter ‘Zotero’ in the search > choose ‘Insert Zotero Citations’ > add a shortcut (I like Ctrl+K)

`brms` package

for running Bayesian models

# brms packages ####

# From https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
# run the next line if you already have rstan installed
# remove.packages(c("StanHeaders", "rstan"))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))

`cmdstanr` package

for running Bayesian models

# and cmdstanr (https://mc-stan.org/cmdstanr/)
remotes::install_github("stan-dev/cmdstanr")
# or
# install cmdstanr
cmdstanr::install_cmdstan(cores = parallel::detectCores(), overwrite = TRUE)

`bcogsci` package

companion package for the textbook An Introduction to Bayesian Data Analysis for Cognitive Science

# run the nextline if you don't have 'devtools' already installed
# install.packages("devtools")
remotes::install_github("bnicenboim/bcogsci")

Optional developer packages

these only need to be installed if specifically wanted

`stargazer` package

these steps were taken when updatin to R v.4.2.1 as a work around to a problem that cropped up; only run this chunk if you start having problems with stargazer
as of March 14, 2023 it’s still needed

# 31.08.2022: updated to R version 4.2.1 (2022-06-23), now stargazer won't compile tables where model names are too long
# Solution: discussed here https://www.reddit.com/r/rstats/comments/ucmtdn/issue_with_stargazer_package_after_update_to_r_420/
# code below from linked solution https://gist.github.com/alexeyknorre/b0780836f4cec04d41a863a683f91b53
## Quick fix for stargazer <= 5.2.3 is.na() issue with long model names in R >= 4.2
# Unload stargazer if loaded
detach("package:stargazer",unload=T)
# Delete it
remove.packages("stargazer")
# Download the source
download.file("https://cran.r-project.org/src/contrib/stargazer_5.2.3.tar.gz", destfile = "stargazer_5.2.3.tar.gz")
# Unpack
untar("stargazer_5.2.3.tar.gz")
# Read the sourcefile with .inside.bracket fun
stargazer_src <- readLines("stargazer/R/stargazer-internal.R")
# Move the length check 5 lines up so it precedes is.na(.)
stargazer_src[1990] <- stargazer_src[1995]
stargazer_src[1995] <- ""
# Save back
writeLines(stargazer_src, con="stargazer/R/stargazer-internal.R")
# Compile and install the patched package
install.packages("stargazer", repos = NULL, type="source")
### FROM NOW ON: shorter model names for stargazer

PsyTeachR `Introdataviz`

can produce violin plots and raincloud plots

# how to install the introdataviz package to get split and half violin plots
remotes::install_github("psyteachr/introdataviz", dependencies = TRUE)

`starpolishr` package

availabile on github
post-polishing of stargazer tables

# install.packages("devtools")
devtools::install_github("ChandlerLutz/starpolishr")

CogSci paper template

used to write CogSci conference proceedings papers

# Install CogSci paper template
remotes::install_github("kemacdonald/cogsci2016")

Loading packages

Moving forward, use the following code at the beginning of your scripts instead of the long list of library(package). This will also check whether packages are installed, if they are it’ll load them, and if they’re not it’ll install them and then load them.

# don't use scientific notation
options(scipen=999)

# copy this chunk at the beginning of new chapters; will automatically load packages and install needed packages

## First specify the packages of interest
packages <- c("here", "tidyverse", "dplyr", "formatR", "stringr",
              "janitor", "dplyr", "ggplot2", "lmerTest", "stargazer",
              "MASS", "afex", "knitr", "gridExtra", "grid",
              "paletteer",
              "remotes",
              "Rmisc")

## Now load or install&load all
package.check <- lapply(
  packages,
  FUN = function(x) {
    if (!require(x, character.only = TRUE)) {
      install.packages(x, dependencies = TRUE)
      library(x, character.only = TRUE)
    }
  }
)

Manual installs

tinyTex

to render documents with LaTeX under the hood, run the following in the terminal: quarto install tinytex

Citations with Zotero

To use the rbbt package installed above, we need to have Zotero installed (and Better BibTex).

install Zotero

https://www.zotero.org/download/

Better BibTex

Install from the [website]{https://retorque.re/zotero-better-bibtex/installation/}

then in Zotero: Tools / Add-ins / Settings wheel / choose downloaded file / Restart Zotero
set your citation keys: Zotero > Settings > Better BibTex > Citation key formula > (I like “zotero.clean”)
- if you need to update the BibTex key in your docs:
  - highlight all your files in the Zotero Library, right-click > Better BibTex > Refresh BibTex key

# UpdateR and (re-)Install Packages ```{r, echo = F} # set global options knitr::opts_chunk$set(eval = F, # run each code chunk? echo = T, # print code chunk? message = F, # print messages (e.g., warnings)? error = F, # print errors? cache = T # cache? (Session > Restart R to clear cache) ) ``` This script is to be run whenever you want to update R and/or install your required packages. Whenever you install a new package, try to remember to add it to this file. This way, whenver you update, you can just run this script and will then have all your required packages ready to go. Newer versions of RStudio automatically check for missing packages when opening a script, so forgetting to install CRAN packages will be less detrimental to your workflow. ## Check for R update: `updateR` Do you need to update R? If using a Mac, you can do this by using the `updateR` package (some steps found [here](https://www.linkedin.com/pulse/3-methods-update-r-rstudio-windows-mac-woratana-ngarmtrakulchol/)): ```{r} # install devtools if you don't have it already install.packages("devtools") ``` ```{r} # install updateR devtools::install_github('andreacirilloac/updateR') ``` ```{r} # run; you will be prompted for admin password updateR::updateR() ``` ::: {.callout-warning} ### `updateR` macOS compatibility As of mid-2023, `updateR()` spits out an error after entering your password: ```{r} #| eval: false Updated ~/.Rprofile Password:Error in if (!compactible) stop(sprintf(e, status$latest, macOS), call. = FALSE) : argument is of length zero ``` This seems to have something to do with the newest Mac OS (see: [discussion on the package GitHub](https://github.com/AndreaCirilloAC/updateR/issues/37)). For now, manual update only directly from [CRAN](https://cran.r-project.org/bin/macosx/). ::: ## Check for R update on Windows: `installR` The `installR` package also has an `updateR()` function which only works on Windows. You will need to run the function in directly in R, *not* RStudio! ```{r} # install installr install.packages("installr") ``` ```{r} # run; you will be prompted for admin password installr::updateR() ``` ## Global options My preferred global options (RStudio > Tools > Global options): - General > Basic - **R Sessions** + uncheck 'Restore previously open source documents at startup' - **Workspace** (for reproducibile workflow!!!) + uncheck 'Restore .RData into workshapce at startup' + Save workspace to .RData on exit: ***Never*** - Code > Display - General + Show whitespace characters + Allow scroll past end of document + highlight selected line - Appearance - Editor theme: Cobalt ## Install packages Packages can be available on CRAN or through developer versions. ### CRAN packages First make a list of your packages available on CRAN. ```{r} # CRAN packages #### # run THIS chunk after updating R/RStudio # from 'install_packages_if_missing.R'; roughly alphabetical required_packages <- c("binom", "bookdown", "broman", "citr", "dplyr", "doBy", "beepr", # to play sounds "emmeans", "EMAtools", "grid", "ggplot2", "ggdark", "ggstatplot", "ggpp", # grammar extension of ggplot2 "ggpubr", "ggrain", "formatR", "janitor", "here", "knitr", "kableExtra", "lme4", "lmerTest", "png", "pryr", "papaja", "performance", "tidyverse", "Rmpfr", "rmarkdown", "rotations", "quarto", "starpolishr", "stargazer", "simr", "xtable") ``` Then, run this list through a for-loop that checks whether you've got these packages installed already. If not, the package will be installed. ```{r} for (package in required_packages) { print(paste0("checking for install of ", package)) if (!requireNamespace(package)) install.packages(package, repos = "http://cran.rstudio.com") } ``` ### Install dev packages: `devtools` and `remotes` Now install the packages that aren't on CRAN. First, install `devtools` and `remotes` if you don't already have them installed. ```{r} # Install remotes package if necessary if(!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") ``` ```{r} # Install remotes package if necessary if(!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") ``` #### `ggrain` package For raincloud plots geom ```{r} if (!require(remotes)) { install.packages("remotes") } remotes::install_github('jorvlan/raincloudplots') library(raincloudplots) ``` #### `papaja` package - APA formatted templates ```{r} # download developer papaja (code https://github.com/crsh/papaja) # Install the stable development version from GitHub remotes::install_github("crsh/papaja") # Install the latest development snapshot from GitHub remotes::install_github("crsh/papaja@devel") ``` #### `rbbt` package - integrates Zotero with RStudio ```{r} # Install rbbt Addin from GitHub to use Zotero remotes::install_github("paleolimbot/rbbt") ``` To set-up a citation entry shortcut: RStudio > Tools > Modify Keyboard Shortcuts > enter 'Zotero' in the search > choose 'Insert Zotero Citations' > add a shortcut (I like Ctrl+K) #### `brms` package - for running Bayesian models ```{r} # brms packages #### # From https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started # run the next line if you already have rstan installed # remove.packages(c("StanHeaders", "rstan")) install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) ``` #### `cmdstanr` package - for running Bayesian models ```{r} # and cmdstanr (https://mc-stan.org/cmdstanr/) remotes::install_github("stan-dev/cmdstanr") # or # install cmdstanr cmdstanr::install_cmdstan(cores = parallel::detectCores(), overwrite = TRUE) ``` #### `bcogsci` package - companion package for the textbook [An Introduction to Bayesian Data Analysis for Cognitive Science](https://vasishth.github.io/bayescogsci/book/) ```{r} # run the nextline if you don't have 'devtools' already installed # install.packages("devtools") remotes::install_github("bnicenboim/bcogsci") ``` ### Optional developer packages - these only need to be installed if specifically wanted #### `stargazer` package - these steps were taken when updatin to R v.4.2.1 as a work around to a problem that cropped up; only run this chunk if you start having problems with stargazer - as of March 14, 2023 it's still needed ```{r} # 31.08.2022: updated to R version 4.2.1 (2022-06-23), now stargazer won't compile tables where model names are too long # Solution: discussed here https://www.reddit.com/r/rstats/comments/ucmtdn/issue_with_stargazer_package_after_update_to_r_420/ # code below from linked solution https://gist.github.com/alexeyknorre/b0780836f4cec04d41a863a683f91b53 ## Quick fix for stargazer <= 5.2.3 is.na() issue with long model names in R >= 4.2 # Unload stargazer if loaded detach("package:stargazer",unload=T) # Delete it remove.packages("stargazer") # Download the source download.file("https://cran.r-project.org/src/contrib/stargazer_5.2.3.tar.gz", destfile = "stargazer_5.2.3.tar.gz") # Unpack untar("stargazer_5.2.3.tar.gz") # Read the sourcefile with .inside.bracket fun stargazer_src <- readLines("stargazer/R/stargazer-internal.R") # Move the length check 5 lines up so it precedes is.na(.) stargazer_src[1990] <- stargazer_src[1995] stargazer_src[1995] <- "" # Save back writeLines(stargazer_src, con="stargazer/R/stargazer-internal.R") # Compile and install the patched package install.packages("stargazer", repos = NULL, type="source") ### FROM NOW ON: shorter model names for stargazer ``` #### PsyTeachR `Introdataviz` - can produce violin plots and raincloud plots ```{r} # how to install the introdataviz package to get split and half violin plots remotes::install_github("psyteachr/introdataviz", dependencies = TRUE) ``` #### `starpolishr` package - availabile on [github](https://github.com/ChandlerLutz/starpolishr) - post-polishing of stargazer tables ```{r} # install.packages("devtools") devtools::install_github("ChandlerLutz/starpolishr") ``` #### CogSci paper template - used to write CogSci conference proceedings papers ```{r} # Install CogSci paper template remotes::install_github("kemacdonald/cogsci2016") ``` ## Loading packages Moving forward, use the following code at the beginning of your scripts instead of the long list of `library(package)`. This will also check whether packages are installed, if they are it'll load them, and if they're not it'll install them and then load them. ```{r, eval = F} # don't use scientific notation options(scipen=999) # copy this chunk at the beginning of new chapters; will automatically load packages and install needed packages ## First specify the packages of interest packages <- c("here", "tidyverse", "dplyr", "formatR", "stringr", "janitor", "dplyr", "ggplot2", "lmerTest", "stargazer", "MASS", "afex", "knitr", "gridExtra", "grid", "paletteer", "remotes", "Rmisc") ## Now load or install&load all package.check <- lapply( packages, FUN = function(x) { if (!require(x, character.only = TRUE)) { install.packages(x, dependencies = TRUE) library(x, character.only = TRUE) } } ) ``` ## Manual installs ### tinyTex - to render documents with LaTeX under the hood, run the following in the *terminal*: `quarto install tinytex` ### Citations with Zotero To use the `rbbt` package installed above, we need to have Zotero installed (and Better BibTex). #### install Zotero https://www.zotero.org/download/ #### Better BibTex Install from the [website]{https://retorque.re/zotero-better-bibtex/installation/} - then in Zotero: Tools / Add-ins / Settings wheel / choose downloaded file / Restart Zotero - set your citation keys: Zotero > Settings > Better BibTex > Citation key formula > (I like "zotero.clean") + if you need to update the BibTex key in your docs: + highlight all your files in the Zotero Library, right-click > Better BibTex > Refresh BibTex key

UpdateR and (re-)Install Packages

Check for R update: updateR

Check for R update on Windows: installR