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https://github.com/GegznaV/RcmdrPlugin.biostat

:heavy_check_mark: BioStat mode for R Commander (Rcmdr): improved functions, menus, and buttons (R package)
https://github.com/GegznaV/RcmdrPlugin.biostat

gui r r-commander rcmdrplugin

Last synced: about 2 months ago
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:heavy_check_mark: BioStat mode for R Commander (Rcmdr): improved functions, menus, and buttons (R package)

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README 

        
---

output: github_document

---



 

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = FALSE, fig.height = 4, fig.width = 6,

  comment = "#>",

  fig.path = "README-"

)

```



***



[![CRAN status](https://www.r-pkg.org/badges/version/RcmdrPlugin.biostat)](https://cran.r-project.org/package=RcmdrPlugin.biostat)

[![GitHub version](https://img.shields.io/badge/GitHub-v`r packageVersion("RcmdrPlugin.biostat")`-brightgreen.svg)](https://github.com/GegznaV/RcmdrPlugin.biostat)

[![R build status](https://github.com/GegznaV/RcmdrPlugin.BioStat/workflows/R-CMD-check/badge.svg)](https://github.com/GegznaV/RcmdrPlugin.BioStat/actions)

[![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)

[![Documentation](https://img.shields.io/badge/Documentation-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)]()



***



```{r include=FALSE}

fig_dir <-

  "https://raw.githubusercontent.com/GegznaV/RcmdrPlugin.biostat/master/inst/etc/fig/"



knitr::opts_chunk$set(fig.align  = "center")

```



```{r logo-local, fig.align='center', out.height='30%', out.width='30%',echo=FALSE} 

knitr::include_graphics(paste0(fig_dir, "logo.png"))

``` 

 



R Commander Plug-in for Basic Data Management and Analysis Tasks {#intro}

==============================================================================









This package is still experimental.


Some features may change.






**RcmdrPlugin.biostat** is an [**Rcmdr**](https://CRAN.R-project.org/package=Rcmdr) plug-in for the most common data wrangling, visualization, and analysis tasks. 

It provides so-called *BioStat* (green) mode.

In this mode, additional button bar appears:



```{r, echo=FALSE, fig.cap=CAPTION}

knitr::include_graphics(paste0(fig_dir, "05--buttons-in-biostat-mode.png"))



CAPTION <- ""

```



**NOTE:** If an active dataset is not selected, some buttons are shaded in gray and are inactive.



This **BioStat** mode enables access to menus that use **tidyverse** family functions, as well as functions from other packages to perform some basic data wrangling, cleaning, plotting, preview and analysis tasks.



The documentation is available at [gegznav.github.io/RcmdrPlugin.biostat](https://gegznav.github.io/RcmdrPlugin.biostat){target="_blank"}.







***



## Install the Package {#install-the-package}



### Preparation



Before you begin installation or updating, make sure that only a single *R*/*RStudio* session is running and restart the current *R* session (to unload the packages).

It is also recommended to close the current *RStudio* project if you use one.

*Mac* users need [*XQuartz*](http://www.xquartz.org/){target="_blank"} to be installed (see also [Notes for *Mac* users only](#notes-for-mac-users-only)) and opened during the installation.

*Windows* users need [*Rtools*](https://cloud.r-project.org/bin/windows/Rtools/){target="_blank"} if they want to install the package form GitHub.



### Installation (Recommended)



The most convenient way is to install the package form CRAN-like repository:



```{r install-biostat, eval=FALSE}

repos <- c("https://mokymai.github.io/download/", getOption("repos"))

install.packages("RcmdrPlugin.biostat", repos = repos)

```



### Installation from GitHub



If you want to install the development version of the package from “GitHub”, use:



```{r install-biostat-github, eval=FALSE}

# Update all necessary CRAN packages

update.packages(ask = "graphics")



# Install required packages

if (!require("remotes")) install.packages("remotes")



# Install RcmdrPlugin.biostat

remotes::install_github(

  "GegznaV/RcmdrPlugin.biostat",

  dependencies = TRUE, upgrade = TRUE

)

```



In case you face installation issues, follow the instructions in the error message.

You may also try removing `upgrade = TRUE`{.r} and manually choose the packages to update.

It is always recommended to restart *R* session before the next installation too.



> **NOTE:** the most common installation issue is related to *R* package **rlang**.

Usually, you have to delete the indicated "*00LOCK*" directory (you may use [`pacman::p_unlock()`{.r}](https://trinker.github.io/pacman/p_unlock.html){target="_blank"}, if you have package [**pacman**](https://trinker.github.io/pacman){target="_blank"} installed, or delete the directory manually), restart the current *R* session and try to install again.



***



## Load the Plug-in {#load}



The easiest way to load **RcmdrPlugin.biostat** in *BioStat* (green) mode is to use RStudio addin:



```{r fig-00, echo=FALSE, fig.cap=CAPTION}

knitr::include_graphics(paste0(fig_dir, "00-addin-to-load-biostat-mode.png"))



CAPTION <- ""

```



Alternatively, use code:



```{r eval=FALSE}

library(Rcmdr)

library(RcmdrPlugin.biostat)

load_rcmdr_biostat_mode()

```



*Mac* users should also read "[Notes for *Mac* users only](#notes-for-mac-users-only)".



When **RcmdrPlugin.biostat** is loaded, you can access its functionality through either the *BioStat* button bar (find figure above) or through `BioStat` menu in the menu bar (shown as `BioStat'19` in the example):



```{r, echo=FALSE, fig.cap=CAPTION}

knitr::include_graphics(paste0(fig_dir, "03--biostat-plugin-loaded.png"))



CAPTION <- ""

```



### Turn on *BioStat* (Green) Mode {#turn-on-biostat-mode}



If you restarted R Commander and "BioStat" menu is present but button bar is missing, you may re-enable *BioStat* mode by selecting option "Mode: BioStat":



```{r, echo=FALSE, fig.cap=CAPTION}

knitr::include_graphics(paste0(fig_dir, "04--activate-biostat-mode.png"))



CAPTION <- ""

```







### Close *BioStat* Mode {#close-biostat-mode}



To close this mode, simply restart the *R Commander*: 



* R Commander menu bar → BioStat → Session → Restart R Commander



You may use the following command as well:



```{r eval=FALSE}

restart_commander()

```



### Notes for *Mac* Users Only {#notes-for-mac-users-only}



For *Mac* users, there at least 2 things to pay attention to:



1) On *Mac*, *R Commander* opens only if [*XQuartz*](http://www.xquartz.org/){target="_blank"} is opened.

So, the first step of using *R Commander* is to make sure that *XQuartz* is opened.

More information on ["Installing R Commander for *Mac* users"](https://murraystate.instructure.com/courses/1252125/pages/installing-r-commander-on-your-mac){target="_blank"}.



2) Some *Mac* users also report that it is impossible to switch between languages while *R Commander* is running.

This means, that some users might not use numbers if in the chosen language the same keys mean some non-English letters. 

Because of this, it is recommended to choose an appropriate language (usually English) before opening *R*/*RStudio*.



# Important



Some functions in the package are based on and modified from functions in packages *Rcmdr*, and *RcmdrPlugin.EZR*.

All of those packages are under the GPL-2/GPL-3 license.



***