{"id":32344179,"url":"https://github.com/gegznav/rcmdrplugin.biostat","last_synced_at":"2026-03-04T11:02:42.451Z","repository":{"id":93361477,"uuid":"73751473","full_name":"GegznaV/RcmdrPlugin.biostat","owner":"GegznaV","description":":heavy_check_mark: BioStat mode for R Commander (Rcmdr): improved functions, menus, and buttons (R package)","archived":false,"fork":false,"pushed_at":"2026-02-28T22:46:22.000Z","size":6619,"stargazers_count":3,"open_issues_count":1,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-02-28T23:43:52.256Z","etag":null,"topics":["gui","r","r-commander","rcmdrplugin"],"latest_commit_sha":null,"homepage":"https://gegznav.github.io/RcmdrPlugin.biostat","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/GegznaV.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-11-14T22:11:03.000Z","updated_at":"2025-12-06T06:58:06.000Z","dependencies_parsed_at":"2023-03-10T15:00:39.393Z","dependency_job_id":"8bece4b8-2759-4ac2-9a3d-45f8b6b4497e","html_url":"https://github.com/GegznaV/RcmdrPlugin.biostat","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/GegznaV/RcmdrPlugin.biostat","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GegznaV%2FRcmdrPlugin.biostat","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GegznaV%2FRcmdrPlugin.biostat/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GegznaV%2FRcmdrPlugin.biostat/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GegznaV%2FRcmdrPlugin.biostat/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/GegznaV","download_url":"https://codeload.github.com/GegznaV/RcmdrPlugin.biostat/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/GegznaV%2FRcmdrPlugin.biostat/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30078415,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-04T08:01:56.766Z","status":"ssl_error","status_checked_at":"2026-03-04T08:00:42.919Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["gui","r","r-commander","rcmdrplugin"],"created_at":"2025-10-24T04:39:04.272Z","updated_at":"2026-03-04T11:02:42.378Z","avatar_url":"https://github.com/GegznaV.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n \n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = FALSE, fig.height = 4, fig.width = 6,\n  comment = \"#\u003e\",\n  fig.path = \"README-\"\n)\n```\n\n***\n\n\u003c!-- badges: start --\u003e\n[![CRAN status](https://www.r-pkg.org/badges/version/RcmdrPlugin.biostat)](https://cran.r-project.org/package=RcmdrPlugin.biostat)\n[![GitHub version](https://img.shields.io/badge/GitHub-v`r packageVersion(\"RcmdrPlugin.biostat\")`-brightgreen.svg)](https://github.com/GegznaV/RcmdrPlugin.biostat)\n[![R build status](https://github.com/GegznaV/RcmdrPlugin.BioStat/workflows/R-CMD-check/badge.svg)](https://github.com/GegznaV/RcmdrPlugin.BioStat/actions)\n[![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)\n[![Documentation](https://img.shields.io/badge/Documentation-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)]()\n\u003c!-- badges: end --\u003e\n\n***\n\n```{r include=FALSE}\nfig_dir \u003c-\n  \"https://raw.githubusercontent.com/GegznaV/RcmdrPlugin.biostat/master/inst/etc/fig/\"\n\nknitr::opts_chunk$set(fig.align  = \"center\")\n```\n\n```{r logo-local, fig.align='center', out.height='30%', out.width='30%',echo=FALSE} \nknitr::include_graphics(paste0(fig_dir, \"logo.png\"))\n``` \n \n\n\n\u003c!-- \nAn *R Commander* Plugin for Basic (Bio)Statistical Routines  \n--\u003e\n\nR Commander Plug-in for Basic Data Management and Analysis Tasks {#intro}\n==============================================================================\n\n\n\u003cbr\u003e\n\u003ccenter\u003e\u003cfont color = \"red\"\u003e\u003cb\u003e\n\nThis package is still experimental.\u003cbr\u003e\nSome features may change.\n\n\u003c/b\u003e\u003c/font\u003e\u003c/center\u003e\n\n\n\n**RcmdrPlugin.biostat** is an [**Rcmdr**](https://CRAN.R-project.org/package=Rcmdr) plug-in for the most common data wrangling, visualization, and analysis tasks. \nIt provides so-called *BioStat* (green) mode.\nIn this mode, additional button bar appears:\n\n```{r, echo=FALSE, fig.cap=CAPTION}\nknitr::include_graphics(paste0(fig_dir, \"05--buttons-in-biostat-mode.png\"))\n\nCAPTION \u003c- \"\"\n```\n\n**NOTE:** If an active dataset is not selected, some buttons are shaded in gray and are inactive.\n\n\nThis **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.\n\n\nThe documentation is available at [gegznav.github.io/RcmdrPlugin.biostat](https://gegznav.github.io/RcmdrPlugin.biostat){target=\"_blank\"}.\n\n\u003cbr\u003e\n\n\n***\n\n## Install the Package {#install-the-package}\n\n### Preparation\n\nBefore 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).\nIt is also recommended to close the current *RStudio* project if you use one.\n*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.\n*Windows* users need [*Rtools*](https://cloud.r-project.org/bin/windows/Rtools/){target=\"_blank\"} if they want to install the package form GitHub.\n\n\n### Installation (Recommended)\n\nThe most convenient way is to install the package form CRAN-like repository:\n\n```{r install-biostat, eval=FALSE}\nrepos \u003c- c(\"https://mokymai.github.io/download/\", getOption(\"repos\"))\ninstall.packages(\"RcmdrPlugin.biostat\", repos = repos)\n```\n\n\n### Installation from GitHub\n\nIf you want to install the development version of the package from “GitHub”, use:\n\n```{r install-biostat-github, eval=FALSE}\n# Update all necessary CRAN packages\nupdate.packages(ask = \"graphics\")\n\n# Install required packages\nif (!require(\"remotes\")) install.packages(\"remotes\")\n\n# Install RcmdrPlugin.biostat\nremotes::install_github(\n  \"GegznaV/RcmdrPlugin.biostat\",\n  dependencies = TRUE, upgrade = TRUE\n)\n```\n\nIn case you face installation issues, follow the instructions in the error message.\nYou may also try removing `upgrade = TRUE`{.r} and manually choose the packages to update.\nIt is always recommended to restart *R* session before the next installation too.\n\n\n\u003e **NOTE:** the most common installation issue is related to *R* package **rlang**.\nUsually, 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.\n\n\n\n***\n\n## Load the Plug-in {#load}\n\nThe easiest way to load **RcmdrPlugin.biostat** in *BioStat* (green) mode is to use RStudio addin:\n\n```{r fig-00, echo=FALSE, fig.cap=CAPTION}\nknitr::include_graphics(paste0(fig_dir, \"00-addin-to-load-biostat-mode.png\"))\n\nCAPTION \u003c- \"\"\n```\n\nAlternatively, use code:\n\n```{r eval=FALSE}\nlibrary(Rcmdr)\nlibrary(RcmdrPlugin.biostat)\nload_rcmdr_biostat_mode()\n```\n\n*Mac* users should also read \"[Notes for *Mac* users only](#notes-for-mac-users-only)\".\n\n\n\n\n\u003c!-- Package **RcmdrPlugin.biostat** can be loaded programmatically or by using menus: --\u003e\n\n\n\u003c!-- a) *Option 1.* Run code: --\u003e\n\n\u003c!--     ```{r eval=FALSE} --\u003e\n\u003c!--     library(RcmdrPlugin.biostat) --\u003e\n\u003c!--     load_rcmdr_biostat_mode() --\u003e\n\u003c!--     ``` --\u003e\n\n\n\u003c!-- b) *Option 2.* Run code: --\u003e\n\n\u003c!--     ```{r eval=FALSE} --\u003e\n\u003c!--     options(Rcmdr = list(plugins = \"RcmdrPlugin.biostat\", console.output = FALSE)) --\u003e\n\u003c!--     library(Rcmdr) --\u003e\n\u003c!--     set_biostat_mode() --\u003e\n\u003c!--     ``` --\u003e\n\n\u003c!-- c) *Option 3:* use *RStudio* and *R Commander* menus (see sections \"[Load by using menus](#load-by-using-menus)\" and \"[Turn on *BioStat* (green) mode](#turn-on-biostat-green-mode)\"). --\u003e\n\n\u003c!-- \u003cbr\u003e --\u003e\n\n\u003c!-- *Mac* users should also read \"[Notes for *Mac* users only](#notes-for-mac-users-only)\". --\u003e\n\n\u003c!-- **Next**, for some of the options above, the *BioStat* mode should be turned on by using commander (see section \"[Turn on *BioStat* (green) mode](#turn-on-biostat-green-mode)\"). --\u003e\n\n\n\u003c!-- ### Load by using menus {#load-by-menu} --\u003e\n\n\u003c!-- 1. Load package **Rcmdr** by either selecting **Rcmdr** in *RStudio* „Packages“ menu: --\u003e\n\n\u003c!--     ```{r, echo=FALSE, fig.cap=CAPTION} --\u003e\n\u003c!--     knitr::include_graphics(paste0(fig_dir, \"01--load-rcmdr-in-rs.png\"))  --\u003e\n\n\u003c!--     CAPTION = \"\" # Figure caption/description. --\u003e\n\u003c!--     ``` --\u003e\n\n\u003c!--     Or by using *R* code:  --\u003e\n\u003c!--     ```{r eval=FALSE} --\u003e\n\u003c!--     library(Rcmdr) --\u003e\n\u003c!--     ``` --\u003e\n\u003c!--     Wait until *R Commander* window opens. --\u003e\n\u003c!--     \u003cbr\u003e --\u003e\n\n\u003c!-- 2. Then load the plug-in (as well as the other necessary plug-ins) through  --\u003e\n\u003c!-- `Tools` → `Load Rcmdr plug-in(s)...` in the *R Commander* menu bar. --\u003e\n\n\u003c!--     ```{r, echo=FALSE, fig.cap=CAPTION} --\u003e\n\u003c!--     knitr::include_graphics(paste0(fig_dir, \"02--load-plugin--biostat.png\"))  --\u003e\n\n\u003c!--     CAPTION = \"\" # Figure caption/description. --\u003e\n\u003c!--     ``` --\u003e\n\n\u003c!--     If you need more than one plug-in to be loaded, hold \u003ckbd\u003eCtrl\u003c/kbd\u003e key while selecting the plug-ins. --\u003e\n\u003c!-- To load the plug-ins, *R Commander* must restart. --\u003e\n\n\u003c!-- \u003e **NOTE:** be aware that some plug-ins are incompatible one to the other and  --\u003e\n\u003c!--         some combinations of plug-ins may break *R Commander*  --\u003e\n\u003c!--         (e.g., \"RcmdrPlugin.EZR\" and \"RcmdrPlugin.EZR.as.menu\"). --\u003e\n\u003c!--         In this kind of situations, you should restart *R* session and try the  --\u003e\n\u003c!--         other combinations of plugins. --\u003e\n\n\n\u003c!-- \u003e **NOTE:** if \"RcmdrPlugin.biostat\" is not between the options of Plugins, it  --\u003e\n\u003c!--         means that the plugin is already chosen but not included in the menus of  --\u003e\n\u003c!--         *R Commander*. This means that you should restart the *R Commander* by  --\u003e\n\u003c!--         using function `restart_commander()`{.r}. --\u003e\n\n\u003c!-- \u003cbr\u003e --\u003e\n\n\nWhen **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):\n\n```{r, echo=FALSE, fig.cap=CAPTION}\nknitr::include_graphics(paste0(fig_dir, \"03--biostat-plugin-loaded.png\"))\n\nCAPTION \u003c- \"\"\n```\n\n\n\n### Turn on *BioStat* (Green) Mode {#turn-on-biostat-mode}\n\nIf 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\":\n\n```{r, echo=FALSE, fig.cap=CAPTION}\nknitr::include_graphics(paste0(fig_dir, \"04--activate-biostat-mode.png\"))\n\nCAPTION \u003c- \"\"\n```\n\n\u003cbr\u003e\n\n\n### Close *BioStat* Mode {#close-biostat-mode}\n\nTo close this mode, simply restart the *R Commander*: \n\n* R Commander menu bar → BioStat → Session → Restart R Commander\n\nYou may use the following command as well:\n\n```{r eval=FALSE}\nrestart_commander()\n```\n\n\n### Notes for *Mac* Users Only {#notes-for-mac-users-only}\n\nFor *Mac* users, there at least 2 things to pay attention to:\n\n1) On *Mac*, *R Commander* opens only if [*XQuartz*](http://www.xquartz.org/){target=\"_blank\"} is opened.\nSo, the first step of using *R Commander* is to make sure that *XQuartz* is opened.\nMore information on [\"Installing R Commander for *Mac* users\"](https://murraystate.instructure.com/courses/1252125/pages/installing-r-commander-on-your-mac){target=\"_blank\"}.\n\n2) Some *Mac* users also report that it is impossible to switch between languages while *R Commander* is running.\nThis means, that some users might not use numbers if in the chosen language the same keys mean some non-English letters. \nBecause of this, it is recommended to choose an appropriate language (usually English) before opening *R*/*RStudio*.\n\n\n\u003c!-- *** --\u003e\n\n\n\u003c!-- # Other Useful Packages {#related-packages} --\u003e\n\n\u003c!-- Other useful **Rcmdr** plug-ins: --\u003e\n\n\u003c!-- a. **RcmdrPlugin.EZR.as.menu** -- an *R Commander* plugin for the most common statistical analyses (functionality is the same as in **RcmdrPlugin.EZR**, except that **RcmdrPlugin.EZR.as.menu** creates a separate \"EZR\" menu in a menu bar and does not reorganize the original **Rcmdr** menus in the menu bar); --\u003e\n\u003c!-- b. **RcmdrPlugin.KMggplot2** -- an *R Commander* plugin for **ggplot2** graphics. --\u003e\n\n\n\u003c!-- To install these packages, use the following code: --\u003e\n\n\n\u003c!-- ```{r Install other packages, eval=FALSE} --\u003e\n\u003c!-- # RcmdrPlugin.EZR.as.menu --\u003e\n\u003c!-- remotes::install_github(\"GegznaV/RcmdrPlugin.EZR\", ref = \"ezr_as_menu\") --\u003e\n\n\u003c!-- # RcmdrPlugin.KMggplot2 --\u003e\n\u003c!-- install.packages(\"RcmdrPlugin.KMggplot2\") --\u003e\n\u003c!-- ``` --\u003e\n\n\u003c!-- After the packages are installed, you can load them programmatically: --\u003e\n\n\u003c!-- ```{r eval=FALSE} --\u003e\n\u003c!-- options(Rcmdr = list( --\u003e\n\u003c!--   plugins = c( --\u003e\n\u003c!--     \"RcmdrPlugin.KMggplot2\", --\u003e\n\u003c!--     \"RcmdrPlugin.EZR.as.menu\", --\u003e\n\u003c!--     \"RcmdrPlugin.biostat\", --\u003e\n\u003c!--     NULL --\u003e\n\u003c!--   ), --\u003e\n\u003c!--   console.output = FALSE --\u003e\n\u003c!-- )) --\u003e\n\n\u003c!-- library(Rcmdr) --\u003e\n\u003c!-- ``` --\u003e\n\n\u003c!-- If package **Rcmdr** is loaded **and R Commander window is closed**, instead of ~~`library(Rcmdr)`~~, use this code **exactly once**: --\u003e\n\n\u003c!-- ```{r eval=FALSE} --\u003e\n\u003c!-- Commander() --\u003e\n\u003c!-- ``` --\u003e\n\n\n# Important\n\nSome functions in the package are based on and modified from functions in packages *Rcmdr*, and *RcmdrPlugin.EZR*.\nAll of those packages are under the GPL-2/GPL-3 license.\n\n\n\n***\n\n\u003c!-- # Previous versions of **RcmdrPlugin.biostat** {#previous-versions-of-rcmdrpluginbiostat} --\u003e\n\n\u003c!-- If you need a previous version of **RcmdrPlugin.biostat**, you can install them from `GitHub`: --\u003e\n\n\u003c!-- - BioStat'19 (Autumn 2019): --\u003e\n\u003c!--     ```{r Install BioStat-19r, eval=FALSE} --\u003e\n\u003c!--     remotes::install_github(\"GegznaV/RcmdrPlugin.biostat\", ref = \"biostat19r\") --\u003e\n\u003c!--     ``` --\u003e\n\u003c!--     (\"r\" -- stands for \"ruduo\" in Lithuanian). --\u003e\n\n\n\u003c!-- - BioStat'19 (Spring 2019): --\u003e\n\u003c!--     ```{r Install BioStat-19, eval=FALSE} --\u003e\n\u003c!--     remotes::install_github(\"GegznaV/RcmdrPlugin.biostat\", ref = \"biostat19\") --\u003e\n\u003c!--     ``` --\u003e\n\n\n\u003c!-- - BioStat'18 (2018): --\u003e\n\u003c!--     ```{r Install BioStat-18, eval=FALSE} --\u003e\n\u003c!--     remotes::install_github(\"GegznaV/RcmdrPlugin.biostat\", ref = \"biostat18\") --\u003e\n\u003c!--     ``` --\u003e\n\n\u003c!-- **NOTE:** these versions are no longer maintained and may not work properly. --\u003e\n\n\n\n\u003c!-- * * * --\u003e\n\n\u003c!--  \u003cp align=\"right\"\u003e \u003c/p\u003e     --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgegznav%2Frcmdrplugin.biostat","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgegznav%2Frcmdrplugin.biostat","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgegznav%2Frcmdrplugin.biostat/lists"}