get rid of MCMCpack

IndrajeetPatil · Dec 16, 2019 · 584e091 · 584e091 · lintr-bot · Dec 16, 2019
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Showing 17 changed files with 39 additions and 40 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -34,7 +34,6 @@ Imports:
     dplyr (>= 0.8.3),
     ez (>= 4.4-0),
     groupedstats (>= 0.1.0),
-    MCMCpack (>= 1.4-5),
     psych (>= 1.8.12),
     rcompanion (>= 2.3.7),
     rlang (>= 0.4.2),

diff --git a/NAMESPACE b/NAMESPACE
@@ -41,7 +41,6 @@ importFrom(BayesFactor,correlationBF)
 importFrom(BayesFactor,extractBF)
 importFrom(BayesFactor,logMeanExpLogs)
 importFrom(BayesFactor,ttestBF)
-importFrom(MCMCpack,rdirichlet)
 importFrom(WRS2,onesampb)
 importFrom(WRS2,pbcor)
 importFrom(WRS2,rmanova)
@@ -120,6 +119,7 @@ importFrom(stats,na.omit)
 importFrom(stats,oneway.test)
 importFrom(stats,pt)
 importFrom(stats,qt)
+importFrom(stats,rgamma)
 importFrom(stats,t.test)
 importFrom(stats,uniroot)
 importFrom(stats,wilcox.test)

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,10 @@
 # statsExpressions 0.1.2.9000
 
+  - Removes `MCMCpack` from `Depends`.
+
 # statsExpressions 0.1.2
 
-  - Maintenance release to fix additional check issues on CRAN.
+  - Maintenance release to fix additional check issues on `CRAN`.
 
 # statsExpressions 0.1.1
 

diff --git a/R/helpers_bf_tests.R b/R/helpers_bf_tests.R
@@ -253,8 +253,7 @@ bf_corr_test <- function(data,
 #'   (1974) `"a"` parameter.
 #'
 #' @importFrom BayesFactor contingencyTableBF logMeanExpLogs
-#' @importFrom stats dmultinom
-#' @importFrom MCMCpack rdirichlet
+#' @importFrom stats dmultinom rgamma
 #' @importFrom dplyr pull select rename mutate
 #' @importFrom tidyr uncount drop_na
 #'
@@ -415,7 +414,16 @@ bf_contingency_tab <- function(data,
 
     # estimate log prob of data under null with Monte Carlo
     M <- 100000
-    p1s <- MCMCpack::rdirichlet(n = M, alpha = prior.concentration * ratio)
+
+    # rdirichlet function
+    rdirichlet_int <- function(n, alpha) {
+      l <- length(alpha)
+      x <- matrix(stats::rgamma(l * n, alpha), ncol = l, byrow = TRUE)
+      sm <- x %*% rep(1, l)
+      return(x / as.vector(sm))
+    }
+    p1s <- rdirichlet_int(n = M, alpha = prior.concentration * ratio)
+
     tmp_pr_h1 <-
       sapply(
         X = 1:M,

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 | [![CRAN Checks](https://cranchecks.info/badges/summary/statsExpressions)](https://cran.r-project.org/web/checks/check_results_statsExpressions.html)                      | [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/IndrajeetPatil/statsExpressions?branch=master&svg=true)](https://ci.appveyor.com/project/IndrajeetPatil/statsExpressions) | [![Weekly downloads badge](https://cranlogs.r-pkg.org/badges/last-week/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions)   | [![Forks](https://img.shields.io/badge/forks-1-blue.svg)](https://github.com/IndrajeetPatil/statsExpressions/)                                                           | [![Rdoc](https://www.rdocumentation.org/badges/version/statsExpressions)](https://www.rdocumentation.org/packages/statsExpressions)                                       |
 | [![minimal R version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg)](https://cran.r-project.org/)                                                                | [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/)                                                                                         | [![Monthly downloads badge](https://cranlogs.r-pkg.org/badges/last-month/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions) | [![Github Issues](https://img.shields.io/badge/issues-7-red.svg)](https://github.com/IndrajeetPatil/statsExpressions/issues)                                             | [![vignettes](https://img.shields.io/badge/vignettes-0.1.2-orange.svg?colorB=FF5722)](https://CRAN.R-project.org/package=statsExpressions/vignettes/)                     |
 | [![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/IndrajeetPatil/statsExpressions.svg)](https://github.com/IndrajeetPatil/statsExpressions) | [![Coverage Status](https://coveralls.io/repos/github/IndrajeetPatil/statsExpressions/badge.svg?branch=master)](https://coveralls.io/github/IndrajeetPatil/statsExpressions?branch=master)             | [![Total downloads badge](https://cranlogs.r-pkg.org/badges/grand-total/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions)  | [![Github Stars](https://img.shields.io/github/stars/IndrajeetPatil/statsExpressions.svg?style=social&label=Github)](https://github.com/IndrajeetPatil/statsExpressions) | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2074621.svg)](https://doi.org/10.5281/zenodo.3386122)                                                                 |
-| [![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)                                                          | [![Codecov test coverage](https://codecov.io/gh/IndrajeetPatil/statsExpressions/branch/master/graph/badge.svg)](https://codecov.io/gh/IndrajeetPatil/statsExpressions?branch=master)                   | [![HitCount](http://hits.dwyl.io/IndrajeetPatil/statsExpressions.svg)](http://hits.dwyl.io/IndrajeetPatil/statsExpressions)                                 | [![Last-changedate](https://img.shields.io/badge/last%20change-2019--12--13-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master)         | [![GitHub last commit](https://img.shields.io/github/last-commit/IndrajeetPatil/statsExpressions.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master) |
+| [![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)                                                          | [![Codecov test coverage](https://codecov.io/gh/IndrajeetPatil/statsExpressions/branch/master/graph/badge.svg)](https://codecov.io/gh/IndrajeetPatil/statsExpressions?branch=master)                   | [![HitCount](http://hits.dwyl.io/IndrajeetPatil/statsExpressions.svg)](http://hits.dwyl.io/IndrajeetPatil/statsExpressions)                                 | [![Last-changedate](https://img.shields.io/badge/last%20change-2019--12--16-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master)         | [![GitHub last commit](https://img.shields.io/github/last-commit/IndrajeetPatil/statsExpressions.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master) |
 | [![status](https://tinyverse.netlify.com/badge/statsExpressions)](https://CRAN.R-project.org/package=statsExpressions)                                                    | [![Covrpage Summary](https://img.shields.io/badge/covrpage-Last_Build_2019_12_12-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/blob/master/tests/README.md)                     | [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/statsExpressions/community)                                                | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)                                                               | [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/IndrajeetPatil/statsExpressions/issues)      |
 
 # Introduction

diff --git a/codemeta.json b/codemeta.json
@@ -15,7 +15,7 @@
   ],
   "issueTracker": "\n    https://github.com/IndrajeetPatil/statsExpressions/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.1.2",
+  "version": "0.1.2.9000",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -219,19 +219,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=groupedstats"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "MCMCpack",
-      "name": "MCMCpack",
-      "version": ">= 1.4-5",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=MCMCpack"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "psych",

diff --git a/docs/articles/stats_details.html b/docs/articles/stats_details.html
diff --git a/docs/articles/tests_and_coverage.html b/docs/articles/tests_and_coverage.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/Titanic_full.html b/docs/reference/Titanic_full.html
diff --git a/docs/reference/VR_dilemma.html b/docs/reference/VR_dilemma.html
diff --git a/docs/reference/bugs_long.html b/docs/reference/bugs_long.html
diff --git a/docs/reference/intent_morality.html b/docs/reference/intent_morality.html
diff --git a/docs/reference/iris_long.html b/docs/reference/iris_long.html