udpate docs

.Rbuildignore

@@ -15,3 +15,5 @@
 ^generate.rb
 ^CRAN-RELEASE$
 ^figs/
+^lastMiKTeXException
+^revdep/

.gitignore

@@ -1,7 +1,8 @@
-.Rproj.user
-.Rhistory
-.RData
-.Ruserdata
-.DS_Store
-*.Rproj
-generate.rb
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+*.Rproj
+generate.rb
+revdep/

DESCRIPTION

@@ -17,8 +17,7 @@ Imports:
     rstan,
     methods,
     overlapping,
-    colorspace,
-    rlang
+    colorspace
 Depends:
     R (>= 3.5.0)
 RoxygenNote: 7.1.2

NEWS.md

@@ -3,7 +3,7 @@ NEWS
 
 0.15.5
 
-- `MCMCplot` fix bug associated with `ref_ovl = TRUE` and the specification of multiple objects. Function also now automatically lightens colors specificied (instead of defaulting to gray) when `ref_ovl = TRUE`
+- `MCMCplot` fix bug associated with `ref_ovl = TRUE` and the specification of multiple objects. Function also now automatically lightens colors specified (instead of defaulting to gray) when `ref_ovl = TRUE`
 
 
 0.15.4

codemeta.json

@@ -1,9 +1,25 @@
 {
-  "@context": [
-    "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
-    "http://schema.org"
-  ],
-  "@type": "Code",
+  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+  "@type": "SoftwareSourceCode",
+  "identifier": "MCMCvis",
+  "description": "Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with 'Stan', 'NIMBLE', 'JAGS', and other software.",
+  "name": "MCMCvis: Tools to Visualize, Manipulate, and Summarize MCMC Output",
+  "codeRepository": "https://github.com/caseyyoungflesh/MCMCvis",
+  "issueTracker": "https://github.com/caseyyoungflesh/MCMCvis/issues",
+  "license": "https://spdx.org/licenses/GPL-3.0",
+  "version": "0.15.5",
+  "programmingLanguage": {
+    "@type": "ComputerLanguage",
+    "name": "R",
+    "url": "https://r-project.org"
+  },
+  "runtimePlatform": "R version 4.1.1 (2021-08-10)",
+  "provider": {
+    "@id": "https://cran.r-project.org",
+    "@type": "Organization",
+    "name": "Comprehensive R Archive Network (CRAN)",
+    "url": "https://cran.r-project.org"
+  },
   "author": [
     {
       "@type": "Person",
@@ -20,29 +36,6 @@
       "@id": "https://orcid.org/0000-0002-7670-2178"
     }
   ],
-  "identifier": "MCMCvis",
-  "codeRepository": "https://github.com/caseyyoungflesh/MCMCvis",
-  "dateModified": "2018-02-16",
-  "dateCreated": "2018-02-16",
-  "description": "Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with 'Stan', 'NIMBLE', 'JAGS', and other software.",
-  "keywords": "MCMC, Bayesian, Visualization, PPO",
-  "license": "https://spdx.org/licenses/GPL-3.0",
-  "title": "MCMCvis",
-  "version": "0.15.3",
-  "name": "MCMCvis: Tools to Visualize, Manipulate, and Summarize MCMC Output",
-  "issueTracker": "https://github.com/caseyyoungflesh/MCMCvis/issues",
-  "programmingLanguage": {
-    "@type": "ComputerLanguage",
-    "name": "R",
-    "url": "https://r-project.org"
-  },
-  "runtimePlatform": "R version 4.0.5 (2021-03-31)",
-  "provider": {
-    "@id": "https://cran.r-project.org",
-    "@type": "Organization",
-    "name": "Comprehensive R Archive Network (CRAN)",
-    "url": "https://cran.r-project.org"
-  },
   "contributor": [
     {
       "@type": "Person",
@@ -97,8 +90,8 @@
       "sameAs": "https://CRAN.R-project.org/package=testthat"
     }
   ],
-  "softwareRequirements": [
-    {
+  "softwareRequirements": {
+    "1": {
       "@type": "SoftwareApplication",
       "identifier": "coda",
       "name": "coda",
@@ -110,7 +103,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=coda"
     },
-    {
+    "2": {
       "@type": "SoftwareApplication",
       "identifier": "rstan",
       "name": "rstan",
@@ -122,12 +115,12 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=rstan"
     },
-    {
+    "3": {
       "@type": "SoftwareApplication",
       "identifier": "methods",
       "name": "methods"
     },
-    {
+    "4": {
       "@type": "SoftwareApplication",
       "identifier": "overlapping",
       "name": "overlapping",
@@ -139,27 +132,27 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=overlapping"
     },
-    {
+    "5": {
       "@type": "SoftwareApplication",
-      "identifier": "rlang",
-      "name": "rlang",
+      "identifier": "colorspace",
+      "name": "colorspace",
       "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=rlang"
+      "sameAs": "https://CRAN.R-project.org/package=colorspace"
     },
-    {
+    "6": {
       "@type": "SoftwareApplication",
       "identifier": "R",
       "name": "R",
       "version": ">= 3.5.0"
-    }
-  ],
-  "releaseNotes": "https://github.com/caseyyoungflesh/MCMCvis/blob/master/NEWS.md",
-  "fileSize": "3289.462KB",
+    },
+    "SystemRequirements": null
+  },
+  "fileSize": "3293.509KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -188,8 +181,7 @@
       }
     }
   ],
-  "relatedLink": "https://CRAN.R-project.org/package=MCMCvis",
-  "copyrightHolder": {},
-  "funder": {},
-  "readme": "https://github.com/caseyyoungflesh/MCMCvis/blob/master/README.md"
+  "releaseNotes": "https://github.com/caseyyoungflesh/MCMCvis/blob/master/NEWS.md",
+  "readme": "https://github.com/caseyyoungflesh/MCMCvis/blob/master/README.md",
+  "relatedLink": "https://CRAN.R-project.org/package=MCMCvis"
 }

cran-comments.md

@@ -3,10 +3,10 @@ CRAN comments
 
 ## Test environments
 * local macOS install - R 4.1.1
-* Ubuntu 20.04.1 (on rhub) - R-release
-* Windows Server 2008 (on rhub) - R-devel
-* Windows Server 2008 (on winbuilder) - R-devel
+* Ubuntu 20.04.1 (on rhub) - R-devel
 * Fedora (on rhub) - R-devel
+* Windows Server 2022 (on winbuilder) - R-devel
+
 
 ## R CMD check results
 

vignettes/MCMCvis.Rmd

@@ -179,7 +179,7 @@ MCMCsummary(MCMC_data,
             round = 2)
 ```
 
-When `exact = FALSE`, the `params` argument reads like a regular expression. Because of this, square brackets must be escaped with `\\`. All other regular expression syntax is accepted, as typically applied in R. This can be useful for returning a specific set of a large number of parameters. A great tools for regular expressions in R can be found <a href ="https://regexr.com/">here</a> (though note two slashes are needed to escape characters in this function rather than one, hence `\\[` as opposed to `\[`). `\\d` can be used to specify any digits in a particular place.
+When `exact = FALSE`, the `params` argument reads like a regular expression. Because of this, square brackets must be escaped with `\\`. All other regular expression syntax is accepted, as typically applied in R. This can be useful for returning a specific set of a large number of parameters. A great tools for regular expressions in R can be found here (https://regexr.com/) (though note two slashes are needed to escape characters in this function rather than one, hence `\\[` as opposed to `\[`). `\\d` can be used to specify any digits in a particular place.
 
 ```{r}
 MCMCsummary(MCMC_data,