diff --git a/.Rbuildignore b/.Rbuildignore index 4656cf1..8753ee5 100755 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -15,3 +15,5 @@ ^generate.rb ^CRAN-RELEASE$ ^figs/ +^lastMiKTeXException +^revdep/ diff --git a/.gitignore b/.gitignore index 5691b29..31893f8 100755 --- a/.gitignore +++ b/.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/ diff --git a/DESCRIPTION b/DESCRIPTION index 23fc4fb..cd40439 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,8 +17,7 @@ Imports: rstan, methods, overlapping, - colorspace, - rlang + colorspace Depends: R (>= 3.5.0) RoxygenNote: 7.1.2 diff --git a/NEWS.md b/NEWS.md index 9d48096..4e20aae 100755 --- a/NEWS.md +++ b/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 diff --git a/codemeta.json b/codemeta.json index f581296..e458ae2 100755 --- a/codemeta.json +++ b/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" } diff --git a/cran-comments.md b/cran-comments.md index ba85f76..d9758ab 100755 --- a/cran-comments.md +++ b/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 diff --git a/vignettes/MCMCvis.Rmd b/vignettes/MCMCvis.Rmd index c21008a..af7b46f 100755 --- a/vignettes/MCMCvis.Rmd +++ b/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 here (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,