diff --git a/DESCRIPTION b/DESCRIPTION index 67f9fdc..1892e76 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,47 +1,39 @@ -Package: Reproducibility.in.Plant.Pathology Type: Package -Title: A Systematic Quantitative Review of Articles Providing a Basis for Identifying Reproducible Research Efforts the Field of Plant Pathology -Version: 1.0.1 +Package: Reproducibility.in.Plant.Pathology +Title: A Systematic Quantitative Review of Articles Providing a Basis for + Identifying Reproducible Research Efforts the Field of Plant Pathology +Version: 1.0.2 Authors@R: c( - person(given = "Adam H.", family = "Sparks", - role = c("aut", "cre"), - email = "adamhsparks@gmail.com", - comment = c(ORCID = "0000-0002-0061-8359")), - person(given = "Emerson M.", family ="Del Ponte", - role = "aut", - email = "edelponte@gmail.com", - comment = c(ORCID = "0000-0003-4398-409X")), - person(given = "Kaique S.", family = "Alves", - role = "aut", - email = "kaiquedsalves@gmail.com", - comment = c(ORCID = "https://orcid.org/0000-0001-9187-0252")), - person(given = "Zachary S. L.", family = "Foster", - role = "aut", - email = "zacharyfoster1989@gmail.com", - comment = c(ORCID = "https://orcid.org/0000-0002-5075-0948")), - person(given = "Niklaus J.", family = "Grünwald", - role = "aut", - email = "grunwaln@science.oregonstate.edu", - comment = c(ORCID = "0000-0003-1656-7602")) + person("Adam H.", "Sparks", , "adamhsparks@gmail.com", role = c("aut", "cre"), + comment = c(ORCID = "0000-0002-0061-8359")), + person("Emerson M.", "Del Ponte", , "edelponte@gmail.com", role = "aut", + comment = c(ORCID = "0000-0003-4398-409X")), + person("Kaique S.", "Alves", , "kaiquedsalves@gmail.com", role = "aut", + comment = c(ORCID = "https://orcid.org/0000-0001-9187-0252")), + person("Zachary S. L.", "Foster", , "zacharyfoster1989@gmail.com", role = "aut", + comment = c(ORCID = "https://orcid.org/0000-0002-5075-0948")), + person("Niklaus J.", "Grünwald", , "grunwaln@science.oregonstate.edu", role = "aut", + comment = c(ORCID = "0000-0003-1656-7602")) ) -URL: https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology -BugReports: https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology/issues Description: A research compendium for a perspectives paper, - "Reproducibility in plant pathology: where we stand and a way forward", - published in "Phytopathology". -DOI: 10.5281/zenodo.1250664 + "Reproducibility in plant pathology: where we stand and a way + forward", published in "Phytopathology". +License: MIT + file LICENSE +URL: + https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology +BugReports: + https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology/issues Depends: R (>= 3.5.0) -License: MIT + file LICENSE Imports: dplyr, magrittr, readODS Suggests: - bib2df, - bibtex, bayesplot, bayestestR, + bib2df, + bibtex, brms, extrafont, flextable, @@ -53,26 +45,28 @@ Suggests: irr, janitor, knitr, + officedown, + officer, + pander, + parallel, patchwork, psych, rcrossref, - report (<= 0.4.0), readr, + report (<= 0.4.0), rmarkdown, roxygen2 (>= 6.0.1), - officedown, - officer, - pander, - parallel, see, sessioninfo, + spelling, stringr, testthat, tibble, - tidyverse, - spelling -RoxygenNote: 7.2.3 + tidyverse +VignetteBuilder: + knitr +DOI: 10.5281/zenodo.1250664 Encoding: UTF-8 -NeedsCompilation: no -VignetteBuilder: knitr Language: en-US +NeedsCompilation: no +RoxygenNote: 7.3.2 diff --git a/codemeta.json b/codemeta.json index 2594b52..1f140f5 100644 --- a/codemeta.json +++ b/codemeta.json @@ -3,17 +3,17 @@ "@type": "SoftwareSourceCode", "identifier": "Reproducibility.in.Plant.Pathology", "description": "A research compendium for a perspectives paper, \"Reproducibility in plant pathology: where we stand and a way forward\", published in \"Phytopathology\".", - "name": "Reproducibility.in.Plant.Pathology: A Systematic Quantitative Review of Articles Providing a Basis for Identifying Reproducible Research Efforts the Field of Plant Pathology", + "name": "Reproducibility.in.Plant.Pathology: A Systematic Quantitative Review of Articles Providing a Basis for\n Identifying Reproducible Research Efforts the Field of Plant Pathology", "codeRepository": "https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology", - "issueTracker": "https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology/issues", + "issueTracker": "\n https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology/issues", "license": "https://spdx.org/licenses/MIT", - "version": "1.0.0", + "version": "1.0.2", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.2.2 (2022-10-31)", + "runtimePlatform": "R version 4.4.1 (2024-06-14)", "author": [ { "@type": "Person", @@ -63,51 +63,51 @@ "softwareSuggestions": [ { "@type": "SoftwareApplication", - "identifier": "bib2df", - "name": "bib2df", + "identifier": "bayesplot", + "name": "bayesplot", "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=bib2df" + "sameAs": "https://CRAN.R-project.org/package=bayesplot" }, { "@type": "SoftwareApplication", - "identifier": "bibtex", - "name": "bibtex", + "identifier": "bayestestR", + "name": "bayestestR", "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=bibtex" + "sameAs": "https://CRAN.R-project.org/package=bayestestR" }, { "@type": "SoftwareApplication", - "identifier": "bayesplot", - "name": "bayesplot", + "identifier": "bib2df", + "name": "bib2df", "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=bayesplot" + "sameAs": "https://CRAN.R-project.org/package=bib2df" }, { "@type": "SoftwareApplication", - "identifier": "bayestestR", - "name": "bayestestR", + "identifier": "bibtex", + "name": "bibtex", "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=bayestestR" + "sameAs": "https://CRAN.R-project.org/package=bibtex" }, { "@type": "SoftwareApplication", @@ -244,130 +244,130 @@ }, { "@type": "SoftwareApplication", - "identifier": "patchwork", - "name": "patchwork", + "identifier": "officedown", + "name": "officedown", "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=patchwork" + "sameAs": "https://CRAN.R-project.org/package=officedown" }, { "@type": "SoftwareApplication", - "identifier": "psych", - "name": "psych", + "identifier": "officer", + "name": "officer", "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=psych" + "sameAs": "https://CRAN.R-project.org/package=officer" }, { "@type": "SoftwareApplication", - "identifier": "rcrossref", - "name": "rcrossref", + "identifier": "pander", + "name": "pander", "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=rcrossref" + "sameAs": "https://CRAN.R-project.org/package=pander" }, { "@type": "SoftwareApplication", - "identifier": "report", - "name": "report", - "version": "<= 0.4.0", + "identifier": "parallel", + "name": "parallel" + }, + { + "@type": "SoftwareApplication", + "identifier": "patchwork", + "name": "patchwork", "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=report" + "sameAs": "https://CRAN.R-project.org/package=patchwork" }, { "@type": "SoftwareApplication", - "identifier": "readr", - "name": "readr", + "identifier": "psych", + "name": "psych", "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=readr" + "sameAs": "https://CRAN.R-project.org/package=psych" }, { "@type": "SoftwareApplication", - "identifier": "rmarkdown", - "name": "rmarkdown", + "identifier": "rcrossref", + "name": "rcrossref", "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=rmarkdown" + "sameAs": "https://CRAN.R-project.org/package=rcrossref" }, { "@type": "SoftwareApplication", - "identifier": "roxygen2", - "name": "roxygen2", - "version": ">= 6.0.1", + "identifier": "readr", + "name": "readr", "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=roxygen2" + "sameAs": "https://CRAN.R-project.org/package=readr" }, { "@type": "SoftwareApplication", - "identifier": "officedown", - "name": "officedown", + "identifier": "report", + "name": "report", + "version": "<= 0.4.0", "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=officedown" + "sameAs": "https://CRAN.R-project.org/package=report" }, { "@type": "SoftwareApplication", - "identifier": "officer", - "name": "officer", + "identifier": "rmarkdown", + "name": "rmarkdown", "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=officer" + "sameAs": "https://CRAN.R-project.org/package=rmarkdown" }, { "@type": "SoftwareApplication", - "identifier": "pander", - "name": "pander", + "identifier": "roxygen2", + "name": "roxygen2", + "version": ">= 6.0.1", "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=pander" - }, - { - "@type": "SoftwareApplication", - "identifier": "parallel", - "name": "parallel" + "sameAs": "https://CRAN.R-project.org/package=roxygen2" }, { "@type": "SoftwareApplication", @@ -393,6 +393,18 @@ }, "sameAs": "https://CRAN.R-project.org/package=sessioninfo" }, + { + "@type": "SoftwareApplication", + "identifier": "spelling", + "name": "spelling", + "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=spelling" + }, { "@type": "SoftwareApplication", "identifier": "stringr", @@ -440,18 +452,6 @@ "url": "https://cran.r-project.org" }, "sameAs": "https://CRAN.R-project.org/package=tidyverse" - }, - { - "@type": "SoftwareApplication", - "identifier": "spelling", - "name": "spelling", - "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=spelling" } ], "softwareRequirements": { @@ -499,7 +499,7 @@ }, "SystemRequirements": null }, - "fileSize": "58918.052KB", + "fileSize": "58893.639KB", "citation": [ { "@type": "SoftwareSourceCode", @@ -533,7 +533,7 @@ "name": "{Reproducibility.in.Plant.Pathology}: A Systematic Quantitative Review of Articles Providing a Basis for Identifying Reproducible Research Efforts the Field of Plant Pathology", "identifier": "10.5281/zenodo.1250664", "url": "https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology", - "description": "R package version 1.0.0", + "description": "R package version 1.0.2", "@id": "https://doi.org/10.5281/zenodo.1250664", "sameAs": "https://doi.org/10.5281/zenodo.1250664" } diff --git a/vignettes/a_reproducibility_criteria.Rmd b/vignettes/a_reproducibility_criteria.Rmd index fe98f87..0484b74 100644 --- a/vignettes/a_reproducibility_criteria.Rmd +++ b/vignettes/a_reproducibility_criteria.Rmd @@ -24,7 +24,7 @@ In the reproducibility score there are two parts, one part is automatically gene The articles' DOIs are looked up manually by Adam and assigned in the "[article_notes](https://docs.google.com/spreadsheets/d/1YrIiQ3OBNjCHMlalkMi1yy8dy4hnj5dnR4PSTj7lDR4/edit#gid=0)" sheet in the googlesheets document, `doi`. -Th five-year impact factor, `IF_5year` for each journal was recorded in a separate sheet in the workbook. +The five-year impact factor, `IF_5year` for each journal was recorded in a separate sheet in the workbook. Other items including `journal`, `year`, and `contains_page` are auto-generated by the ["Assigning Articles"](https://github.com/phytopathology/Reproducibility_in_Plant_Pathology/blob/master/vignettes/Assigning_Articles.Rmd) vignette.