From 233b8bfbfbf464804a7112b5a79529169b3e307c Mon Sep 17 00:00:00 2001 From: sbalci Date: Sun, 3 Apr 2022 21:48:04 +0300 Subject: [PATCH] update --- ClinicoPathLinuxDescriptives.Rproj | 1 + DESCRIPTION | 6 +++--- R/00jmv.R | 10 +++++++++- R/agepyramid.h.R | 4 +++- R/benford.h.R | 3 ++- R/crosstable.h.R | 4 +++- R/reportcat.h.R | 4 +++- R/summarydata.h.R | 4 +++- R/tableone.h.R | 4 +++- R/venn.h.R | 3 ++- jamovi/0000.yaml | 4 ++-- jamovi/00refs.yaml | 8 ++++++++ jamovi/agepyramid.r.yaml | 4 ++++ jamovi/benford.r.yaml | 2 ++ jamovi/crosstable.r.yaml | 5 +++++ jamovi/reportcat.r.yaml | 4 +++- jamovi/summarydata.r.yaml | 3 ++- jamovi/tableone.r.yaml | 4 ++++ jamovi/venn.r.yaml | 1 + man/agepyramidClass.Rd | 1 + man/crosstableClass.Rd | 1 + man/reportcatClass.Rd | 1 + man/summarydataClass.Rd | 1 + man/tableoneClass.Rd | 1 + man/vennClass.Rd | 1 + 25 files changed, 69 insertions(+), 15 deletions(-) diff --git a/ClinicoPathLinuxDescriptives.Rproj b/ClinicoPathLinuxDescriptives.Rproj index 497f8bf..bb57690 100644 --- a/ClinicoPathLinuxDescriptives.Rproj +++ b/ClinicoPathLinuxDescriptives.Rproj @@ -17,4 +17,5 @@ StripTrailingWhitespace: Yes BuildType: Package PackageUseDevtools: Yes +PackageCleanBeforeInstall: Yes PackageInstallArgs: --no-multiarch --with-keep.source diff --git a/DESCRIPTION b/DESCRIPTION index 2f7a42f..916e963 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: ClinicoPathDescriptives Title: Descriptives Functions for Clinicopathological Research -Version: 0.0.2.0084 -Date: 2021-02-14 +Version: 0.0.2.04 +Date: 2021-04-03 Authors@R: person(given = "Serdar", family = "Balci", @@ -48,4 +48,4 @@ Remotes: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.1 +RoxygenNote: 7.1.2 diff --git a/R/00jmv.R b/R/00jmv.R index b549021..8d9ee45 100644 --- a/R/00jmv.R +++ b/R/00jmv.R @@ -423,4 +423,12 @@ `year`=2020, `title`=" Venn Diagram by ggplot2, with really easy-to-use API", `publisher`="[R package]. Retrieved from https://github.com/yanlinlin82/ggvenn", - `url`="https://github.com/yanlinlin82/ggvenn")) + `url`="https://github.com/yanlinlin82/ggvenn"), + `ClinicoPathJamoviModule`=list( + `type`="software", + `author`="Serdar Balci", + `year`=2022, + `title`="ClinicoPath jamovi Module doi:10.5281/zenodo.3997188", + `publisher`="[R package]. Retrieved from https://github.com/sbalci/ClinicoPathJamoviModule", + `doi`="10.17605/OSF.IO/9SZUD", + `url`="https://www.serdarbalci.com/ClinicoPathJamoviModule/")) diff --git a/R/agepyramid.h.R b/R/agepyramid.h.R index 5e9da2a..8d77ee9 100644 --- a/R/agepyramid.h.R +++ b/R/agepyramid.h.R @@ -62,7 +62,9 @@ agepyramidResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( super$initialize( options=options, name="", - title="Age Pyramid") + title="Age Pyramid", + refs=list( + "ClinicoPathJamoviModule")) self$add(jmvcore::Table$new( options=options, name="pyramidTable", diff --git a/R/benford.h.R b/R/benford.h.R index 144254f..12dbc68 100644 --- a/R/benford.h.R +++ b/R/benford.h.R @@ -46,7 +46,8 @@ benfordResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( name="", title="Benford Analysis", refs=list( - "benford.analysis")) + "benford.analysis", + "ClinicoPathJamoviModule")) self$add(jmvcore::Html$new( options=options, name="todo", diff --git a/R/crosstable.h.R b/R/crosstable.h.R index fa603ce..c7117fb 100644 --- a/R/crosstable.h.R +++ b/R/crosstable.h.R @@ -98,7 +98,9 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( super$initialize( options=options, name="", - title="`Cross Table - ${group}`") + title="`Cross Table - ${group}`", + refs=list( + "ClinicoPathJamoviModule")) self$add(jmvcore::Html$new( options=options, name="todo", diff --git a/R/reportcat.h.R b/R/reportcat.h.R index e4b2936..0299bcd 100644 --- a/R/reportcat.h.R +++ b/R/reportcat.h.R @@ -44,7 +44,9 @@ reportcatResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( options=options, name="", title="Summary of Categorical Variables", - refs="report") + refs=list( + "report", + "ClinicoPathJamoviModule")) self$add(jmvcore::Html$new( options=options, name="todo", diff --git a/R/summarydata.h.R b/R/summarydata.h.R index ec618bf..f9d8a17 100644 --- a/R/summarydata.h.R +++ b/R/summarydata.h.R @@ -42,7 +42,9 @@ summarydataResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class super$initialize( options=options, name="", - title="Summary of Continuous Variables") + title="Summary of Continuous Variables", + refs=list( + "ClinicoPathJamoviModule")) self$add(jmvcore::Html$new( options=options, name="todo", diff --git a/R/tableone.h.R b/R/tableone.h.R index eba6c48..20e10f6 100644 --- a/R/tableone.h.R +++ b/R/tableone.h.R @@ -62,7 +62,9 @@ tableoneResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( super$initialize( options=options, name="", - title="Table One") + title="Table One", + refs=list( + "ClinicoPathJamoviModule")) self$add(jmvcore::Html$new( options=options, name="todo", diff --git a/R/venn.h.R b/R/venn.h.R index b3b6645..edd400d 100644 --- a/R/venn.h.R +++ b/R/venn.h.R @@ -113,7 +113,8 @@ vennResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( name="", title="Venn Diagram", refs=list( - "venn"), + "venn", + "ClinicoPathJamoviModule"), clearWith=list( "var1", "var2", diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml index 8eeb8a7..7528028 100644 --- a/jamovi/0000.yaml +++ b/jamovi/0000.yaml @@ -1,12 +1,12 @@ --- title: Descriptives Functions for Clinicopathological Research name: ClinicoPathLinuxDescriptives -version: 0.0.2.0084 +version: 0.0.2.4 jms: '1.0' authors: - Serdar Balci maintainer: Serdar Balci -date: '2021-04-14' +date: '2022-04-03' type: R description: >- Descriptives Functions for Clinicopathological Research Descriptive functions diff --git a/jamovi/00refs.yaml b/jamovi/00refs.yaml index 13fbede..71f0620 100644 --- a/jamovi/00refs.yaml +++ b/jamovi/00refs.yaml @@ -511,6 +511,14 @@ refs: url: https://github.com/yanlinlin82/ggvenn + ClinicoPathJamoviModule: + type: 'software' + author: Serdar Balci + year: 2022 + title: "ClinicoPath jamovi Module doi:10.5281/zenodo.3997188" + publisher: '[R package]. Retrieved from https://github.com/sbalci/ClinicoPathJamoviModule' + doi: 10.17605/OSF.IO/9SZUD + url: https://www.serdarbalci.com/ClinicoPathJamoviModule/ diff --git a/jamovi/agepyramid.r.yaml b/jamovi/agepyramid.r.yaml index 89046f6..876b3c2 100644 --- a/jamovi/agepyramid.r.yaml +++ b/jamovi/agepyramid.r.yaml @@ -41,4 +41,8 @@ items: - female +refs: + - ClinicoPathJamoviModule + + ... diff --git a/jamovi/benford.r.yaml b/jamovi/benford.r.yaml index 84e7344..68c2394 100644 --- a/jamovi/benford.r.yaml +++ b/jamovi/benford.r.yaml @@ -29,4 +29,6 @@ items: refs: - benford.analysis + - ClinicoPathJamoviModule + ... diff --git a/jamovi/crosstable.r.yaml b/jamovi/crosstable.r.yaml index 20719fd..e790918 100644 --- a/jamovi/crosstable.r.yaml +++ b/jamovi/crosstable.r.yaml @@ -62,4 +62,9 @@ items: visible: (sty:nejm || sty:lancet || sty:hmisc) refs: tangram + +refs: + - ClinicoPathJamoviModule + + ... diff --git a/jamovi/reportcat.r.yaml b/jamovi/reportcat.r.yaml index eff9656..034cca7 100644 --- a/jamovi/reportcat.r.yaml +++ b/jamovi/reportcat.r.yaml @@ -15,6 +15,8 @@ items: title: '' type: Preformatted -refs: report +refs: + - report + - ClinicoPathJamoviModule ... diff --git a/jamovi/summarydata.r.yaml b/jamovi/summarydata.r.yaml index 9079142..801c95e 100644 --- a/jamovi/summarydata.r.yaml +++ b/jamovi/summarydata.r.yaml @@ -14,6 +14,7 @@ items: type: Preformatted -# refs: +refs: + - ClinicoPathJamoviModule ... diff --git a/jamovi/tableone.r.yaml b/jamovi/tableone.r.yaml index 06f32d5..49c2de6 100644 --- a/jamovi/tableone.r.yaml +++ b/jamovi/tableone.r.yaml @@ -47,4 +47,8 @@ items: visible: (sty:t4) refs: janitor +refs: + - ClinicoPathJamoviModule + + ... diff --git a/jamovi/venn.r.yaml b/jamovi/venn.r.yaml index ad15bad..0585325 100644 --- a/jamovi/venn.r.yaml +++ b/jamovi/venn.r.yaml @@ -33,5 +33,6 @@ items: refs: - venn + - ClinicoPathJamoviModule ... diff --git a/man/agepyramidClass.Rd b/man/agepyramidClass.Rd index 73f31d0..cc4f70e 100644 --- a/man/agepyramidClass.Rd +++ b/man/agepyramidClass.Rd @@ -46,6 +46,7 @@ Age Pyramid \item \out{}\href{../../jmvcore/html/Analysis.html#method-serialize}{\code{jmvcore::Analysis$serialize()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setError}{\code{jmvcore::Analysis$setError()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setStatus}{\code{jmvcore::Analysis$setStatus()}}\out{} +\item \out{}\href{../../jmvcore/html/Analysis.html#method-translate}{\code{jmvcore::Analysis$translate()}}\out{} \item \out{}\href{../../ClinicoPathDescriptives/html/agepyramidBase.html#method-initialize}{\code{ClinicoPathDescriptives::agepyramidBase$initialize()}}\out{} } \out{} diff --git a/man/crosstableClass.Rd b/man/crosstableClass.Rd index 12ec1dc..c090178 100644 --- a/man/crosstableClass.Rd +++ b/man/crosstableClass.Rd @@ -46,6 +46,7 @@ Cross Table \item \out{}\href{../../jmvcore/html/Analysis.html#method-serialize}{\code{jmvcore::Analysis$serialize()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setError}{\code{jmvcore::Analysis$setError()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setStatus}{\code{jmvcore::Analysis$setStatus()}}\out{} +\item \out{}\href{../../jmvcore/html/Analysis.html#method-translate}{\code{jmvcore::Analysis$translate()}}\out{} \item \out{}\href{../../ClinicoPathDescriptives/html/crosstableBase.html#method-initialize}{\code{ClinicoPathDescriptives::crosstableBase$initialize()}}\out{} } \out{} diff --git a/man/reportcatClass.Rd b/man/reportcatClass.Rd index 88f5908..8aa1fdb 100644 --- a/man/reportcatClass.Rd +++ b/man/reportcatClass.Rd @@ -49,6 +49,7 @@ Summary of Categorical Variables \item \out{}\href{../../jmvcore/html/Analysis.html#method-serialize}{\code{jmvcore::Analysis$serialize()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setError}{\code{jmvcore::Analysis$setError()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setStatus}{\code{jmvcore::Analysis$setStatus()}}\out{} +\item \out{}\href{../../jmvcore/html/Analysis.html#method-translate}{\code{jmvcore::Analysis$translate()}}\out{} \item \out{}\href{../../ClinicoPathDescriptives/html/reportcatBase.html#method-initialize}{\code{ClinicoPathDescriptives::reportcatBase$initialize()}}\out{} } \out{} diff --git a/man/summarydataClass.Rd b/man/summarydataClass.Rd index b5696d1..c5c2f3c 100644 --- a/man/summarydataClass.Rd +++ b/man/summarydataClass.Rd @@ -46,6 +46,7 @@ Summary of Continuous Variables \item \out{}\href{../../jmvcore/html/Analysis.html#method-serialize}{\code{jmvcore::Analysis$serialize()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setError}{\code{jmvcore::Analysis$setError()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setStatus}{\code{jmvcore::Analysis$setStatus()}}\out{} +\item \out{}\href{../../jmvcore/html/Analysis.html#method-translate}{\code{jmvcore::Analysis$translate()}}\out{} \item \out{}\href{../../ClinicoPathDescriptives/html/summarydataBase.html#method-initialize}{\code{ClinicoPathDescriptives::summarydataBase$initialize()}}\out{} } \out{} diff --git a/man/tableoneClass.Rd b/man/tableoneClass.Rd index fded311..bbdfc3f 100644 --- a/man/tableoneClass.Rd +++ b/man/tableoneClass.Rd @@ -49,6 +49,7 @@ Table One \item \out{}\href{../../jmvcore/html/Analysis.html#method-serialize}{\code{jmvcore::Analysis$serialize()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setError}{\code{jmvcore::Analysis$setError()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setStatus}{\code{jmvcore::Analysis$setStatus()}}\out{} +\item \out{}\href{../../jmvcore/html/Analysis.html#method-translate}{\code{jmvcore::Analysis$translate()}}\out{} \item \out{}\href{../../ClinicoPathDescriptives/html/tableoneBase.html#method-initialize}{\code{ClinicoPathDescriptives::tableoneBase$initialize()}}\out{} } \out{} diff --git a/man/vennClass.Rd b/man/vennClass.Rd index 638bdb1..8453e61 100644 --- a/man/vennClass.Rd +++ b/man/vennClass.Rd @@ -46,6 +46,7 @@ Venn Diagram \item \out{}\href{../../jmvcore/html/Analysis.html#method-serialize}{\code{jmvcore::Analysis$serialize()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setError}{\code{jmvcore::Analysis$setError()}}\out{} \item \out{}\href{../../jmvcore/html/Analysis.html#method-setStatus}{\code{jmvcore::Analysis$setStatus()}}\out{} +\item \out{}\href{../../jmvcore/html/Analysis.html#method-translate}{\code{jmvcore::Analysis$translate()}}\out{} \item \out{}\href{../../ClinicoPathDescriptives/html/vennBase.html#method-initialize}{\code{ClinicoPathDescriptives::vennBase$initialize()}}\out{} } \out{}