diff --git a/.Rprofile b/.Rprofile index 48d941ae..43eece16 100644 --- a/.Rprofile +++ b/.Rprofile @@ -9,6 +9,26 @@ options(repos = c("https://cran.microsoft.com/snapshot/2020-05-01")) # .libPaths(new = "~/histopathRprojects/ClinicoPathLibrary") + +# options(repos = c("https://cran.microsoft.com/snapshot/2020-05-01")) + +# .libPaths(new = "C:\\ClinicoPathLibrary") + +# Sys.setenv(TZ = "Europe/Istanbul") + +# Sys.setenv(TEMP = "C:\\temp") + +# Sys.setenv(TMP = "C:\\temp") + + +# jmvtools::check("C://Program Files//jamovi//bin") +# jmvtools::install(home = "C://Program Files//jamovi//bin") +# +# +# + + + # source( # "renv/activate.R" # "~/histopathRprojects/ClinicoPath/renv/activate.R" diff --git a/DESCRIPTION b/DESCRIPTION index 7a31e295..3554a1d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: ClinicoPath Title: Analysis for Clinicopathological Research -Version: 0.0.2.0015 -Date: 2020-06-28 +Version: 0.0.2.0016 +Date: 2020-06-29 Authors@R: person(given = "Serdar", family = "Balci", diff --git a/NEWS.md b/NEWS.md index 59c03839..208276df 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,24 @@ +# ClinicoPath 0.0.2.0016 + +- See: https://github.com/sbalci/jjstatsplot/releases/ + +- See: https://github.com/sbalci/ClinicoPath/releases/ + +- crosstable function partially resolves https://github.com/jamovi/jamovi/issues/443 + +- survival function resolves https://github.com/jonathon-love/deathwatch/issues/2 + +- added export html to crosstables to bypass https://github.com/jamovi/jamovi/issues/892 + + + + # ClinicoPath 0.0.2.0015 - Added tangram statistical results - Added options to finalfit crosstables fixes: https://github.com/sbalci/ClinicoPathJamoviModule/issues/24 -fixes: https://github.com/jamovi/jamovi/issues/901 +Partially fixes: https://github.com/jamovi/jamovi/issues/901 fixes: https://github.com/ewenharrison/finalfit/issues/52 - Added experimental biblometrics functions diff --git a/R/00jmv.R b/R/00jmv.R index 01d86137..5d4ad9b7 100644 --- a/R/00jmv.R +++ b/R/00jmv.R @@ -314,22 +314,23 @@ `url`="https://CRAN.R-project.org/package=hrbrthemes"), `retractcheck`=list( `type`="software", - `author`=NULL, - `year`=NULL, - `title`="", - `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", - `url`="https://CRAN.R-project.org/package="), + `author`="Chris Hartgerink and Frederik Aust", + `year`=2019, + `title`="retractcheck: Retraction Scanner", + `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=retractcheck", + `url`="https://CRAN.R-project.org/package=retractcheck"), `RefManageR`=list( `type`="software", - `author`=NULL, - `year`=NULL, - `title`="", - `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", - `url`="https://CRAN.R-project.org/package="), + `author`="McLean MW", + `year`=2017, + `title`="RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.", + `doi`="10.21105/joss.00338", + `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=RefManageR", + `url`="https://CRAN.R-project.org/package=RefManageR"), `rcrossref`=list( `type`="software", - `author`=NULL, - `year`=NULL, - `title`="", - `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", - `url`="https://CRAN.R-project.org/package=")) + `author`="Scott Chamberlain and Hao Zhu and Najko Jahn and Carl Boettiger and Karthik Ram", + `year`=2020, + `title`="rcrossref: Client for Various 'CrossRef' 'APIs'", + `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=rcrossref", + `url`="https://CRAN.R-project.org/package=rcrossref")) diff --git a/R/crosstable.b.R b/R/crosstable.b.R index 3be0f0e0..75051e6c 100644 --- a/R/crosstable.b.R +++ b/R/crosstable.b.R @@ -268,10 +268,29 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class( if (export) { + + + + if (.Platform$OS.type == "windows") { + + stopifnot(file.exists("C:\\temp2")) + + write( + x = tabletangram, + file = "C:\\temp2\\ClinicoPathCrossTable.html" + ) + + + } else { + + write(x = tabletangram, file = "~/Documents/ClinicoPathCrossTable.html" - ) + + } + + } diff --git a/R/tree.b.R b/R/tree.b.R index d881e4a8..8cd1cdee 100644 --- a/R/tree.b.R +++ b/R/tree.b.R @@ -85,7 +85,7 @@ treeClass <- if (requireNamespace('jmvcore')) R6::R6Class( tree <- rpart::rpart(myformula, data = mydata, cp = .02) - # self$results$text2$setContent(tree) + self$results$text2$setContent(tree) # FFTrees ---- @@ -113,7 +113,7 @@ treeClass <- if (requireNamespace('jmvcore')) R6::R6Class( - # self$results$text2$setContent(mydata) + self$results$text2$setContent(mydata) } @@ -200,6 +200,7 @@ treeClass <- if (requireNamespace('jmvcore')) R6::R6Class( myformula <- as.formula(myformula) # FFTrees ---- + # https://ndphillips.github.io/useR2017_pres/#1 mytree.fft <- FFTrees::FFTrees( formula = myformula, @@ -250,7 +251,9 @@ treeClass <- if (requireNamespace('jmvcore')) R6::R6Class( myformula <- as.formula(myformula) - tree <- rpart::rpart(myformula, data = mydata, cp = .02) + tree <- rpart::rpart(myformula, + data = mydata, + cp = .02) plot3 <- rpart.plot::rpart.plot(tree, diff --git a/README.Rmd b/README.Rmd index 3978c569..44317aa4 100644 --- a/README.Rmd +++ b/README.Rmd @@ -4,7 +4,7 @@ output: github_document -```{r, include = FALSE} +```{r global options, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>", @@ -64,17 +64,41 @@ Then you can install this module directly inside the jamovi, using library. ## Installation via sideload [jamovi](https://www.jamovi.org) -- Step 1: Download and install [jamovi](https://www.jamovi.org). +**Step 1: Download and install [jamovi](https://www.jamovi.org).** -- Step 2: Download the relevant `jmo` file for your operating system from +**Step 2: Download the relevant `jmo` file for your operating system from** + +*a: For development version* - - a: For development version - [releases](https://github.com/sbalci/ClinicoPathJamoviModule/releases/) - [sourceforge](https://sourceforge.net/projects/clinicopathjamovimodule/files/latest/download). - - b: For stable version + +*b: For smaller modules* + + +- ClinicoPath: + + +https://github.com/sbalci/ClinicoPath + + +https://github.com/sbalci/ClinicoPath/releases + + +- JJStatsPlot: + + +https://github.com/sbalci/jjstatsplot + +https://github.com/sbalci/jjstatsplot/releases/ + + +*c: For stable version* + + - windows: https://library.jamovi.org/win64/R3.6.3/ClinicoPath-0.0.2.jmo @@ -84,7 +108,7 @@ Then you can install this module directly inside the jamovi, using library. -- Step 3: And install using side-load as shown below: +**Step 3: And install using side-load as shown below:** diff --git a/README.md b/README.md index bf31ab71..6a1a5f2f 100644 --- a/README.md +++ b/README.md @@ -45,18 +45,31 @@ library. ## Installation via sideload [jamovi](https://www.jamovi.org) - - Step 1: Download and install [jamovi](https://www.jamovi.org). +**Step 1: Download and install [jamovi](https://www.jamovi.org).** - - Step 2: Download the relevant `jmo` file for your operating system - from - - - a: For development version +**Step 2: Download the relevant `jmo` file for your operating system +from** - - [releases](https://github.com/sbalci/ClinicoPathJamoviModule/releases/) +*a: For development version* + - [releases](https://github.com/sbalci/ClinicoPathJamoviModule/releases/) - [sourceforge](https://sourceforge.net/projects/clinicopathjamovimodule/files/latest/download). - - - b: For stable version + +*b: For smaller modules* + + - ClinicoPath: + + + + + + - JJStatsPlot: + + + + + +*c: For stable version* - windows: @@ -66,7 +79,7 @@ library. - - Step 3: And install using side-load as shown below: +**Step 3: And install using side-load as shown below:** @@ -293,21 +306,23 @@ Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/sbalci/C Ready-to-Code](https://img.shields.io/badge/Gitpod-Ready--to--Code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/sbalci/ClinicoPathJamoviModule) [![Download ClinicoPathJamoviModule](https://img.shields.io/sourceforge/dt/clinicopathjamovimodule.svg)](https://sourceforge.net/projects/clinicopathjamovimodule/files/latest/download) -[![Project Status: WIP – Initial development is in progress, but there -has not yet been a stable, usable release suitable for the -public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) 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welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/sbalci/clinicopathjamovimodule/issues) ![GitHub diff --git a/codemeta.json b/codemeta.json index 4e753a62..937c3254 100644 --- a/codemeta.json +++ b/codemeta.json @@ -14,7 +14,7 @@ ], "issueTracker": "\n https://github.com/sbalci/ClinicoPathJamoviModule/issues/", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "0.0.2.15", + "version": "0.0.2.16", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -657,6 +657,6 @@ "survival-analysis", "natural-language-summaries" ], - "fileSize": "301.543KB", + "fileSize": "302.144KB", "readme": "https://github.com/sbalci/ClinicoPathJamoviModule/blob/master/README.md" } diff --git a/data/histopathology.omv b/data/histopathology.omv index 11ef86ca..4b3cbd89 100644 Binary files a/data/histopathology.omv and b/data/histopathology.omv differ diff --git a/inst/extdata/histopathology.omv b/inst/extdata/histopathology.omv index 61b27bf2..11ef86ca 100644 Binary files a/inst/extdata/histopathology.omv and b/inst/extdata/histopathology.omv differ diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml index ab12a056..8567fa92 100644 --- a/jamovi/0000.yaml +++ b/jamovi/0000.yaml @@ -1,12 +1,12 @@ --- title: Common Analysis for Clinicopathological Research name: ClinicoPath -version: 0.0.2.0015 +version: 0.0.2.0016 jms: '1.0' authors: - Serdar Balci maintainer: Serdar Balci -date: '2020-06-28' +date: '2020-06-29' type: R description: >- ClinicoPath help researchers to generate natural language summaries of their diff --git a/jamovi/00refs.yaml b/jamovi/00refs.yaml index ac5b2bf7..ec7ceaaa 100644 --- a/jamovi/00refs.yaml +++ b/jamovi/00refs.yaml @@ -365,29 +365,30 @@ refs: retractcheck: type: 'software' - author: - year: - title: "" - publisher: '[R package]. Retrieved from https://CRAN.R-project.org/package=' - url: https://CRAN.R-project.org/package= + author: Chris Hartgerink and Frederik Aust + year: 2019 + title: "retractcheck: Retraction Scanner" + publisher: '[R package]. Retrieved from https://CRAN.R-project.org/package=retractcheck' + url: https://CRAN.R-project.org/package=retractcheck RefManageR: type: 'software' - author: - year: - title: "" - publisher: '[R package]. Retrieved from https://CRAN.R-project.org/package=' - url: https://CRAN.R-project.org/package= + author: McLean MW + year: 2017 + title: 'RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.' + doi: 10.21105/joss.00338 + publisher: '[R package]. Retrieved from https://CRAN.R-project.org/package=RefManageR' + url: https://CRAN.R-project.org/package=RefManageR rcrossref: type: 'software' - author: - year: - title: "" - publisher: '[R package]. Retrieved from https://CRAN.R-project.org/package=' - url: https://CRAN.R-project.org/package= + author: Scott Chamberlain and Hao Zhu and Najko Jahn and Carl Boettiger and Karthik Ram + year: 2020 + title: "rcrossref: Client for Various 'CrossRef' 'APIs'" + publisher: '[R package]. Retrieved from https://CRAN.R-project.org/package=rcrossref' + url: https://CRAN.R-project.org/package=rcrossref ... diff --git a/tododata/todo.Rmd b/tododata/todo.Rmd index f37956ae..ff48ea6d 100644 --- a/tododata/todo.Rmd +++ b/tododata/todo.Rmd @@ -1065,24 +1065,13 @@ readyfunctions <- c( "^oddsratio", # "^competingsurvival", -# JJ Functions - "statsplot2", - "^jjbarstats\\.", - "^jjbetweenstats", - "^jjcorrmat", - "^jjdotplotstats", - "^jjhistostats", - "^jjpiestats", - "^jjscatterstats", - "^jjwithinstats", - # Agreement - "^agreement" + "^agreement", # "^icccoeff", # Decision - # "^decision", - # "^decisioncalculator", + "^decision", + "^decisioncalculator" # "^roc", # "^tree" )