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# ClinicoPath 0.0.2.0015
- Added tangram statistical results - Added options to finalfit crosstables fixes: #24 fixes: jamovi/jamovi#901 fixes: ewenharrison/finalfit#52 - Added experimental biblometrics functions - includes experimental changes
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‎DESCRIPTION‎

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Type: Package
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Package: ClinicoPath
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Title: Analysis for Clinicopathological Research
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Version: 0.0.2.0013
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Date: 2020-06-12
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Version: 0.0.2.0015
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Date: 2020-06-28
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Authors@R:
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person(given = "Serdar",
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family = "Balci",
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rpart,
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rpart.plot,
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plotROC,
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arsenal,
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easyalluvial,
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corrr,
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correlation,
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pkgnet,
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hrbrthemes,
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gtsummary,
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vctrs
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vctrs,
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retractcheck,
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RefManageR,
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rcrossref
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Remotes:
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ndphillips/FFTrees,
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easystats/report,
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spgarbet/tangram,
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cran/rmngb,
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mixOmicsTeam/mixOmics
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mixOmicsTeam/mixOmics,
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mayoverse/arsenal
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VignetteBuilder:
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knitr
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Encoding: UTF-8

‎NAMESPACE‎

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export(oddsratio)
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export(pairchi2)
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export(reportcat)
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export(retracted)
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export(roc)
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export(statsplot2)
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export(summarydata)

‎NEWS.md‎

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# ClinicoPath 0.0.2.0015
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- Added tangram statistical results
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- Added options to finalfit crosstables
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fixes: https://github.com/sbalci/ClinicoPathJamoviModule/issues/24
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fixes: https://github.com/jamovi/jamovi/issues/901
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fixes: https://github.com/ewenharrison/finalfit/issues/52
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- Added experimental biblometrics functions
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- includes experimental changes
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# ClinicoPath 0.0.2.0014
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- Added footnote to arsenal crosstable
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# ClinicoPath 0.0.2.0012
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- jjstatsplot is the wrapper functions for using ggstatsplot in jamovi.

‎R/00jmv.R‎

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`year`=2020,
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`title`="hrbrthemes: Additional Themes, Theme Components and Utilities for 'ggplot2'.",
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`publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=hrbrthemes",
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`url`="https://CRAN.R-project.org/package=hrbrthemes"))
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`url`="https://CRAN.R-project.org/package=hrbrthemes"),
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`retractcheck`=list(
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`type`="software",
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`author`=NULL,
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`year`=NULL,
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`title`="",
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`publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=",
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`url`="https://CRAN.R-project.org/package="),
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`RefManageR`=list(
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`type`="software",
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`author`=NULL,
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`year`=NULL,
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`title`="",
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`publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=",
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`url`="https://CRAN.R-project.org/package="),
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`rcrossref`=list(
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`type`="software",
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`author`=NULL,
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`year`=NULL,
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`title`="",
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`publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=",
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`url`="https://CRAN.R-project.org/package="))

‎R/crosstable.b.R‎

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@@ -13,13 +13,20 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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.run = function() {
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# Select Style ----
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sty <- self$options$sty
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if (is.null(self$options$vars) || is.null(self$options$group)) {
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# ToDo Message ----
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todo <- glue::glue("
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<br>
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<br>Welcome to ClinicoPath.<br>
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This tool will help you form a Cross Table.<br>
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The functions select hypothesis tests automatically. You may see different results with different tables. Please verify your data distribution and appropriateness of the test accordingly. You may find Statkat module useful.<br>
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html <- self$results$todo
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html$setContent(todo)
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if (sty == "finalfit") {
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todo <- glue::glue("
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<br>
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<b>finalfit</b> uses
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<em>aov (analysis of variance) or t.test for Welch two sample t-test. Note continuous non-parametric test is always Kruskal Wallis (kruskal.test) which in two-group setting is equivalent to Mann-Whitney U /Wilcoxon rank sum test</em>. See full documentation <a href= 'https://finalfit.org/reference/summary_factorlist.html'>here</a>.
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"
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)
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html <- self$results$todo
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html$setContent(todo)
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}
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# Error Message ----
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if (nrow(self$data) == 0) stop("Data contains no (complete) rows")
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if (excl) {mydata <- jmvcore::naOmit(mydata)}
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# Select Style ----
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sty <- self$options$sty
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# tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
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tablearsenal <- summary(tablearsenal,
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text = 'html',
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pfootnote = TRUE
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pfootnote = 'html'
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)
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# tablearsenal_output <- capture.output(tablearsenal)
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tablearsenal <-
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kableExtra::kable(tablearsenal,
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format = "html",
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digits = 1,
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escape = FALSE
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)
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# self$results$tablearsenal_output$setContent(tablearsenal_output)
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# tablearsenal <-
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# kableExtra::kable(tablearsenal,
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# format = "html",
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# digits = 1,
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# escape = FALSE
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# )
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tablearsenal <- capture.output(tablearsenal)
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self$results$tablestyle1$setContent(tablearsenal)
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} else if (sty == "finalfit") {
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# FinalFit ----
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# https://finalfit.org/articles/tables_gallery.html#cross-tables
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# https://finalfit.org/reference/summary_factorlist.html
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myvars <- jmvcore::composeTerm(components = self$options$vars)
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.data = .,
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dependent = self$options$group,
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explanatory = myvars,
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# column = TRUE,
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total_col = TRUE,
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p = TRUE,
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add_dependent_label = TRUE,
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na_include = FALSE,
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na_to_p = FALSE
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na_to_p = FALSE,
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cont = self$options$cont,
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cont_range = TRUE,
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p_cont_para = "aov",
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p_cat = self$options$pcat,
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cont_nonpara = NULL,
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cont_cut = 5,
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dependent_label_prefix = "Dependent: ",
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dependent_label_suffix = "",
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row_totals_colname = "Total N",
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row_missing_colname = "Missing N",
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column = TRUE,
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orderbytotal = FALSE,
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digits = c(1, 1, 3, 1),
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na_include_dependent = FALSE,
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na_complete_cases = FALSE,
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fit_id = FALSE,
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add_col_totals = FALSE,
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include_col_totals_percent = TRUE,
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col_totals_rowname = NULL,
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col_totals_prefix = "",
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add_row_totals = FALSE,
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include_row_missing_col = TRUE
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# catTest = catTestfisher
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) -> tablefinalfit
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tablefinalfit <- kableExtra::kable(tablefinalfit,
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digits = 1,
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mydata,
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transform=tangram::hmisc,
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id = "tbl3",
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test = TRUE,
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digits = 1,
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include_p = TRUE
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),
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self$results$tablestyle4$setContent(tabletangram)
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}
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# tableone ----
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# tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
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}
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})
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‎R/crosstable.h.R‎

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@@ -9,7 +9,9 @@ crosstableOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
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vars = NULL,
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group = NULL,
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sty = "nejm",
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excl = TRUE, ...) {
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excl = TRUE,
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cont = "mean",
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pcat = "chisq", ...) {
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super$initialize(
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package='ClinicoPath',
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"excl",
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default=TRUE)
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private$..cont <- jmvcore::OptionList$new(
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"cont",
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cont,
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options=list(
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"mean",
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"median"),
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default="mean")
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private$..pcat <- jmvcore::OptionList$new(
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"pcat",
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pcat,
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options=list(
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"chisq",
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"fisher"),
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default="chisq")
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self$.addOption(private$..vars)
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self$.addOption(private$..group)
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self$.addOption(private$..sty)
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self$.addOption(private$..excl)
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self$.addOption(private$..cont)
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self$.addOption(private$..pcat)
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}),
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active = list(
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vars = function() private$..vars$value,
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group = function() private$..group$value,
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sty = function() private$..sty$value,
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excl = function() private$..excl$value),
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excl = function() private$..excl$value,
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cont = function() private$..cont$value,
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pcat = function() private$..pcat$value),
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private = list(
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..vars = NA,
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..group = NA,
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..sty = NA,
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..excl = NA)
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..excl = NA,
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..cont = NA,
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..pcat = NA)
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crosstableResults <- if (requireNamespace('jmvcore')) R6::R6Class(
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title="To Do",
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clearWith=list(
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"group")))
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"group",
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"cont",
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"pcat")))
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self$add(jmvcore::Html$new(
87111
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name="tablestyle1",
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title="`Cross Table - ${group}`",
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clearWith=list(
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"vars",
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"group"),
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"group",
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"cont",
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"pcat"),
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visible="(sty:finalfit)",
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refs="finalfit"))
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self$add(jmvcore::Html$new(
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#' @param group variable in the column
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#' @param sty .
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#' @param excl .
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#' @param cont .
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#' @param pcat .
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#' @return A results object containing:
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#' \tabular{llllll}{
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#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
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excl = TRUE) {
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excl = TRUE,
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cont = "mean",
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pcat = "chisq") {
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if ( ! requireNamespace('jmvcore'))
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stop('crosstable requires jmvcore to be installed (restart may be required)')
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excl = excl)
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excl = excl,
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cont = cont,
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pcat = pcat)
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analysis <- crosstableClass$new(
193225
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‎R/multisurvival.b.R‎

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finalfit::finalfit(.data = mydata,
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dependent = myformula,
120120
explanatory = formula2,
121-
# ,
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122122
# metrics = TRUE
123123
) -> tMultivariate
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