finalfit, survival, survival plot, multivariate survival works

sbalci · Jan 31, 2020 · b50269d · b50269d
1 parent 08473bf
commit b50269d
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Showing 40 changed files with 415 additions and 251 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -46,3 +46,4 @@ build
 ^\.github/
 ^docs$
 ^pkgdown$
+^img$
diff --git a/R/00jmv.R b/R/00jmv.R
@@ -146,17 +146,17 @@
         `doi`="10.5281/zenodo.2074621"), 
     `report`=list(
         `type`="software", 
-        `author`=NULL, 
-        `year`=2018, 
-        `title`="", 
-        `publisher`="", 
-        `url`="https://CRAN.R-project.org/package=report"), 
+        `author`="Makowski, Dominique, L\u00FCdecke, Daniel", 
+        `year`=2019, 
+        `title`="The report package for R: Ensuring the use of best practices for results reporting", 
+        `publisher`="[R package]. Retrieved from https://github.com/easystats/report", 
+        `url`="https://github.com/easystats/report"), 
     `arsenal`=list(
         `type`="software", 
-        `author`=NULL, 
+        `author`="Heinzen, E Sinnwell, J Atkinson, E Gunderson, T Dougherty, G", 
         `year`=2018, 
-        `title`="", 
-        `publisher`="", 
+        `title`="arsenal: An Arsenal of 'R' Functions for Large-Scale Statistical Summaries", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=arsenal", 
         `url`="https://CRAN.R-project.org/package=arsenal"), 
     `tangram`=list(
         `type`="software", 
@@ -167,7 +167,7 @@
         `url`="https://CRAN.R-project.org/package=tangram"), 
     `irr`=list(
         `type`="software", 
-        `author`="Matthias Gamer, Jim Lemon and Ian Fellows Puspendra Singh", 
+        `author`="Matthias Gamer, Jim Lemon, Ian Fellows, Puspendra Singh", 
         `year`=2019, 
         `title`="Various Coefficients of Interrater Reliability and Agreement.", 
         `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=irr", 
@@ -185,4 +185,18 @@
         `year`=2019, 
         `title`="janitor: Simple Tools for Examining and Cleaning Dirty Data.", 
         `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=janitor", 
-        `url`="https://CRAN.R-project.org/package=janitor"))
+        `url`="https://CRAN.R-project.org/package=janitor"), 
+    `finalfit`=list(
+        `type`="software", 
+        `author`="Ewen Harrison and Tom Drake and Riinu Ots", 
+        `year`=2019, 
+        `title`="finalfit: Quickly Create Elegant Regression Results Tables and Plots when Modelling", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=finalfit", 
+        `url`="https://CRAN.R-project.org/package=finalfit"), 
+    `caret`=list(
+        `type`="software", 
+        `author`="Max Kuhn", 
+        `year`=2020, 
+        `title`="caret: Classification and Regression Training", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=caret", 
+        `url`="https://CRAN.R-project.org/package=caret"))
diff --git a/R/agreement.h.R b/R/agreement.h.R
@@ -70,10 +70,6 @@ agreementBase <- if (requireNamespace('jmvcore')) R6::R6Class(
 #' Interrater Intrarater Reliability
 #'
 #' Function for Interrater Intrarater Reliability.
-#'
-#' @examples
-#' # example will be added
-#'
 #' @param data .
 #' @param vars a string naming the variable from \code{data} that contains the
 #'   diagnosis given by the observer, variable can be categorical, ordinal or

diff --git a/R/correlation.h.R b/R/correlation.h.R
@@ -88,7 +88,7 @@ correlationBase <- if (requireNamespace('jmvcore')) R6::R6Class(
                 completeWhenFilled = FALSE)
         }))
 
-#' correlation
+#' Correlation
 #'
 #' 
 #' @param data .

diff --git a/R/crosstable.b.R b/R/crosstable.b.R
@@ -10,7 +10,7 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
         .run = function() {
 
 
-            if (length(self$options$vars) == 0)
+            if (length(self$options$vars) == 0 | length(self$options$group) == 0)
                 return()
 
             # Arsenal Table
@@ -20,6 +20,7 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             formulaL <- jmvcore::constructFormula(terms = self$options$group)
 
             formula <- paste(formulaL, '~', formulaR)
+
             formula <- as.formula(formula)
 
             table1 <- arsenal::tableby(formula, self$data)
@@ -45,10 +46,10 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                 tangram::html5(
                     tangram::tangram(
                         formula, self$data),
-                    fragment=TRUE,
-                    inline="nejm.css",
+                    fragment = TRUE,
+                    inline = "nejm.css",
                     caption = "Cross Table NEJM Style",
-                    id="tbl3")
+                    id = "tbl3")
 
             results3 <- table3
 
@@ -61,17 +62,44 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                 tangram::html5(
                     tangram::tangram(
                         formula, self$data),
-                    fragment=TRUE,
-                    inline="lancet.css",
+                    fragment = TRUE,
+                    inline = "lancet.css",
                     caption = "Cross Table Lancet Style",
-                    id="tbl4")
+                    id = "tbl4")
 
             results4 <- table4
 
             self$results$text4$setContent(results4)
 
 
 
+            # Table FinalFit
+
+            # https://finalfit.org/articles/tables_gallery.html#cross-tables
+
+
+            myvars <- jmvcore::decomposeFormula(formula = formulaR)
+
+            myvars <- unlist(myvars)
+
+            self$data %>%
+                summary_factorlist(dependent = self$options$group,
+                                   explanatory = myvars,
+                                   # column = TRUE,
+                                   total_col = TRUE,
+                                   p = TRUE,
+                                   add_dependent_label = TRUE,
+                                   na_include = FALSE
+                                   # catTest = catTestfisher
+                ) -> table5
+
+            # knitr::kable(table5, row.names = FALSE, align = c('l', 'l', 'r', 'r', 'r'))
+
+
+            results5 <- table5
+
+            self$results$text5$setContent(results5)
+
 
 
 

diff --git a/R/crosstable.h.R b/R/crosstable.h.R
@@ -49,15 +49,16 @@ crosstableResults <- if (requireNamespace('jmvcore')) R6::R6Class(
         text1 = function() private$.items[["text1"]],
         text2 = function() private$.items[["text2"]],
         text3 = function() private$.items[["text3"]],
-        text4 = function() private$.items[["text4"]]),
+        text4 = function() private$.items[["text4"]],
+        text5 = function() private$.items[["text5"]]),
     private = list(),
     public=list(
         initialize=function(options) {
             super$initialize(
                 options=options,
                 name="",
                 title="CrossTable",
-                refs="tangram, arsenal")
+                refs="tangram, arsenal, finalfit")
             self$add(jmvcore::Preformatted$new(
                 options=options,
                 name="text1",
@@ -73,7 +74,11 @@ crosstableResults <- if (requireNamespace('jmvcore')) R6::R6Class(
             self$add(jmvcore::Html$new(
                 options=options,
                 name="text4",
-                title="CrossTable Tangram Lancet"))}))
+                title="CrossTable Tangram Lancet"))
+            self$add(jmvcore::Preformatted$new(
+                options=options,
+                name="text5",
+                title="CrossTable FinalFit"))}))
 
 crosstableBase <- if (requireNamespace('jmvcore')) R6::R6Class(
     "crosstableBase",
@@ -94,7 +99,7 @@ crosstableBase <- if (requireNamespace('jmvcore')) R6::R6Class(
                 completeWhenFilled = FALSE)
         }))
 
-#' CrossTable
+#' CrossTables
 #'
 #' Function for making Cross Tables.
 #' @param data .
@@ -106,6 +111,7 @@ crosstableBase <- if (requireNamespace('jmvcore')) R6::R6Class(
 #'   \code{results$text2} \tab \tab \tab \tab \tab a preformatted \cr
 #'   \code{results$text3} \tab \tab \tab \tab \tab a html \cr
 #'   \code{results$text4} \tab \tab \tab \tab \tab a html \cr
+#'   \code{results$text5} \tab \tab \tab \tab \tab a preformatted \cr
 #' }
 #'
 #' @export
-Original file line number
+Diff line change
@@ Expand Up / @@ -46,3 +46,4 @@ build @@
     ^\.github/
     ^docs$
     ^pkgdown$
+    ^img$