update for WINratio,

added fct flex2rmd, conditional on interactive

DESCRIPTION

@@ -10,7 +10,7 @@ Description: The main functionalities of 'wrappedtools' are:
     descriptive statistics and p-values; creating specialized plots for 
     correlation matrices. Functions were mainly written for my own daily work or 
     teaching, but may be of use to others as well.
-Version: 0.9.4
+Version: 0.9.4.2
 Date: 2023-12-23
 Authors@R: c(
     person(given = "Andreas",
@@ -45,7 +45,8 @@ Imports:
     lifecycle,
     broom,
     rlist,
-    DescTools
+    DescTools,
+    flextable
 Depends: 
     R (>= 4.2)
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -14,6 +14,7 @@ export(compare_n_numvars)
 export(compare_n_qualvars)
 export(cortestR)
 export(detect_outliers)
+export(flex2rmd)
 export(formatP)
 export(ggcormat)
 export(glmCI)
@@ -52,6 +53,7 @@ import(stringr)
 import(tibble)
 importFrom(DescTools,BinomRatioCI)
 importFrom(broom,tidy)
+importFrom(flextable,flextable_to_rmd)
 importFrom(forcats,fct_drop)
 importFrom(forcats,fct_lump_n)
 importFrom(grDevices,boxplot.stats)

NEWS.md

@@ -3,6 +3,7 @@
 - new function label_outliers to extend boxplots
 - new function detect_outliers for compatibility with geom_boxplot
 - new function WINratio to calculate the ratio of wins to losses in clinical trials
+- new function flex2rmd to convert flextable to rmarkdown table if non-interactive
 
 # wrappedtools 0.9.3
 - compare2numvars checks indep. variables for 2 levels

R/basefunctions.R

@@ -554,3 +554,20 @@ tab.search <- function(searchdata = rawdata, pattern,
 surprisal <- function(p, precision = 1){
   round(-log2(as.numeric(p)),precision) |> as.character()
 }
+
+
+#' Transform flextable to rmd if non-interactive
+#' 
+#' \code{flex2rmd} takes a flextable and returns a markdown table if not in an interactive session
+#' 
+#' @param ft a flextable
+#' 
+#' @return either a markdown table or the flextable
+#' @export
+flex2rmd <- function(ft){
+  if(interactive()){
+    return(ft)
+  } else {
+    return(flextable_to_rmd(ft))
+  }
+}

R/pkgstart.R

@@ -51,3 +51,6 @@ NULL
 
 #' @importFrom DescTools BinomRatioCI
 NULL
+
+#' @importFrom flextable flextable_to_rmd
+NULL

R/tests.R

@@ -1189,6 +1189,8 @@ utils::globalVariables('p_wcox_t_out')
 #' 
 #' WINratio=vector with WINratio and CIs,
 #' 
+#' WINodds=odds ratio of wins and losses, taking ties into account,
+#' 
 #' p.value=p.value from prop.test,
 #' 
 #' WINratioCI=character with merged WINratio, CI, and p
@@ -1261,26 +1263,31 @@ WINratio <- function(data,groupvar,testvars,rules, idvar=NULL,
                              .default=.x))) |>
     mutate(rule=c(paste(testvars,rules, sep=": "),"all"))
 
-  pT <- WINners |>
+  p_w <- WINners |>
+    filter(rule=="all") |>
+    pull("Wins")# / nrow(testdata)
+  p_l <- WINners |>
     filter(rule=="all") |>
-    pull(Wins)# / nrow(testdata)
-  pC <- WINners |>
+    pull("Losses")# / nrow(testdata)
+  p_t <- WINners |>
     filter(rule=="all") |>
-    pull(Losses)# / nrow(testdata)
+    pull("Ties")# / nrow(testdata)
   # WINratio=pT/pC
-  p.value <- prop.test(pT,pT+pC)$p.value
-  WINratio <- DescTools::BinomRatioCI(pT,nrow(testdata),
-                                      pC,nrow(testdata),
+  p.value <- prop.test(p_w,p_w+p_l)$p.value
+  WINratio <- DescTools::BinomRatioCI(p_w,nrow(testdata),
+                                      p_l,nrow(testdata),
                                       method = 'katz') |>
     roundR(3)
+  WINodds <- (p_w+p_t*.5) / (p_l+p_t*.5)
   WINratioCI <- paste0(roundR(WINratio[1],3)," (",
                        roundR(WINratio[2],3),"/",
                        roundR(WINratio[3],3),")",
                        " p ",formatP(p.value, ndigits=p_digits, pretext=TRUE))
   return(list(WIN=WINners,
               WINratio=WINratio,
+              WINodds=WINodds,
               p.value=p.value,
               WINratioCI=WINratioCI,
               testdata=testdata))
 }
-utils::globalVariables(c('outcome',"Wins","Losses","rule"))
+utils::globalVariables(c('outcome',"rule"))