Clearing errors from get.ggplot

R/hypoAfrica.R

@@ -119,7 +119,7 @@ add.p.values.fisher<-function(df,dfRef,var,timeVar='visitid',nVar='total'){
 #' @param var target fraction variable
 #' @param timeVar variable measuring time
 #' @param doseVar variable for selecting datasets
-#' @param countVar variable where counts are stored
+#' @param nVar variable where counts are stored
 #' @param doseBreaks values to break plots to
 #' @param doseLabels labels for legend for breaks
 #' @param doseColors colors to use for different plots
@@ -135,7 +135,7 @@ add.p.values.fisher<-function(df,dfRef,var,timeVar='visitid',nVar='total'){
 get.ggplot<-function(df,dfRef,var,timeVar='visitid',doseVar='dose',nVar='ntotal',
    doseBreaks=base::c(60,62,100),doseLabels=base::c('60 Gy','62 Gy','all'),doseColors=base::c('red','magenta','blue'),
    timeBreaks=base::c(0,1,3,4),timeLabels=base::c('beforeRT','at20','at3mo','at12mo')){
-   df<-add.conf.int(df,var)
+   df<-add.conf.int(df,var,nVar)
    dfRef<-add.conf.int(dfRef,var,nVar)
 
    ghigh<-base::sprintf("%s_high",var)

man/get.ggplot.Rd

@@ -10,6 +10,7 @@ get.ggplot(
   var,
   timeVar = "visitid",
   doseVar = "dose",
+  nVar = "ntotal",
   doseBreaks = base::c(60, 62, 100),
   doseLabels = base::c("60 Gy", "62 Gy", "all"),
   doseColors = base::c("red", "magenta", "blue"),
@@ -28,6 +29,8 @@ get.ggplot(
 
 \item{doseVar}{variable for selecting datasets}
 
+\item{nVar}{variable where counts are stored}
+
 \item{doseBreaks}{values to break plots to}
 
 \item{doseLabels}{labels for legend for breaks}