How to use Pivottabler on concatenated strings in R - r

Question

I have a table that looks like this-
LDAutGroup PatientDays ExposedDays sex Ageband DrugGroup Prop LowerCI UpperCI concat
Group1 100 23 M 5 to 10 PSY 23 15.84 32.15 23 (15.84 -32.15) F
Group2 500 56 F 11 to 17 HYP 11.2 8.73 14.27 11.2 (8.73 -14.27)
Group3 300 89 M 18 and over PSY 29.67 24.78 35.07 29.67 (24.78 -35.07)
Group1 200 34 F 5 to 10 PSY 17 12.43 22.82 17 (12.43 -22.82)
Group2 456 78 M 11 to 17 ANX 17.11 13.93 20.83 17.11 (13.93 -20.83)
Following this, I want a pivot table to lay out the concat column as the valuename. However, the pivottabler only works on integers or numeric values. The following code runs right with either of the Prop, LowerCI or UpperCI columns on their own, but gives an error message for the concat column-
library(readr)
library(dplyr)
library(epitools)
library(gtools)
library(reshape2)
library(binom)
library(pivottabler)
pt <- PivotTable$new()
pt$addData(a)
pt$addColumnDataGroups("LDAutGroup")
pt$addColumnDataGroups("sex")
pt$addRowDataGroups("DrugGroup")
pt$addRowDataGroups("Ageband")
pt$defineCalculation(calculationName="TotalTrains", type="value", valueName="Prop")
pt$renderPivot()
Is there a way I can make this work on the concat column? I want a table that has the following layout and the cells populated with the strings in concat column in the table above
Group1 Group2 Group3
M F M F M F
ANX 11 to 17
18 and over
Total
HYP 11 to 17
18 and over
5 to 10
Total
PSY 18 and over
5 to 10
Total

Answer 1

I am the pivottabler package author.
As you say, pivottabler currently only pivots integer/numerical columns. A workaround exists however, using a custom cell calculation function to calculate the value in each cell. Custom calculation functions were intended for more complex use cases, so using them in this way is a sledgehammer approach, but it does the job, and I suppose makes sense in some scenarios, e.g. if you have other numerical pivot tables and want a uniform appearance for the pivot tables in your output.
Adapting an example from the package vignettes:
library(pivottabler)
library(dplyr)
trainsConcatendated <- mutate(bhmtrains, ConcatValue = paste(TOC, TrainCategory, sep=" "))
getConcatenatedValue <- function(pivotCalculator, netFilters, format, baseValues, cell) {
# get the data frame
trains <- pivotCalculator$getDataFrame("trainsConcatendated")
# apply the filters coming from the headers in the pivot table
filteredTrains <- pivotCalculator$getFilteredDataFrame(trains, netFilters)
# get the distinct values
distinctValues <- distinct(filteredTrains, ConcatValue)
# get the value of the concatenated column
# this just returns the first concatenated value for the cell
# if there are multiple values, the others are ignored
if(length(distinctValues$ConcatValue)==0) { tv <- "" }
else { tv <- distinctValues$ConcatValue[1] }
# build the return value
# the raw value must be numerical, so simply set this to zero
value <- list()
value$rawValue <- 0
value$formattedValue <- tv
return(value)
}
pt <- PivotTable$new()
pt$addData(trainsConcatendated)
pt$addColumnDataGroups("TrainCategory", addTotal=FALSE)
pt$addRowDataGroups("TOC", addTotal=FALSE)
pt$defineCalculation(calculationName="ConcatValue",
type="function", calculationFunction=getConcatenatedValue)
pt$renderPivot()
Results:

Answer 2

It is speculative to apply the same function for CI (lower or upper) as it could be for mean statistics to report subtotal levels, as well as no sense for concat to report subtotals (at least in the simple way of pivot table).
With no subtotal you can easily use tidyr library and report variable with character type in spread format of table : here is 2 line code. First is create groups for columns and second line is to change table format to spread version
library(tidyr)
Table_Original <- unite(Table_Original, "Col_pivot", c("LDAutGroup", "sex"), sep = "_", remove = F)
Table_Pivot <- spread(Table_Original[ ,c("Col_pivot","DrugGroup", "Ageband", "concat")], Col_pivot, concat)