format not being applied to data frame - r

Question

I try to apply formatting to a data frame created from a printed TableOne object but it won't "stick"
Sample
library(dplyr)
library(tableone)
data(ovarian)
data <- ovarian
data$futime <- data$futime * 100
vars <- c("futime","fustat")
catvars <- c("fustat")
table1 <- CreateTableOne(vars = vars, factorVars = catvars,strata = "rx", data = data)
print(table1, printToggle = F, quote = F) %>%as.data.frame() %>% format(big.mark = ",")
Result:
1 2 p test
n 13 13
futime (mean (SD)) 51730.77 (34688.14) 68176.92 (32467.63) 0.224
fustat = 1 (%) 7 (53.8) 5 (38.5) 0.694
This behaves similar to simply creating my own data frame
c(1213,2,3,1213,2,3) %>% table()%>% as.data.frame() %>% format(big.mark = ",")
Result:
. Freq
1 2 2
2 3 2
3 1213 2
This is unlike when simply using the format option on a numeric variable or even a one column data frame
123321789 %>% format(big.mark = ",")
Result:
[1] "123,321,789"
or
c(1213,2,3,1213,2,3) %>% as.data.frame() %>% format(big.mark = ",")
Result:
1 1,213
2 2
3 3
4 1,213
5 2
6 3

Answer 1

This is linked to the fact that table returns factors.
The examples you provided apply to numeric data.
Try:
library(dplyr)
result <- c(1213,2,3,1213,2,3) %>% table() %>% as.data.frame
class(result$.)
#> [1] "factor"
result %>% mutate_all( ~format(as.numeric(as.character(.x)),big.mark=','))
#> . Freq
#> 1 2 2
#> 2 3 2
#> 3 1,213 2

Answer 2

OK, so this one lead me down a rabbit hole of text formatting.
Ended up writing a function to address the matter, used address some weird rounding issues.
styleTableOne <- function(x){
if(!is.na(as.numeric(x))){return(format(as.numeric(x),big.mark = ","))}
if(x == ""){return(x)}
if(x == "<0.001"){return(x)}
if(x == "0.0"){return(x)}
if(x == " "){return(x)}
if (length(strsplit(x, split = "(", fixed = T)[[1]]) == 2){
set1 <- strsplit(x, split = "(",fixed = T)[[1]][1] %>% as.numeric()
set2 <- strsplit(x, split = "(",fixed = T)[[1]][2] %>% str_remove(fixed(")")) %>% as.numeric()
set1 <- case_when(
set1 > 100 ~ round(set1,0),
set1 > 25 ~ round(set1,1),
T ~ round(set1,2)
)
set2 <- case_when(
set1 > 100 ~ round(set2,0),
set1 > 25 ~ round(set2,1),
T ~ round(set2,2)
)
set1 %<>% format(big.mark = ",")
set2 %<>% format(big.mark = ",")
set <- paste(set1,set2,sep = " (")
set <- paste0(set,")")
return(set)}
x %>% strsplit(split = " ",fixed = T) %>% .[[1]] -> x
x <- subset(x, x != "")
set1 <- strsplit(x, split = " ",fixed = T)[1] %>% as.numeric()
set2 <- strsplit(x, split = " ",fixed = T)[2] %>% str_remove(fixed("[")) %>% str_remove(fixed(",")) %>% as.numeric()
set3 <- strsplit(x, split = " ",fixed = T)[3] %>% str_remove(fixed("]")) %>% as.numeric()
set1 <- case_when(
set1 > 100 ~ round(set1,0),
set1 > 25 ~ round(set1,1),
T ~ round(set1,2)
)
set2 <- case_when(
set1 > 100 ~ round(set2,0),
set1 > 25 ~ round(set2,1),
T ~ round(set2,2)
)
set3 <- case_when(
set1 > 100 ~ round(set3,0),
set1 > 25 ~ round(set3,1),
T ~ round(set3,2)
)
set1 %<>% format(big.mark = ",")
set2 %<>% format(big.mark = ",")
set3 %<>% format(big.mark = ",")
set <- paste0(set1," (",set2,"-",set3,")")
return(set)
}
Then you can do:
library(survival)
library(dplyr)
library(tableone)
data(ovarian)
data <- ovarian
data$futime <- data$futime * 100
vars <- c("futime","fustat")
catvars <- c("fustat")
table1 <- CreateTableOne(vars = vars, factorVars = catvars,strata = "rx", data = data)
print(table1, printToggle = F) %>%
as.data.frame() %>%
sapply(sapply, styleTableOne) %>%
as.data.frame(row.names = row.names(print(table1)))
result:
1 2 p test
n 13 13
futime (mean (SD)) 51,731 (34,688) 68,177 (32,468) 0.224
fustat = 1 (%) 7 (53.8) 5 (38.5) 0.694