Using dplyr to create summary proportion table with several categorical/factor variables

One way to solve this, is to turn your data to a long(er) format. You can then use the same code to calculate the outcomes you want, with one extra group_by:

library(reshape2)
library(dplyr)

m_mtcars <- melt(mtcars,measure.vars=c("gear","carb","cyl"))

res <- m_mtcars %>%
  group_by(am, variable, value) %>%
  summarise (n = n()) %>%
  mutate(freq = n / sum(n))

Building on this, the desired output can be obtained using more reshaping and some string formatting

#make an 'export' variable
res$export <- with(res, sprintf("%i (%.1f%%)", n, freq*100))

#reshape again
output <- dcast(variable+value~am, value.var="export", data=res, fill="missing") #use drop=F to prevent silent missings 
#'silent missings'
output$variable <- as.character(output$variable)
#make 'empty lines' 
empties <- data.frame(variable=unique(output$variable), stringsAsFactors=F)
empties[,colnames(output)[-1]] <- ""

#bind them together
output2 <- rbind(empties,output)
output2 <- output2[order(output2$variable,output2$value),]

#optional: 'remove' variable if value present

output2$variable[output2$value!=""] <- ""

This results in:

   variable value          0         1
2      carb                           
7               1  3 (15.8%) 4 (30.8%)
8               2  6 (31.6%) 4 (30.8%)
9               3  3 (15.8%)   missing
10              4  7 (36.8%) 3 (23.1%)
11              6    missing  1 (7.7%)
12              8    missing  1 (7.7%)
3       cyl                           
13              4  3 (15.8%) 8 (61.5%)
14              6  4 (21.1%) 3 (23.1%)
15              8 12 (63.2%) 2 (15.4%)
1      gear                           
4               3 15 (78.9%)   missing
5               4  4 (21.1%) 8 (61.5%)
6               5    missing 5 (38.5%)

With tidyr/dplyr combination, here is how you would do it:

library(tidyr)
library(dplyr)

mtcars %>%
  gather(variable, value, gear, carb, cyl) %>%
  group_by(am, variable, value) %>%
  summarise (n = n()) %>%
  mutate(freq = n / sum(n))