is there a simple way to recode levels of a factor variable so that levels occuring below a given fr-CodePudding

theshold <- c(0.001, 0.5, 0.1)

df$a df$b df$c - Recode levels based on level frequency of less than first threshold

df$x df$y df$x - Recode levels based on level frequency of less than second threshold

df$d df$e df$f - Recode levels based on level frequency of less than third threshold

CodePudding user response：

You're looking for fct_lump_prop() from forcats.

library(forcats)
library(dplyr)

dat <- data.frame(base = c("A", "A", "A",
                           "B", "B",
                           "C",
                           "D"))

dat |> mutate(base0.2 = fct_lump_prop(base, 0.2),
              base0.3 = fct_lump_prop(base, 0.3))

Output

#>   base base0.2 base0.3
#> 1    A       A       A
#> 2    A       A       A
#> 3    A       A       A
#> 4    B       B   Other
#> 5    B       B   Other
#> 6    C   Other   Other
#> 7    D   Other   Other

^{Created on 2022-03-31 by the reprex package (v2.0.0)}

CodePudding user response：

There may be an easier tidy way of doing this, but you could write a little function that would implement this:

set.seed(519)
x <- sample(LETTERS[1:5], 1000, prob=c(.01,.1,.29,.3,.3), replace=TRUE)
x <- as.factor(x)
recode_thresh <- function(x, threshold = .15){
  tab <- table(x)/sum(table(x))
  levs <- levels(x)
  levs <- c(levs, "other")
  x <- as.character(x)
  if(any(tab < threshold)){
    x <- ifelse(x %in% names(tab)[which(tab < threshold)], "other", x)
  }
  levs <- intersect(levs, unique(x))
  factor(x, levels=levs)
}
x2 <- recode_thresh(x, threshold=.15)
table(x)/1000
#> x
#>     A     B     C     D     E 
#> 0.014 0.106 0.294 0.276 0.310
table(x2)/1000
#> x2
#>     C     D     E other 
#> 0.294 0.276 0.310 0.120

^{Created on 2022-03-31 by the reprex package (v2.0.1)}