# R/combine.levels.r In harrelfe/Hmisc: Harrell Miscellaneous

#### Documented in combine.levels

```##' Combine Infrequent Levels of a Categorical Variable
##'
##' After turning `x` into a `factor` if it is not one already, combines
##' levels of `x` whose frequency falls below a specified relative frequency `minlev` or absolute count `m`.  When `x` is not treated as ordered, all of the
##' small frequency levels are combined into `"OTHER"`, unless `plevels=TRUE`.
##' When `ord=TRUE` or `x` is an ordered factor, only consecutive levels
##' are combined.  New levels are constructed by concatenating the levels with
##' `sep` as a separator.  This is useful when comparing ordinal regression
##' with polytomous (multinomial) regression and there are too many
##' categories for polytomous regression.  `combine.levels` is also useful
##' when assumptions of ordinal models are being checked empirically by
##' computing exceedance probabilities for various cutoffs of the
##' dependent variable.
##' @title combine.levels
##' @param x a factor, `ordered` factor, or numeric or character variable that will be turned into a `factor`
##' @param minlev the minimum proportion of observations in a cell before that cell is combined with one or more cells.  If more than one cell has fewer than minlev*n observations, all such cells are combined into a new cell labeled `"OTHER"`.  Otherwise, the lowest frequency cell is combined with the next lowest frequency cell, and the level name is the combination of the two old level levels. When `ord=TRUE` combinations happen only for consecutive levels.
##' @param m alternative to `minlev`, is the minimum number of observations in a cell before it will be combined with others
##' @param ord set to `TRUE` to treat `x` as if it were an ordered factor, which allows only consecutive levels to be combined
##' @param plevels by default `combine.levels` pools low-frequency levels into a category named `OTHER` when `x` is not ordered and `ord=FALSE`.  To instead name this category the concatenation of all the pooled level names, separated by a comma, set `plevels=TRUE`.
##' @param sep the separator for concatenating levels when `plevels=TRUE`
##' @return a factor variable, or if `ord=TRUE` an ordered factor variable
##' @author Frank Harrell
##' @examples
##' x <- c(rep('A', 1), rep('B', 3), rep('C', 4), rep('D',1), rep('E',1))
##' combine.levels(x, m=3)
##' combine.levels(x, m=3, plevels=TRUE)
##' combine.levels(x, ord=TRUE, m=3)
##' x <- c(rep('A', 1), rep('B', 3), rep('C', 4), rep('D',1), rep('E',1),
##'        rep('F',1))
##' combine.levels(x, ord=TRUE, m=3)

## Modified 27Feb23 - added ord
combine.levels <- function(x, minlev=.05, m, ord=is.ordered(x),
plevels=FALSE, sep=',') {

x  <- as.factor(x)
i  <- ! is.na(x)
nu <- length(unique(x[i]))
if(nu < 2) return(x)
notna <- sum(i)
if(notna == 0) return(x)
lev <- levels(x)
n   <- table(x)   # excludes NAs in tabulation
f   <- n / notna
if(! missing(m)) minlev <- m / notna
i   <- f < minlev
si  <- sum(i)
if(si == 0) return(x)

if(ord) {
if(nu > 250) warning('combine.levels with ord=TRUE is slow with more than 250 distinct values.\nConsider using cut2().')
if(missing(m)) m <- round(minlev * notna)
if(sum(n) < 2 * m)
stop(paste('with m=', m, 'must have >=', 2 * m,
'non-missing observations'))
levs <- newlevs <- names(n)
names(n) <- NULL
l <- length(levs)
while(TRUE) {
## Find first value of x having < m observations when counting
## by the current combined levels
## If it's the first level, combine it with the 2nd level
## If it's the last level, combine it with the next-to-last level
## Otherwise, combine it with the smaller of the previous level
## and the next level
## factor() below makes tapply keep levels in order
freq <- tapply(n, factor(newlevs, unique(newlevs)), sum)
i    <- which.min(freq)
if(freq[i] >= m) break
l <- length(freq)
j <- if(i == 1) 1:2
else if(i == l) (l-1) : l
else if(freq[i-1] < freq[i+1]) (i-1) : i else i : (i+1)
## freq,i,j are aligned with unique(newlevs)
## Need to make changes index into the longer newlevs
unewlevs <- names(freq)
newlevs[newlevs %in% unewlevs[j]] <- paste(unewlevs[j], collapse=sep)
}
levels(x) <- newlevs
return(ordered(x))
}

comb <- if(si == 1) names(sort(f))[1 : 2]
else names(f)[i]

keepsep <- setdiff(names(f), comb)
names(keepsep) <- keepsep
w <- c(list(OTHER=comb), keepsep)
if(plevels) names(w)[1] <- paste(comb, collapse=sep)
levels(x) <- w
x
}
```
harrelfe/Hmisc documentation built on May 19, 2024, 4:13 a.m.