How to write and document %special% functions in R

November 26, 2016 Code R functions special

I spend a considerable portion of my working hours with data processing where I often use the %in% R function as x %in% y. Whenever I need the negation of that, I used to write !(x %in% y). Not much of a hassle, but still, wouldn’t it be nicer to have x %notin% y instead? So I decided to code it for my mefa4 package that I maintain primarily to make my data munging time shorter and more efficient. Coding a %special% function was no big deal. But I had to do quite a bit of research and trial-error until I figured out the proper documentation. So here it goes.

The function

The function name needs quotes and exactly two arguments, one for the left and one for the right hand side of the operator in the middle:

"%notin%" <- function(x, table) !(match(x, table, nomatch = 0) > 0)

Let us see what it does:

1:4 %in% 3:5
## [1] FALSE FALSE  TRUE  TRUE
1:4 %notin% 3:5
## [1]  TRUE  TRUE FALSE FALSE

The NAMESPACE entry

We need to export the function, so just add the following entry to the NAMESPACE file:

export("%notin%")

The Rd file

This is where things get are a bit more interesting. The LaTeX engine needs the percent sign to be escaped (\%) throughout the whole documentation. Also pay close attention to the usage section (x \%notin\% table).

\name{\%notin\%}
\alias{\%notin\%}
\title{
Negated Value Matching
}
\description{
\code{\%notin\%} is the negation of \code{\link{\%in\%}},
which returns a logical vector indicating if there is a non-match or not
for its left operand.
}
\usage{
x \%notin\% table
}
\arguments{
  \item{x}{
vector or \code{NULL}: the values to be matched.
}
  \item{table}{
vector or \code{NULL}: the values to be matched against.
}
}
\value{
A logical vector, indicating if a non-match was located for each element of
\code{x}: thus the values are \code{TRUE} or \code{FALSE} and never \code{NA}.
}
\author{
Peter Solymos <solymos@ualberta.ca>
}
\seealso{
All the opposite of what is written for \code{\link{\%in\%}}.
}
\examples{
1:10 \%notin\% c(1,3,5,9)
sstr <- c("c","ab","B","bba","c",NA,"@","bla","a","Ba","\%")
sstr[sstr \%notin\% c(letters, LETTERS)]
}
\keyword{manip}
\keyword{logic}

UPDATE

Some updates from the comments:

  • From Marcin: One can use roxygen2 for writing package documentation, see the magrittr package docs on the %>% (pipe) operator.
  • From Andrey: The Hmisc package also has a similar %nin% function ({match(x, table, nomatch = 0) == 0}). (Note that the unexported Matrix:::"%nin%" is defined as {is.na(match(x, table))}.)

Statistical computing meets biodiversity conservation and natural resource management

Phylogeny and species traits predict bird detectability

It all started with this paper in Methods in Ecol. Evol. where we looked at detectability of many species. So we wanted to use life history traits to validate our results. But we had to cut the manuscript, and there was this leftover with some neat patterns, but without much focus. It took a few years, and the most positive peer-review experience ever, and the paper is now early view in Ecography. This post is a quick summary of the goodies stuffed inside the lhreg R package that makes the whole analysis reproducible, and provides some functions for similar PGLMM models.

ABMI (6) ARU (1) C (1) CRAN (1) Hungary (2) JOSM (2) PVA (2) PVAClone (1) QPAD (1) R (18) R packages (1) bioacoustics (1) biodiversity (1) birds (2) course (2) data (1) data cloning (4) dclone (3) dependencies (1) detect (2) detectability (1) footprint (3) forecasting (1) functions (3) intrval (3) lhreg (1) mefa4 (1) monitoring (2) pbapply (5) phylogeny (1) plyr (1) poster (2) processing time (2) progress bar (4) publications (2) report (1) sector effects (1) single visit (1) site (1) slides (2) special (3) species (1) trend (1) tutorials (2) video (4)