roxygen2

I have the following file cumsum_bounded.cpp #include <Rcpp.h> using namespace Rcpp; //' Cumulative sum. //' @param x numeric vector //' @param low lower bound //' @param high upper bound //' @param res bounded numeric vector //' @export //' @return bounded numeric vector // [[Rcpp::export]] NumericVector cumsum_bounded(NumericVector x, double low, double high) { NumericVector res(x.size()); double acc = 0; for (int i=0; i < x.size(); ++i) { acc += x[i]; if (acc < low) acc = low; else if (acc > high) acc = high; res[i] = acc; } return res; } I then Build & Reload and test out my new function.

I ran into following problem already multiple times. Say you have two classes, classA and classB described in the following files classA.R : #' the class classA #' #' This is a class A blabla #' \section{Slots}{\describe{\item{\code{A}}{a Character}}} #' @ name classA #' @rdname classA #' @exportClass classA setClass("classA",representation(A="character")) And classB.R #' the class classB #' #' This is a class B blabla #' \section{Slots}{\describe{\item{\code{B}}{an object of class A}}} #' @ name classB #' @rdname classB #' @exportClass classB setClass("classB",representation(B="classA")) I

Suppose I have a function closure in my package, for example f = function(x) { x = x g = function(y) x <<- y h = function() x list(g = g, h = h) } l = f(5) l$g(10) l$h() What is the correct (in the official CRAN sense) way of documenting this function? In particular, I would like to use roxygen2 I would like to provide documentation for the functions g and h One way would be to do something similar to ?family where you document g() and h() in the Value section of the .Rd file. Then provide extended documentation about g() and h() in a bespoke \section{foo} , which you point to in the Value

I am using devtools to build R package, and there are some functions that are NOT designed to be visible to end-users. However, since these functions involve calling C codes by .Call , so that I have to write @useDynLib above the function for automatic generation of .Rd files. In that way, when I build the package, even I did NOT include the @export for those functions, they nonetheless appear in the help document... Is there a way to suppress those functions even if they have been documented? Thanks! alittleboy According to Hadley's comments, use @keywords internal will make the function

I'm trying to document some datasets in an R package using roxygen2. Considering just one of these: I have mypkg/data/CpG.human.GRCh37.RDa which contains an object called CpG.human.GRCh37 and a file called: mypkg/R/cpg-data.R , which contains: #' @name CpG.human.GRCh37 #' @title CpG islands - human - genome build: GRCh37/hg19 #' @description This data set list the genomic locations of human CpG islands, #' with coordinates based on the GRCh37 / hg19 genome build. #' @docType data #' @usage CpG.human.GRCh37 #' @format a \code{RangedData} instance, 1 row per CpG island. #' @source UCSC Table

I am trying to follow closely @hadley's book to learn best practices in writing R packages. And I was thrilled to read these lines about the philosophy of the book: anything that can be automated, should be automated. Do as little as possible by hand. Do as much as possible with functions. So when I was reading about dependencies and the (sort of) confusing differences between import directives in the NAMESPACE file and the "Imports:" field in the DESCRIPTION file, I was hoping that roxygen2 would automatically handle both of them. After all Every package mentioned in NAMESPACE must also be