[R] documenting s4 methods in package

[Duncan Murdoch]

On 4/4/2006 1:58 PM, Steven Lacey wrote:
> Thomas, 
> 
> Correction! If I remove the \seealso line the missing ~~fun~~ disppears
> (thank you!), but now "chm" appears at the end of the line decribing the
> help page building. Most lines do not have that, only "text htm1 latex
> example". What does the chm signify and how does one get rid of it?

"chm" indicates that you have built a compiled HTML version of your man 
page.  It will be shown in Windows if you ask for help after 
options(chmhelp=TRUE).

You can edit the MkRules file to disable production of this kind of help 
page.

Duncan Murdoch
> 
> Thanks,
> Steve 
> 
> -----Original Message-----
> From: Steven Lacey [mailto:slacey at umich.edu] 
> Sent: Tuesday, April 04, 2006 1:54 PM
> To: 'Thomas Lumley'
> Cc: 'r-help at stat.math.ethz.ch'
> Subject: RE: [R] documenting s4 methods in package
> 
> 
> Thomas, 
> 
> If I delete the \seealso section, I still get the same strange behavior.
> Shouldn't removing that line fix the problem?
> 
> Thanks,
> Steve
> 
> -----Original Message-----
> From: Thomas Lumley [mailto:tlumley at u.washington.edu] 
> Sent: Tuesday, April 04, 2006 10:13 AM
> To: Steven Lacey
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] documenting s4 methods in package
> 
> 
> On Tue, 4 Apr 2006, Steven Lacey wrote:
> 
>> Hi,
>>
>> I have written a package that contains many s4 generic functions and
>> associated methods. I am having a lot of trouble getting R to build 
>> the help pages for these generic functions without reporting, "missing 
>> link(s): ~~fun~~, which means that it cannot find the appropriate 
>> function when code in the example section of the help is run. Right?
> 
> No.  It means that you still have \link{~~fun~~} in the \seealso 
> section.
> 
>  	-thomas
> 
> 
>> After some playing around I can get it to build the help without
>> missing a link, but often I am not sure what I have done to correct 
>> the "problem" and it takes a lot of time.
>>
>> For instance, I had the package build the help without missing a
>> function link. I then added a argument to two different functions and 
>> updated the corresponding .rd help files and now when R build the help 
>> pages it reports "missing link(s):  ~~fun~~. What is going on?
>>
>> Below is the code from the help file and the associated s4 method.
>>
>> Any help would be greatly appreciated.
>>
>> Steve
>>
>> GENERIC FUNCTION AND METHODS
>>
>> setGeneric("getRemovedDf.OAD",function(x,y,z,simplify=TRUE,descrip=FAL
>> SE){st
>> andardGeneric("getRemovedDf.OAD")})
>>
>> setMethod("getRemovedDf.OAD","status.or.rm.v1",
>>    function(x,y,z,simplify,descrip){
>>        if(length(0">x at removed) <mailto:x at removed)> >0){
>>            pred <- unlist(lapply(x at removed,function(x)x[1]))
>>            resp <- unlist(lapply(x at removed,function(x)x[2]))
>>            out  <- data.frame(pred,resp)
>>            names(out) <- c(y,z)
>>            return(out)
>>        } else {
>>            return(data.frame())
>>        }
>>    }
>> )
>>
>> setMethod("getRemovedDf.OAD","sa",
>>    function(x,y,z,simplify,descrip){
>>        i <- unlist(lapply(x at outlier.removal,function(x)length(x at removed)))
>>        if(all(i==0)){
>>            return(list())
>>        } else {
>>            if(simplify) x at outlier.removal[seq(along=i)[i==0]]
>> <mailto:x at outlier.removal[seq(along=i)[i==0]]<-NULL> <-NULL
>>            tmp <-
>> lapply(x at outlier.removal,getRemovedDf.OAD,x at predictorName,x at responseName)
>>            if(descrip){
>>                f <- as.data.frame(descrip[!"history"%in%names(x at descrip)])
>>                return(lapply(tmp,function(x)cbind(f,x)))
>>            } else {
>>                return(tmp)
>>            }
>>        }
>>    }
>> )
>>
>>
>> MAN FILE
>> \name{getRemovedDf.OAD}
>> \alias{getRemovedDf.OAD}
>> %- Also NEED an '\alias' for EACH other topic documented here. \title{
>> ~~function to do ... ~~ } \description{
>>  ~~ A concise (1-5 lines) description of what the function does. ~~
>> }
>> \usage{
>> getRemovedDf.OAD(x, y, z, simplify = TRUE, descrip=FALSE)
>> }
>> %- maybe also 'usage' for other objects documented here.
>> \arguments{
>>  \item{x}{ ~~Describe \code{x} here~~ }
>>  \item{y}{ ~~Describe \code{y} here~~ }
>>  \item{z}{ ~~Describe \code{z} here~~ }
>>  \item{simplify}{ ~~Describe \code{simplify} here~~ }
>>  \item{descrip}{ ~~Describe \code{descrip} here~~ }
>> }
>> \details{
>>  ~~ If necessary, more details than the __description__  above ~~
>> }
>> \value{
>>  ~Describe the value returned
>>  If it is a LIST, use
>>  \item{comp1 }{Description of 'comp1'}
>>  \item{comp2 }{Description of 'comp2'}
>>  ...
>> }
>> \references{ ~put references to the literature/web site here ~ }
>> \author{ ~~who you are~~ }
>> \note{ ~~further notes~~ }
>>
>> ~Make other sections like Warning with \section{Warning }{....} ~
>>
>> \seealso{ ~~objects to See Also as \code{\link{~~fun~~}}, ~~~ }
>> \examples{
>> ##---- Should be DIRECTLY executable !! ----
>> ##-- ==>  Define data, use random,
>> ##--    or do  help(data=index)  for the standard data sets.
>>
>> ## The function is currently defined as
>> function(x,y,z,simplify=TRUE,descrip=FALSE){standardGeneric("getRemove
>> dDf.OA
>> D")}
>> }
>> \keyword{ ~kwd1 }% at least one, from doc/KEYWORDS
>> \keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
>>
>>
>> 	[[alternative HTML version deleted]]
>>
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>>
> 
> Thomas Lumley			Assoc. Professor, Biostatistics
> tlumley at u.washington.edu	University of Washington, Seattle
> 
> ______________________________________________
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