Re: [Rd] R CMD check WARNING \usage question

From: Jeff Hamann <jeff.hamann_at_forestinformatics.com>
Date: Fri, 06 Jan 2012 11:48:25 -0800

I know I should provide a better answer, but I think it's really for a function.

For this package, we simply pass a list object about, but have to obfuscate it using a domain familiar nomenclature for the users.

So, not a data set, but a function. I think.

Here's the file in it's entirety:

%% $Id $

\name{sample.data}
\alias{sample.data}

\title{CONIFERS forest growth model sample data}

\description{ A list object of type \code{sample.data} stores all of
the basic information about a \code{\link{data.frame}} object representing a sample of plants.}

\usage{

x <- list( plots=data.frame(), plants=data.frame(), age=0, x0=0.0, n.years.projected=0 ) class(x) <- "sample.data"
}

\details{

	To create the basic data type used in rconifers, you create a
	list object with the following elements (order is not
	important):

\describe{
\item{plots}{is a \link{data.frame} with the the same elements as \code{\link{plots.swo}}.}
\item{plants}{is a \link{data.frame} with the the same elements as \code{\link{plants.swo}}.}
\item{age}{is an integer value that represents the age of the plants,
in years.}
\item{x0}{is the $x_{0}$ coefficient for the Hann and Wang (1990) mortality model.}
\item{n.years.projected}{is the number of years that $x$ has been

        projected forward in time.}
}
}

\references{

Ritchie, M.W. 2008. User's Guide and Help System for CONIFERS: A Simulator for Young Conifer Plantations Version 4.10. See \url{http://www.fs.fed.us/psw/programs/ecology_of_western_forests/projects/conifers/}

}

\author{Jeff D. Hamann \email{jeff.hamann_at_forestinformatics.com},\cr

             Martin W. Ritchie \email{mritchie_at_fs.fed.us} }

\seealso{ \code{\link{plants.smc}},

	     \code{\link{plots.smc}}
	     \code{\link{plants.swo}},
	     \code{\link{plots.swo}},
	     \code{\link{sample.data}},
	     \code{\link{set.species.map}},		  
	     \code{\link{set.variant}},		  
 	     \code{\link{smc}}, 
 	     \code{\link{summary.sample.data}},
	     \code{\link{swo}}, 
	     \code{\link{thin}}

}

\examples{

library( rconifers )

## Example for SWO variant
## set the variant to the SWO variant and set species map
##set.species.map( set.variant(0) )

set.variant(0)

## grow the data that was originally swo in the smc variant # load and display CONIFERS example plots data( plots.swo )
print( plots.swo )

# load and display CONIFERS example plants data( plants.swo )
print( plants.swo )

# create the sample.data list object
sample.swo.3 <- list( plots=plots.swo, plants=plants.swo, age=3, x0=0.0,n.years.projected=0) class(sample.swo.3) <- "sample.data"

}

\keyword{models}

and the WARNING:

Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See the chapter 'Writing R documentation files' in manual 'Writing R Extensions'.
* checking Rd contents ... OK

Respectfully,
Jeff.

Jeff Hamann, PhD
PO Box 1421
Corvallis, Oregon 97339-1421
541-754-2457
jeff.hamann[at]forestinformatics[dot]com jeff.d.hamann[at]gmail[dot]com
http://www.forestinformatics.com
http://en.wikipedia.org/wiki/Forest_informatics

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On Jan 6, 2012, at 11:38 AM, Bryan Hanson wrote:

> Jeff, quick question: is this a data set or a function you are documenting?  What you say sounds like it's data, but the Rd file reads more like a function.  Or are you trying to document a data format/object which stores specific data sets?
> 
> Let us know, and I'll bet the answer will appear pretty quickly. Bryan
> 
> ***********
> Bryan Hanson
> Professor of Chemistry & Biochemistry
> DePauw University
> 
> On Jan 6, 2012, at 2:11 PM, Jeff Hamann wrote:
> 
>> I'm trying to update a package and would like to crush a WARNING message for a clean build. 
>> 
>> I've been struggling with this question and haven't gotten any traction on the web either.
>> 
>> I've got a document file (Rd) that contains the following \usage statement:
>> 
>> \name{sample.data}
>> \alias{sample.data}
>> 
>> \title{CONIFERS forest growth model sample data}
>> 
>> \description{ A list object of type \code{sample.data} stores all of
>> the basic information about a \code{\link{data.frame}} object
>> representing a sample of plants.}
>> 
>> \usage{
>> x <- list( plots=data.frame(), plants=data.frame(), age=0, x0=0.0, n.years.projected=0 )
>> class(x)  <- "sample.data"
>> }
>> 
>> When I run R CMD check [pkg], I get the following WARNING:
>> 
>> * checking Rd \usage sections ... WARNING
>> Assignments in \usage in documentation object 'sample.data':
>> x <- list(plots, plants, age = 0, x0 = 0, n.years.projected = 0)
>> class(x) <- "sample.data"
>> 
>> Functions with \usage entries need to have the appropriate \alias
>> entries, and all their arguments documented.
>> The \usage entries must correspond to syntactically valid R code.
>> See the chapter 'Writing R documentation files' in manual 'Writing R
>> Extensions'.
>> * checking Rd contents ... OK
>> 
>> I'm not sure if there's a problem with the \alias section or the \usage section or both sections (I'm assuming this is the case).
>> 
>> I've read the Chapter 2 of R-ext.pdf plenty and just can't seem to see where I'm blowing it.
>> 
>> Respectfully,
>> Jeff.
>> 
>> 
>> Jeff Hamann, PhD
>> PO Box 1421
>> Corvallis, Oregon 97339-1421
>> 541-754-2457
>> jeff.hamann[at]forestinformatics[dot]com
>> jeff.d.hamann[at]gmail[dot]com
>> http://www.forestinformatics.com
>> http://en.wikipedia.org/wiki/Forest_informatics
>> 
>> To ensure that your email is processed, include a subject entry in your email.
>> 
>> 
>> 
>> 
>> 
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>> 
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> 
> 


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