I’m in the process of preparing a package for CRAN.
The package is called “exportR” and since it really just consists of one
function, I found it natural to call it “exportR” too.
The function returns a function that does the actual job, but it is set up to
work in different ways, depending on the arguments given to its creator. In
short:
library( exportR )
exporter <- exportR( the, arguments )
exporter( its, own, arguments )
When I run R CMD check I get two warnings:
-----------------
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'exportR' but not in
code:
exporter
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'exportR':
exporter <- exportR(fname, type = "latex", format = "4", prefix = "",
append = FALSE)
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 the ‘Writing R
Extensions’ manual.
————————
The first warning I understand, but I don’t know how to proceed to rid myself
of it. Indeed it is nowhere in my code, as exportR creates it, but I still need
to document it. I would very much appreciate advice.
The second warning I don’t understand. I do have both \name{exportR} and
\alias{exportR} (as well as \alias{exporter}) at the top of the .Rd file. The
function name, arguments, and default values are copied directly from the
source, so they are identical. I changed the package name to exporteR to see if
the problem was that the package name and the function name were the same, but
that did not remove the warning. I used package.skeleton to create a .Rd
template for the function and it was syntactically identical. Installing the
package and running it works, obviously. I’m running out of ideas and any help
is appreciated. I have this nagging feeling that I’m missing something obvious…?
I post the entire contents of the .Rd file at the bottom.
Best regards,
Peder Axensten
Research engineer
Swedish University of Agricultural Sciences
Department of Forest Resource Management
Remote Sensing
SE-901 83 Umeå
Visiting address: Skogsmarksgränd
Phone: +46 90 786 85 00
peder.axens...@slu.se, www.slu.se/srh
The Department of Forest Resource Management is environmentally certified in
accordance with ISO 14001.
——————————————————————————————————
\name{exportR}
\alias{exportR}
\alias{export}
\alias{exporter}
\alias{latex}
\alias{conversion}
\alias{exportR.latex}
\title{Easy export of R results}
\description{A flexible and simple way to export R results to LaTeX and [maybe
later] other formats.}
\usage{
exporter <- exportR( fname, type="latex", format="4", prefix="", append=FALSE )
exporter( ..., format=NA, prefix=NA, named=FALSE )
}
\arguments{
\item{...}{The value[s] to be exported. To name them, use the normal R
convention: \code{exporter(first=123, second=456)}. If no such name is given,
the variable name is used: \code{exporter(myvar, second=456)}. For other
expressions the naming is undetermined, be sure to name them:
\code{exporter(myname=2*pi/sqrt(2))}. Non-valid characters will be substituted
by \code{x}, i.e. \code{my_var1} will result in \code{\\myxvarx} in LaTeX.}
\item{fname}{The path to the destination file.}
\item{type}{The name of export file type, e.g. \code{exporter}. May be
a string vector to export to more than one format at once. But presently, only
\code{exporter} is implemented.}
\item{format}{The numerical format to use. When given to
\code{exportR}, it sets the default \code{.format} to be used by
\code{exporter}. When used in a call to \code{exporter}, it is used for the
present value[s]. The number suffix is the number of significant digits to use.
The formats are: \tabular{llll}{
\tab Format \tab
Example \tab \cr
sprintf expression \tab \%<expr.> \tab \%.5e
\tab 10000*pi -> 3.14159*10^4\cr
flexible \tab <n> \tab 8
\tab 10000*pi -> 31415.927\cr
integer \tab i
\tab i \tab 10000*pi -> 31415\cr
float \tab f<n> \tab f4
\tab 10000*pi -> 3.142*10^4\cr
float, factor 3 exponent \tab e<n> \tab e4
\tab 10000*pi -> 31.42*10^3\cr
float, with suffix \tab s<n> \tab s4
\tab 10000*pi -> 31.42 k\cr
float, with 2^10 suffix \tab b<n> \tab b3
\tab 10000*pi -> 12.06 Ki\cr
fraction \tab d or d<n> \tab d6
\tab pi -> 1146408/364913\cr
fraction, with integer \tab D or D<n> \tab D6
\tab pi -> 3+51669/364913\cr
}
}
\item{prefix}{If a naming prefix is to be used. When given to
\code{exportR}, it sets the default \code{.prefix} to be used by
\code{exporter}. When used in a call to \code{exporter}, it is used for the
present and following value[s].}
\item{append}{If \code{TRUE}, values will be appended to the
\code{fname} file, instead of rewriting it.}
\item{named}{If \code{TRUE}, the row names of a 2-d data structure
(i.e. a \code{data.frame}) will be included as the first column. if
\code{TRUE}, the item names of a 1-d data structure (i.e. a \code{list}) will
be included.}
}
\details{
It's actually the function returned by \code{exportR} that does the job, so
typically \code{exportR} is called only once. But more than one such function
can be active at the same time.
When the returned function (called \code{exporter}, above) is created, a header
is written to the file \code{fname}. During subsequent calls, actual values are
appended to the file.
Presently, the following classes are recognized: \code{NULL}, \code{logical}
(including \code{NA}), \code{character}, \code{factor}, \code{call} (it's
evaluated through \code{eval}), \code{numeric} (including \code{INF} and
\code{NaN}), \code{complex} (including \code{INF}), \code{matrix},
\code{array}, \code{list}, \code{pairlist}, \code{table}, \code{data.frame},
\code{lm}, \code{randomForest}, \code{randomForest.formula}, \code{ts},
\code{bigz} and \code{bigq} from package \code{gmp}, \code{int64} and
\code{uint64} from package \code{int64}, and \code{integer64} from package
\code{bit64}. Other classes are processed with \code{as.character( value )}.
Table-like structures defines three commands for each structure:
\code{nameColumns,} that can be used as a column-format,
\code{nameHeader,} contains the column names, and
\code{nameBody} contains the actual table contents.
Example: \code{\\begin{tabular}{\\nameColumns}\\nameHeader\\hline
\\nameBody\\end{tabular}}
Some structures, like \code{lm}, may define even more variants. Try, and see
what is generated!
Support for more classes can be implemented by defining functions
\code{as.exportR.<your-class>}. Call \code{as.exportR} on each item in your
class to get the correct output. See \code{as.exportR.lm} in file \code{R/exportR.R}
as an example on how to do this.
Output formats presently supported: only \code{LaTeX}. Support for more formats can
be implemented by writing a function \code{exportR.<your-format>} in the same
manner as \code{exportR.latex}, present in the file \code{R/latexR.R}.
}
\value{
\code{exportR} returns a function that is used to output formatted values.
This [returned] function returns no value, when called.
}
\author{Peder Axensten}
\examples{
library(exporteR)
ltx <- exportR( tempfile( pattern = "test", fileext = ".tex" ) )
x <- 2*pi
ltx(x) # Writes \newcommand{\x}{6.283}
ltx(two_pi=2*pi) # Writes \newcommand{\twoxpi}{6.283}
# Alternatively, in one go:
ltx(x, two_pi=2*pi)
}
\keyword{export}
\keyword{latex}
\keyword{utilities}
\keyword{conversion}
——————————————————————————————————
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