From a0c2cce48d33b4db971b12ba7d062b86d74b426c Mon Sep 17 00:00:00 2001 From: guiastrennec Date: Sun, 28 Jan 2024 23:00:08 +0000 Subject: [PATCH] Update documentation --- man/read_nm_files.Rd | 4 ++-- man/read_nm_model.Rd | 14 ++++++++++---- man/xpose_data.Rd | 14 ++++++++++---- 3 files changed, 22 insertions(+), 10 deletions(-) diff --git a/man/read_nm_files.Rd b/man/read_nm_files.Rd index 9ec71143..0e9586c9 100755 --- a/man/read_nm_files.Rd +++ b/man/read_nm_files.Rd @@ -33,11 +33,11 @@ Quickly import NONMEM output files into R. } \section{File path generation}{ The rules for model file names generation are - as follow: \itemize{ + as follow: \itemize{ \item with \code{runno}: the full path is generated as \code{/.} e.g. with \code{dir = 'model/pk'}, \code{prefix = 'run'}, \code{runno = '001'}, \code{ext = '.lst'} the - resulting path would be \code{model/pk/run001.lst} + resulting path would be \code{model/pk/run001.lst} \item with \code{file}: the full path is generated as \code{/} e.g. with \code{dir = 'model/pk'}, \code{file = 'run001.lst'} the resulting path would also be diff --git a/man/read_nm_model.Rd b/man/read_nm_model.Rd index 7c727961..3a3ff64c 100755 --- a/man/read_nm_model.Rd +++ b/man/read_nm_model.Rd @@ -9,7 +9,8 @@ read_nm_model( prefix = "run", ext = ".lst", file = NULL, - dir = NULL + dir = NULL, + check_ext = TRUE ) } \arguments{ @@ -19,7 +20,7 @@ combination with \code{prefix} and \code{ext}.} \item{prefix}{Prefix to be used to generate model file name. Used in combination with \code{runno} and \code{ext}.} -\item{ext}{Extension to be used to generate model file name.Should be one of +\item{ext}{Extension to be used to generate model file name. Should be one of '.lst' (default), '.out', '.res', '.mod' or '.ctl' for NONMEM.} \item{file}{Model file name (preferably a '.lst' file) containing the file @@ -27,6 +28,11 @@ extension. Alternative to \code{prefix}, \code{runno} and \code{ext} arguments.} \item{dir}{Location of the model files.} + +\item{check_ext}{Logical, if \code{TRUE} will provide an error message if the +extension of the NONMEM input file is not one of '.lst', '.out', '.res', +'.mod' or '.ctl' for NONMEM. If \code {FALSE} any file extension can be +used.} } \value{ A \code{\link[dplyr]{tibble}} of class \code{model} containing the following columns: @@ -53,11 +59,11 @@ associated with run001.mod. } \section{File path generation}{ The rules for model file names generation are - as follow: \itemize{ + as follow: \itemize{ \item with \code{runno}: the full path is generated as \code{/.} e.g. with \code{dir = 'model/pk'}, \code{prefix = 'run'}, \code{runno = '001'}, \code{ext = '.lst'} the - resulting path would be \code{model/pk/run001.lst} + resulting path would be \code{model/pk/run001.lst} \item with \code{file}: the full path is generated as \code{/} e.g. with \code{dir = 'model/pk'}, \code{file = 'run001.lst'} the resulting path would also be diff --git a/man/xpose_data.Rd b/man/xpose_data.Rd index 8d8e9bf8..21014946 100755 --- a/man/xpose_data.Rd +++ b/man/xpose_data.Rd @@ -15,6 +15,7 @@ xpose_data( simtab = NULL, manual_import = NULL, ignore = NULL, + check_ext = TRUE, extra_files, quiet, ... @@ -27,7 +28,7 @@ combination with \code{prefix} and \code{ext}.} \item{prefix}{Prefix to be used to generate model file name. Used in combination with \code{runno} and \code{ext}.} -\item{ext}{Extension to be used to generate model file name.Should be one of +\item{ext}{Extension to be used to generate model file name. Should be one of '.lst' (default), '.out', '.res', '.mod' or '.ctl' for NONMEM.} \item{file}{Model file name (preferably a '.lst' file) containing the file @@ -55,8 +56,13 @@ in previous versions of xpose, the check the function \item{ignore}{Character vector be used to ignore the import/generation of: 'data', 'files', 'summary' or any combination of the three.} +\item{check_ext}{Logical, if \code{TRUE} will provide an error message if the +extension of the NONMEM input file is not one of '.lst', '.out', '.res', +'.mod' or '.ctl' for NONMEM. If \code {FALSE} any file extension can be +used.} + \item{extra_files}{A vector of additional output file extensions to be -imported. Default is '.ext', '.cov', '.cor', '.phi', ".grd" for NONMEM.} +imported. Default is '.ext', '.cov', '.cor', '.phi', '.grd' for NONMEM.} \item{quiet}{Logical, if \code{FALSE} messages are printed to the console.} @@ -68,11 +74,11 @@ Gather model outputs into a R database } \section{File path generation}{ The rules for model file names generation are - as follow: \itemize{ + as follow: \itemize{ \item with \code{runno}: the full path is generated as \code{/.} e.g. with \code{dir = 'model/pk'}, \code{prefix = 'run'}, \code{runno = '001'}, \code{ext = '.lst'} the - resulting path would be \code{model/pk/run001.lst} + resulting path would be \code{model/pk/run001.lst} \item with \code{file}: the full path is generated as \code{/} e.g. with \code{dir = 'model/pk'}, \code{file = 'run001.lst'} the resulting path would also be