Minor documentation improvements

R/ReadIgorBinary.R

@@ -54,14 +54,20 @@
 # 2009-07-09
 # Fixed handling of dates in ReadNclampLogTable
 
-#' Read binary files in the Igor Binary Wave format (IBW) 
-#' @param wavefile Either a character vector containing the path to a file or an R \link{connection} 
-#' @param Verbose Whether to print status information while reading the file
-#' @param ReturnTimeSeries Return as an R time series (package \code{\link{ts}})
-#' @param MakeWave Assign wave to a list in the global user environment
-#' @param HeaderOnly Only return the header of the Igor Wave 
-#' @return returns a vector containing the wave data OR returns the name of a 
-#'  new R vector containing the data which has been made in the user environment
+#' Read binary files in the Igor Binary Wave format (IBW)
+#' 
+#' @param wavefile either a character vector containing the path to a file or an
+#'   R \link{connection}.
+#' @param Verbose if \code{TRUE}, print status information while reading the
+#'   file.
+#' @param ReturnTimeSeries if \code{TRUE}, return as an R time series (package
+#'   \code{\link{ts}}).
+#' @param MakeWave if \code{TRUE}, assign wave to a list in the global user
+#'   environment.
+#' @param HeaderOnly if \code{TRUE}, only return the header of the Igor Wave.
+#' @return A vector containing the wave data or, if \code{MakeWave == TRUE},
+#'   returns the name of a new R vector containing the data which has been made
+#'   in the user environment
 #' @author jefferis
 #' @export
 #' @examples
@@ -72,7 +78,6 @@
 #' # make a list containing the wave's data in the users's environment
 #' wavename=read.ibw(system.file("igor","version5.ibw",package="IgorR"),MakeWave=TRUE) 
 #' sum(get(wavename))
-#' 
 read.ibw<-function(wavefile,Verbose=FALSE,ReturnTimeSeries=FALSE,
     MakeWave=FALSE,HeaderOnly=FALSE){
   if (is.character(wavefile)) {
@@ -117,32 +122,33 @@ read.ibw<-function(wavefile,Verbose=FALSE,ReturnTimeSeries=FALSE,
 
 #' Reads an Igor Pro Packed Experiment (.pxp) file
 #' 
-#' Note that pxp files are only partially documented so some contents cannot be 
+#' Note that PXP files are only partially documented so some contents cannot be 
 #' parsed (e.g. image data). This function currently reads data records (Igor 
-#' waves and variables), history, procedures, recreation macros and plain text
+#' waves and variables), history, procedures, recreation macros and plain text 
 #' notebooks. Formatted notebooks cannot be read.
 #' 
 #' \code{IgorPlatform} will determine in which encoding text is read 
 #' (WINDOWS-1252 for windows and macintosh for macintosh). Unique abbreviations 
-#' are acceptable. Defaults to "windows" on windows, "macintosh" otherwise. Note
-#' that Igor Pro 5.5 added a PlatformRecord to the pxp file format which is used
-#' to determine the file's platform of origin when available. Since this is 
-#' informatino straight from the horse's mouth it will override the 
-#' \code{IgorPlatform} argument.
-#' @param pxpfile Character vector naming a PXP file or an R \link{connection}
-#' @param regex only read records (e.g. waves) in the pxp file whose names match
-#'   a \link{regex}
-#' @param ReturnTimeSeries Igor waves are returned as a ts object with  sensible
-#'   x scaling (FALSE by default)
+#' are acceptable. Defaults to \code{"windows"} on Windows, \code{"macintosh"}
+#' otherwise. Note that Igor Pro 5.5 added a PlatformRecord to the PXP file
+#' format which is used to determine the file's platform of origin when
+#' available. Since this is information straight from the horse's mouth it will
+#' override the \code{IgorPlatform} argument.
+#' @param pxpfile character vector naming a PXP file or an R \link{connection}.
+#' @param regex if \code{TRUE}, only read records (e.g. waves) in the PXP file
+#'   whose names match a \link{regex}.
+#' @param ReturnTimeSeries if \code{TRUE}, Igor waves are returned as a
+#'   \code{link{ts}} object with sensible x scaling (\code{FALSE} by default).
 #' @param Verbose whether to print information to console during loading 
-#'   (numeric values are also allowed 0=none, 1=basic, 2=all)
-#' @param StructureOnly TODO Only the structure of the pxp file for inspection
-#' @param ExtractText Whether to extract procedures, recreation macros, history 
-#'   and plain text notebooks (FALSE by default)
-#' @param IgorPlatform OS on which Igor file was saved (windows or macintosh)
-#' @param ... Optional parameters passed to \link{read.ibw}
-#' @return A list containing all the individual waves or variables in the pxp 
-#'   file
+#'   (numeric values are also allowed 0=none, 1=basic, 2=all).
+#' @param StructureOnly (TODO) if \code{TRUE}, only the structure of the PXP
+#'   file for inspection.
+#' @param ExtractText whether to extract procedures, recreation macros, history 
+#'   and plain text notebooks (\code{FALSE} by default).
+#' @param IgorPlatform OS on which Igor file was saved (windows or macintosh).
+#' @param ... optional parameters passed to \link{read.ibw}.
+#' @return A list containing all the individual waves or variables in the PXP 
+#'   file.
 #' @author jefferis
 #' @export
 #' @import bitops

R/ReadNclamp.R

@@ -6,9 +6,9 @@
 #' log tables are special Igor .pxp files that contain only variables.
 #' Each entry corresponds to a single run of an Nclamp protocol, 
 #' storing information like protocol name, run time etc.  
-#' @param f Path to the log file
-#' @param Verbose Whether to print status information while reading the file
-#' @return A dataframe containing a row for each acquisition protocol run
+#' @param f path to the log file.
+#' @param Verbose whether to print status information while reading the file.
+#' @return A dataframe containing a row for each acquisition protocol run.
 #' @author jefferis
 #' @export
 ReadNclampLogTable<-function(f,Verbose=FALSE){
@@ -44,16 +44,17 @@ ReadNclampLogTable<-function(f,Verbose=FALSE){
   d
 }
 
-#' Read all Nclamp log tables from a directory into a list 
-#' @param logfiledir Path to directory containing log files (pxp files)
-#' @param pattern Optional regular expression - see \code{\link{list.files}}
-#' @param ... additional parameters for ReadNclampLogTable
-#' @return named list containing one dataframe for each parsed log file
+#' Read all Nclamp log tables from a directory into a list
+#' 
+#' @param logfiledir path to directory containing log files (pxp files).
+#' @param pattern optional regular expression -- see \code{\link{list.files}}.
+#' @param ... additional parameters for \code{\link{ReadNclampLogTable}}.
+#' @return A named list containing one dataframe for each parsed log file.
 #' @author jefferis
 #' @export
 #' @examples
 #' \dontrun{
-#' ReadAllNclampLogTables("/GD/projects/PhysiologyData/logs")
+#' logfiles <- ReadAllNclampLogTables("/GD/projects/PhysiologyData/logs")
 #' str(logfiles)
 #' }
 ReadAllNclampLogTables<-function(logfiledir,pattern="_log[0-9]+[.]pxp$",...){
@@ -81,17 +82,18 @@ ReadAllNclampLogTables<-function(logfiledir,pattern="_log[0-9]+[.]pxp$",...){
 #' Extract summary information from an Nclamp/Igor Sweep File
 #' 
 #' e.g. for import into Physiology database
-#' @param f path to an Nclamp/Igor pxp format sweep file
-#' @param Verbose print details while parsing underlying pxp file
-#' @return a list of about 25 fields summarising the sweep file 
+#' @param f path to an Nclamp/Igor PXP format sweep file.
+#' @param Verbose if \code{TRUE}, print details while parsing underlying PXP
+#'   file.
+#' @return A list of about 25 fields summarising the sweep file.
 #' @author jefferis
 #' @export
 #' @import tools
 #' @examples
-#' l=SummariseSweepFile(system.file("igor","WedJul407c2_001.pxp",package="IgorR"))
-#' cat("There are",l$NumWaves,"waves in the file each of total duration",l$StimWaveLength,
-#'  "ms and sample duration",l$StimSampleInterval,"ms \n") 
-SummariseSweepFile<-function(f,Verbose=F){
+#' l <- SummariseSweepFile(system.file("igor", "WedJul407c2_001.pxp", package="IgorR"))
+#' cat("There are", l$NumWaves, "waves in the file each of total duration", l$StimWaveLength, 
+#'  "ms and sample duration", l$StimSampleInterval, "ms \n") 
+SummariseSweepFile<-function(f,Verbose=FALSE){
   s=read.pxp(f,Verbose=Verbose)
 
   fileinfo=file.info(f)
@@ -120,9 +122,9 @@ SummariseSweepFile<-function(f,Verbose=F){
 #' Summarise multiple sweep files into a single dataframe
 #' 
 #' Note that this is still a little fragile if the lists produced by 
-#' SummariseSweepFile do not have consistent field names
-#' @param ff paths to a set of sweep files 
-#' @return dataframe with rows for each sweep file  
+#' \code{\link{SummariseSweepFile}} do not have consistent field names.
+#' @param ff paths to a set of sweep files.
+#' @return A dataframe with rows for each sweep file.
 #' @author jefferis
 #' @seealso SummariseSweepFile
 #' @export
@@ -137,13 +139,14 @@ SweepFilesToDataFrame<-function(ff){
   do.call(rbind,lapply(ll,as.data.frame,stringsAsFactors=FALSE))
 }
 
-#' Update the csv file summarising the sweeps in an Nclamp data folder
+#' Update the CSV file summarising the sweeps in an Nclamp data folder
 #' 
-#' @param folder Path to the folder
-#' @param outfile Path to outfile (default: /path/to/datafolder/datafolder.csv) 
-#' @param action TODO update newer (default) or force update (not implemented)
-#' @param DryRun Report which files would be processed, but do nothing
-#' @return TRUE if something happened, FALSE otherwise
+#' @param folder path to the folder.
+#' @param outfile path to outfile (default: \code{/path/to/datafolder/datafolder.csv}).
+#' @param action update newer (default) or force update (not yet implemented).
+#' @param DryRun if \code{TRUE}, report which files would be processed, but do
+#'   nothing.
+#' @return \code{TRUE} if something happened, \code{FALSE} otherwise.
 #' @author jefferis
 #' @export
 UpdateSweepDataFrame<-function(folder,outfile=NULL,action=c("update","force"),DryRun=FALSE){

man/ReadAllNclampLogTables.Rd

@@ -5,24 +5,25 @@
 ReadAllNclampLogTables(logfiledir, pattern = "_log[0-9]+[.]pxp$", ...)
 }
 \arguments{
-  \item{logfiledir}{Path to directory containing log files
-  (pxp files)}
+  \item{logfiledir}{path to directory containing log files
+  (pxp files).}
 
-  \item{pattern}{Optional regular expression - see
-  \code{\link{list.files}}}
+  \item{pattern}{optional regular expression -- see
+  \code{\link{list.files}}.}
 
-  \item{...}{additional parameters for ReadNclampLogTable}
+  \item{...}{additional parameters for
+  \code{\link{ReadNclampLogTable}}.}
 }
 \value{
-named list containing one dataframe for each parsed log
-file
+A named list containing one dataframe for each parsed log
+file.
 }
 \description{
 Read all Nclamp log tables from a directory into a list
 }
 \examples{
 \dontrun{
-ReadAllNclampLogTables("/GD/projects/PhysiologyData/logs")
+logfiles <- ReadAllNclampLogTables("/GD/projects/PhysiologyData/logs")
 str(logfiles)
 }
 }

man/ReadNclampLogTable.Rd

@@ -5,14 +5,14 @@
 ReadNclampLogTable(f, Verbose = FALSE)
 }
 \arguments{
-  \item{f}{Path to the log file}
+  \item{f}{path to the log file.}
 
-  \item{Verbose}{Whether to print status information while
-  reading the file}
+  \item{Verbose}{whether to print status information while
+  reading the file.}
 }
 \value{
 A dataframe containing a row for each acquisition protocol
-run
+run.
 }
 \description{
 log tables are special Igor .pxp files that contain only

man/SummariseSweepFile.Rd

@@ -2,24 +2,24 @@
 \alias{SummariseSweepFile}
 \title{Extract summary information from an Nclamp/Igor Sweep File}
 \usage{
-SummariseSweepFile(f, Verbose = F)
+SummariseSweepFile(f, Verbose = FALSE)
 }
 \arguments{
-  \item{f}{path to an Nclamp/Igor pxp format sweep file}
+  \item{f}{path to an Nclamp/Igor PXP format sweep file.}
 
-  \item{Verbose}{print details while parsing underlying pxp
-  file}
+  \item{Verbose}{if \code{TRUE}, print details while
+  parsing underlying PXP file.}
 }
 \value{
-a list of about 25 fields summarising the sweep file
+A list of about 25 fields summarising the sweep file.
 }
 \description{
 e.g. for import into Physiology database
 }
 \examples{
-l=SummariseSweepFile(system.file("igor","WedJul407c2_001.pxp",package="IgorR"))
-cat("There are",l$NumWaves,"waves in the file each of total duration",l$StimWaveLength,
- "ms and sample duration",l$StimSampleInterval,"ms \\n")
+l <- SummariseSweepFile(system.file("igor", "WedJul407c2_001.pxp", package="IgorR"))
+cat("There are", l$NumWaves, "waves in the file each of total duration", l$StimWaveLength,
+ "ms and sample duration", l$StimSampleInterval, "ms \\n")
 }
 \author{
 jefferis

man/SweepFilesToDataFrame.Rd

@@ -5,15 +5,15 @@
 SweepFilesToDataFrame(ff)
 }
 \arguments{
-  \item{ff}{paths to a set of sweep files}
+  \item{ff}{paths to a set of sweep files.}
 }
 \value{
-dataframe with rows for each sweep file
+A dataframe with rows for each sweep file.
 }
 \description{
 Note that this is still a little fragile if the lists
-produced by SummariseSweepFile do not have consistent field
-names
+produced by \code{\link{SummariseSweepFile}} do not have
+consistent field names.
 }
 \author{
 jefferis

man/UpdateSweepDataFrame.Rd

@@ -1,27 +1,27 @@
 \name{UpdateSweepDataFrame}
 \alias{UpdateSweepDataFrame}
-\title{Update the csv file summarising the sweeps in an Nclamp data folder}
+\title{Update the CSV file summarising the sweeps in an Nclamp data folder}
 \usage{
 UpdateSweepDataFrame(folder, outfile = NULL, action = c("update", "force"),
   DryRun = FALSE)
 }
 \arguments{
-  \item{folder}{Path to the folder}
+  \item{folder}{path to the folder.}
 
-  \item{outfile}{Path to outfile (default:
-  /path/to/datafolder/datafolder.csv)}
+  \item{outfile}{path to outfile (default:
+  \code{/path/to/datafolder/datafolder.csv}).}
 
-  \item{action}{TODO update newer (default) or force update
-  (not implemented)}
+  \item{action}{update newer (default) or force update (not
+  yet implemented).}
 
-  \item{DryRun}{Report which files would be processed, but
-  do nothing}
+  \item{DryRun}{if \code{TRUE}, report which files would be
+  processed, but do nothing.}
 }
 \value{
-TRUE if something happened, FALSE otherwise
+\code{TRUE} if something happened, \code{FALSE} otherwise.
 }
 \description{
-Update the csv file summarising the sweeps in an Nclamp
+Update the CSV file summarising the sweeps in an Nclamp
 data folder
 }
 \author{

man/read.ibw.Rd

@@ -6,25 +6,25 @@ read.ibw(wavefile, Verbose = FALSE, ReturnTimeSeries = FALSE,
   MakeWave = FALSE, HeaderOnly = FALSE)
 }
 \arguments{
-  \item{wavefile}{Either a character vector containing the
-  path to a file or an R \link{connection}}
+  \item{wavefile}{either a character vector containing the
+  path to a file or an R \link{connection}.}
 
-  \item{Verbose}{Whether to print status information while
-  reading the file}
+  \item{Verbose}{if \code{TRUE}, print status information
+  while reading the file.}
 
-  \item{ReturnTimeSeries}{Return as an R time series
-  (package \code{\link{ts}})}
+  \item{ReturnTimeSeries}{if \code{TRUE}, return as an R
+  time series (package \code{\link{ts}}).}
 
-  \item{MakeWave}{Assign wave to a list in the global user
-  environment}
+  \item{MakeWave}{if \code{TRUE}, assign wave to a list in
+  the global user environment.}
 
-  \item{HeaderOnly}{Only return the header of the Igor
-  Wave}
+  \item{HeaderOnly}{if \code{TRUE}, only return the header
+  of the Igor Wave.}
 }
 \value{
-returns a vector containing the wave data OR returns the
-name of a new R vector containing the data which has been
-made in the user environment
+A vector containing the wave data or, if \code{MakeWave ==
+TRUE}, returns the name of a new R vector containing the
+data which has been made in the user environment
 }
 \description{
 Read binary files in the Igor Binary Wave format (IBW)