R/gphys-package.R

In jefferis/gphys: Analyse Electrophysiology Data Acquired by 'Neuromatic' / 'Igor Pro'

#' Analyse electrophysiology data acquired by Neuromatic / Igor Pro
#' 
#' gphys = Greg's ephys (and perhaps gee whiz)
#' 
#' You can use functions such as
#' \code{\link{PlotRasterFromSweeps}} to view spike data. This function and others
#' depend on spike times stored in Igor Pro text files. For details of how to make
#' these files in Igor see:
#' 
#' \url{http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=protocols:analysing_spikes}
#' 
#' Spike times read in from Igor Pro text files by \code{\link{CollectSpikesFromSweeps}}
#' are stored in R a modified list of S3 class \code{spiketimes}.
#' You can add, subset and split these lists - see \code{\link{spiketimes}}
#' and links therein for details.
#' 
#' You can also add continuous traces such as membrane voltage, PID signals etc
#' to your raster plots. See \code{\link{AddLinesToRasterPlot}}.
#' 
#' If you have a mistake in the assignments of your ODD channels (e.g. you were
#' opening channel 27 when you thought you were opening 29) you will likely need
#' to use the function \code{\link{fix.odd}} to make the correct assignments. If
#' you simply want to relabel a channel you can use the \code{relabelfun}
#' argument of \code{\link{PlotRasterFromSweeps}} - see function documentation for
#' examples.
#' 
#' Note that you may find it useful to set e.g.
#' \code{options(gphys.datadir='/Volumes/JData/JPeople/Jonny/physiology/data')}
#' appropriately at the start of a session or in your 
#' \code{\link[=Startup]{.Rprofile}} file. You can then use relative paths to
#' your Igor data folders in the plot functions.
#' 
#' Finally \code{\link{as.repeatedTrain}} provides a bridge to the \code{\link{STAR}}
#' package which includes many spike analysis functions including (smoothed)
#' peristimulus time histograms.
#' 
#' @name gphys-package
#' @aliases gphys
#' @seealso \code{\link{options}, \link{spiketimes}, \link{PlotRasterFromSweeps},
#'   \link{CollectSpikesFromSweeps}}
#' and \code{\link{STAR}} package for further analysis.
#' @docType package
#' @keywords package
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