[Zooimage-commits] r176 - in pkg/zooimage: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jul 3 09:53:58 CEST 2009
Author: kevin
Date: 2009-07-03 09:53:57 +0200 (Fri, 03 Jul 2009)
New Revision: 176
Added:
pkg/zooimage/man/RealTime.Rd
Modified:
pkg/zooimage/R/capabilities.R
pkg/zooimage/R/zzz.r
Log:
Small fine-tunings
Modified: pkg/zooimage/R/capabilities.R
===================================================================
--- pkg/zooimage/R/capabilities.R 2009-07-02 11:51:45 UTC (rev 175)
+++ pkg/zooimage/R/capabilities.R 2009-07-03 07:53:57 UTC (rev 176)
@@ -32,7 +32,7 @@
#' utility that checks if the zip program is available
checkZipAvailable <- function( ){
checkCapabilityAvailable( "zip",
- sprintf('"%s" -h %s', ZIpgm("zip", "misc"), if( !isWin() ) " > /dev/null" ),
+ sprintf('"%s" -h %s', ZIpgm("zip", "misc"), if( !isWin() ) " > /dev/null" else "" ),
"zip - program from Info-Zip not found!" )
}
# }}}
@@ -40,7 +40,7 @@
#{{{ checkUnzipAvailable
checkUnzipAvailable <- function( ){
checkCapabilityAvailable( "unzip",
- sprintf('"%s" -h %s', ZIpgm("unzip", "misc"), if( !isWin() ) " > /dev/null" ),
+ sprintf('"%s" -h %s', ZIpgm("unzip", "misc"), if( !isWin() ) " > /dev/null" else "" ),
"unzip - program from Info-Zip not found!" )
}
#}}}
@@ -48,7 +48,7 @@
#{{{ checkZipnoteAvailable
checkZipnoteAvailable <- function( ){
checkCapabilityAvailable( "zipnote",
- sprintf('"%s" -h %s', ZIpgm("zipnote", "misc"), if( !isWin() ) " > /dev/null" ),
+ sprintf('"%s" -h %s', ZIpgm("zipnote", "misc"), if( !isWin() ) " > /dev/null" else "" ),
"zipnote - program from Info-Zip not found!" )
}
# }}}
@@ -137,7 +137,7 @@
#{{{ checkCapabilityAvailable
checkCapabilityAvailable <- function( cap, cmd, msg ){
- program <- cap
+ program <- cap
if( program == "dc_raw" && !isWin() ) {
program <- "dcraw"
}
@@ -161,7 +161,7 @@
# and we do not want this warning to be captured by our
# error trapping
ok <- if( isWin() ){
- system(cmd, invisible = TRUE) == 0
+ system(cmd, invisible = TRUE) == 0
} else {
length(
system( sprintf( " which %s 2> /dev/null" , program ), intern = TRUE )
Modified: pkg/zooimage/R/zzz.r
===================================================================
--- pkg/zooimage/R/zzz.r 2009-07-02 11:51:45 UTC (rev 175)
+++ pkg/zooimage/R/zzz.r 2009-07-03 07:53:57 UTC (rev 176)
@@ -19,7 +19,8 @@
# {{{ Loading ZooImage
".onAttach" <- function(libname, pkgname) {
- # {{{ check package dependencies
+
+ # {{{ check package dependencies
(require(utils) || stop("Package 'utils' is required!"))
(require(svMisc) || stop("Package 'svMisc' from SciViews bundle is required!"))
(require(svWidgets) || stop("Package 'svWidgets' is required!"))
@@ -29,9 +30,8 @@
# {{{ check capabilities
checkZipAvailable()
- checkUnzipAvailable()
+ checkUnzipAvailable()
checkZipnoteAvailable()
- # }}}
# {{{
if (!interactive()) options(ZIAssistant = FALSE)
Added: pkg/zooimage/man/RealTime.Rd
===================================================================
--- pkg/zooimage/man/RealTime.Rd (rev 0)
+++ pkg/zooimage/man/RealTime.Rd 2009-07-03 07:53:57 UTC (rev 176)
@@ -0,0 +1,138 @@
+\name{RealTime}
+\alias{read.lst}
+\alias{predict.ZIClass.Real.Time}
+\alias{Biomass}
+\alias{hist.spectrum}
+\alias{loop.opts}
+\alias{SampleCurrent}
+\alias{CompaSamplePrev}
+\alias{CompaSampleList}
+\alias{process}
+\alias{plotLines}
+\alias{Export}
+\alias{SelectGroups}
+\alias{SmpToComp}
+\alias{save.loop.res}
+\alias{tclFun_}
+\alias{loopAsynch}
+
+\title{ The ZooImage Real time recognition functions for FlowCAM parameters }
+\description{
+ These functions allow the user to recognize in near real time partciles digitized with the FlowCAM.
+ Some functions are currently developed for the AMORE III project.
+}
+
+\usage{
+read.lst(x, skip = 2)
+predict.ZIClass.Real.Time(object, ZIDat, calc.vars = TRUE, class.only = FALSE, type = "class", na.rm = NULL, ...)
+Biomass(tab)
+hist.spectrum(spect, breaks = seq(0.05, 0.6, by = 0.05),
+ width = 0.1, xlab = "classes (mm)", ylab = "log(abundance + 1)", main = "",
+ ylim = c(0, 10))
+loop.opts(lst = ".",
+ classif = ZIC,
+ type = NULL,
+ SizeThreshold = NULL,
+ Export_Collages = NULL,
+ ZIprevSmp = NULL,
+ ZIlist = NULL,
+ Abd.all = TRUE,
+ Abd.gp = NULL,
+ Spec.all = NULL,
+ Spec.gp = NULL,
+ Bio.all = NULL,
+ Bio.gp = NULL,
+ breaks = seq(0.05, 3, by = 0.1),
+ conv = ".",
+ ZICompAbd = NULL,
+ ZICompSpectra = NULL,
+ ZICompBiomass = NULL,
+ ZICompSlope = NULL,
+ ZICompAbd.gp = NULL,
+ ZICompBio.gp = NULL
+ )
+SampleCurrent()
+CompaSamplePrev()
+CompaSampleList()
+process()
+plotLines()
+Export()
+SelectGroups(ZIC)
+SmpToComp(Prev = NULL, Samples = NULL, Table = NULL)
+save.loop.res(lst, Classif, breaks = seq(0.25, 2, by = 0.1), conv = c(1, 0, 1), save.dir = NULL)
+tclFun_(f, name = deparse(substitute(f)))
+loopAsynch()
+}
+
+\arguments{
+ \item{x}{ a connection or a character string giving the name of the 'list' file to read. }
+ \item{skip}{ number of row to skip in the 'list' file. }
+ \item{object}{ the classifier to use for automatic recognition (ZIClass object). }
+ \item{ZIDat}{data.frame of the 'list' file which contains measurements made by the FlowCAM. }
+ \item{calc.vars}{ If \code{TRUE}, A function to use to calculate variables from the original data frame. }
+ \item{class.only}{ If \code{TRUE}, return a vector with classification, otherwise, return a 'ZIDat' object with 'Ident' column appended to it. }
+ \item{type}{ If \code{"prob"}, return probabilities only if random Forest is the used algorithm, else only classes are returned }
+ \item{na.rm}{ If \code{TRUE}, rows with NA values are not classified by the algorithm }
+ \item{tab}{ a data.frame resulting of the automatic recognition with a 'Ident' column }
+ \item{spect}{ vector of log transformed abundance of particles per size classes }
+ \item{breaks}{ Limits for the classes where to break the spectrum }
+ \item{width}{ width of bars on the barplot }
+ \item{xlab}{ legend of x axis }
+ \item{ylab}{ Legend of y axis }
+ \item{main}{ General legend of the barplot }
+ \item{ylim}{ numeric vector of y axis limits }
+ \item{lst}{ a connection or a character string giving the name of the 'list' file to read. }
+ \item{classif}{ the classifier to use for automatic recognition (ZIClass object). }
+ \item{type}{ If \code{"NULL"} barplot are provided, else \code{"l"} lines are provided -- not implemented yet --. }
+ \item{SizeThreshold}{ Size threshold in microns to filter particles, if \code{"NULL"} no size threshold is applied -- not implemented yet --. }
+ \item{Export_Collages}{ number of collages to copy in artificial subsamples, if \code{"NULL"} no artificial subsample created -- not implemented yet --. }
+ \item{ZIprevSmp}{ a connection or a character string giving the name of the 'list' file to compare, else \code{"NULL"} no comparison. }
+ \item{ZIlist}{ a list of character strings giving the name of the 'list' files to compare, else \code{"NULL"} no comparison. }
+ \item{Abd.all}{ If \code{"TRUE"} only total relative abundance is measured on the current sample, else \code{"NULL"}. }
+ \item{Abd.gp}{ a character vector with names of groups to compare in relative abundance, else \code{"NULL"}. }
+ \item{Spec.all}{ If \code{"TRUE"} only total size spectra is provided for the current sample, else \code{"NULL"}. }
+ \item{Spec.gp}{ a character vector with names of groups to compare in size spectra, else \code{"NULL"}. }
+ \item{Bio.all}{ If \code{"TRUE"} only total biomass is provided for the current sample, else \code{"NULL"}. }
+ \item{Bio.gp}{ a character vector with names of groups to compare in relative abundance, else \code{"NULL"}. }
+ \item{conv}{ Conversion parameters :a table with 4 column: group and the 3 parameters per group. }
+ \item{ZICompAbd}{ If \code{"TRUE"} only total relative abundance is compared between the current sample and other(s), else \code{"NULL"}. }
+ \item{ZICompSpectra}{ If \code{"TRUE"} only total size spectra is compared between the current sample and other(s), else \code{"NULL"}. }
+ \item{ZICompBiomass}{ If \code{"TRUE"} only total biomass is compared between the current sample and other(s), else \code{"NULL"}. }
+ \item{ZICompSlope}{ If \code{"TRUE"} slope of log transformed size spectra are compared between the current sample and other(s), else \code{"NULL"}. }
+ \item{ZICompAbd.gp}{ a character vector with names of groups to compare in relative abundance between the current sample and other(s), else \code{"NULL"}. }
+ \item{ZICompBio.gp}{ a character vector with names of groups to compare in relative biomass between the current sample and other(s), else \code{"NULL"}. }
+ \item{ZIC}{ a classifier (ZIClass object). }
+ \item{Prev}{ a connection or a character string giving the name of the 'list' file to compare. }
+ \item{Samples}{ a connection or a character string giving the name of the directory containing samples to compare. }
+ \item{Table}{ a connection or a character string giving the name table to compare -- not implemented yet --. }
+ \item{Classif}{ the classifier to use for automatic recognition (ZIClass object). }
+ \item{save.dir}{ a connection or a character string giving the name of the directory to save the results. }
+}
+
+\value{
+ \code{read.lst()} is called to read a 'list' file at regular interval.
+ \code{predict.ZIClass.Real.Time()} is used to recognize the read 'list' file at regular interval.
+ \code{Biomass()} is used to calculate biomass of a sample.
+ \code{hist.spectrum()} is used to calculate barplot of log transformed size spectra.
+ \code{loop.opts()} is used to provide argument to the loop applied at regular interval.
+ \code{SampleCurrent()} is used to analyze the current sample in near-real time.
+ \code{CompaSamplePrev()} is used to analyze and compare the current sample with one sample already digitized in near-real time.
+ \code{CompaSampleList()} is used to analyze and compare the current sample with several samples already digitized in near-real time.
+ \code{process()} is used to recognize the current sample in near-real time.
+ \code{plotLines()} is used to plot abundance of the current sample in near-real time on line graph. -- currently developed --
+ \code{Export()} is used to create artificial sub sample for transect. -- currently developed --
+ \code{SelectGroups()} is used to select groups to plot.
+ \code{SmpToComp()} is used to select the sample to compare with the current sample.
+ \code{save.loop.res()} is used to save results of the automatic recognition of the current sample.
+ \code{tclFun_()} is used to control the loop.
+ \code{loopAsynch()} is the loop which applies functions for the real time recogntion.
+}
+
+\author{ Kevin Denis <Kevin.Denis at umons.ac.be> and Philippe Grosjean <Philippe.Grosjean at umons.ac.be> }
+
+\seealso{ \code{\link{Bio.sample}} }
+\examples{
+# TO DO
+#
+}
+\keyword{ iteration }
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