[Zooimage-commits] r243 - pkg/zooimage/man

[noreply at r-forge.r-project.org]

Author: phgrosjean
Date: 2013-12-01 15:04:02 +0100 (Sun, 01 Dec 2013)
New Revision: 243

Added:
   pkg/zooimage/man/import.Rd
Modified:
   pkg/zooimage/man/utilities.Rd
   pkg/zooimage/man/zid.Rd
   pkg/zooimage/man/zooimage.package.Rd
Log:
Wrong path in zidUncompress() and zidUncompressAll() solved. Addition of calcVarsVIS().

Added: pkg/zooimage/man/import.Rd
===================================================================
--- pkg/zooimage/man/import.Rd	                        (rev 0)
+++ pkg/zooimage/man/import.Rd	2013-12-01 14:04:02 UTC (rev 243)
@@ -0,0 +1,47 @@
+\name{import}
+\alias{readFlowCAMctx}
+\alias{readFlowCAMlst}
+\alias{importFlowCAM}
+
+\title{ Function to import data from the FlowCAM }
+\description{
+  These functions read data and metadata from FlowCAM runs and import them into
+  ZooImage objects.
+}
+
+\usage{
+readFlowCAMctx(ctx, stop.it = TRUE)
+readFlowCAMlst(lst, skip = 2, read.ctx = TRUE)
+importFlowCAM(lst)
+}
+
+\arguments{
+  \item{ctx}{ the path to a .ctx FlowCAM file. }
+  \item{stop.it}{ should the process stop in case of an error? Set this to
+    \code{FALSE} when you run in batch mode and want the error to be repported
+	back to the calling code. }
+  \item{lst}{ the path to a .lst FlowCAM file. }
+  \item{skip}{ the number of lines to skip in the .lst table before reading the
+    data. This is usally two lines. }
+  \item{read.ctx}{ should we also read the .ctx file with \code{readFlowCAMctx()}? }
+}
+
+\value{
+  A \code{zidb} object with the converted data, metadata and images.
+}
+
+\details{
+  The Visual Spreadsheet software provided with the FlowCAM is constantly
+  changing specifications from version to version. This is mainly testes with
+  VS 1.5.14.
+}
+
+\author{Philippe Grosjean <Philippe.Grosjean at umons.ac.be>}
+
+\seealso{\code{\link{selectObject}}}
+
+\examples{
+## TODO...
+}
+
+\keyword{ utilities }


Property changes on: pkg/zooimage/man/import.Rd
___________________________________________________________________
Added: svn:executable
   + *

Modified: pkg/zooimage/man/utilities.Rd
===================================================================
--- pkg/zooimage/man/utilities.Rd	2013-09-15 20:08:52 UTC (rev 242)
+++ pkg/zooimage/man/utilities.Rd	2013-12-01 14:04:02 UTC (rev 243)
@@ -6,6 +6,7 @@
 \alias{makeId}
 \alias{addClass}
 \alias{calcVars}
+\alias{calcVarsVIS}
 \alias{dropVars}
 \alias{ecd}
 \alias{parseIni}
@@ -31,6 +32,7 @@
 makeId(ZIDat)
 addClass(ZIDat, ZIobj)
 calcVars(x, drop.vars = NULL, drop.vars.def = dropVars())
+calcVarsVIS(x, drop.vars = NULL, drop.vars.def = dropVars()) 
 dropVars()
 
 ecd(area)
@@ -89,10 +91,10 @@
   element found.
 
   The data.frame with additional columns for calculated variables with
-  \code{calcVars()}. Variables to drop are gathered using \code{dropVars()},
-  altogether with a list provided explicitly in the \code{drop.vars =} argument.
-  The list of variable names to drop automatically and silently can be stored in
-  a variable named \code{ZI.dropVarsDef} or in
+  \code{calcVars()} or \code{calcVarsVIS()}. Variables to drop are gathered
+  using \code{dropVars()}, altogether with a list provided explicitly in the
+  \code{drop.vars =} argument. The list of variable names to drop automatically
+  and silently can be stored in a variable named \code{ZI.dropVarsDef} or in
   \code{options(ZI.dropVarsDef = ....)}.
 
   A vector of numerical values for \code{ecd()}.

Modified: pkg/zooimage/man/zid.Rd
===================================================================
--- pkg/zooimage/man/zid.Rd	2013-09-15 20:08:52 UTC (rev 242)
+++ pkg/zooimage/man/zid.Rd	2013-12-01 14:04:02 UTC (rev 243)
@@ -26,8 +26,8 @@
 zidDatRead(zidfile)
 
 zidUncompress(zidfile, path = dirname(zidfile), delete.source = FALSE)
-zidUncompressAll(path = ".", zidfiles = zidList(path), path.extract = path,
-    skip.existing.dirs = TRUE, delete.source = FALSE)
+zidUncompressAll(path = ".", zidfiles = zidList(path, full.names = TRUE),
+    path.extract = path, skip.existing.dirs = TRUE, delete.source = FALSE)
 
 zidVerify(zidir, type = c("ZI1", "ZI2", "ZI3"), check.vignettes = TRUE)
 zidVerifyAll(path = ".", samples = NULL, type = c("ZI1", "ZI2", "ZI3"),

Modified: pkg/zooimage/man/zooimage.package.Rd
===================================================================
--- pkg/zooimage/man/zooimage.package.Rd	2013-09-15 20:08:52 UTC (rev 242)
+++ pkg/zooimage/man/zooimage.package.Rd	2013-12-01 14:04:02 UTC (rev 243)
@@ -16,8 +16,8 @@
   \tabular{ll}{
     Package: \tab zooimage\cr
     Type: \tab Package\cr
-    Version: \tab 3.0-4\cr
-    Date: \tab 2013-02-12\cr
+    Version: \tab 3.0-6\cr
+    Date: \tab 2013-12-01\cr
     License: \tab GPL 2 or above at your convenience.\cr
   }
   Everytime you publish results that use ZooImage, you must place a reference