Renewed documentation

DESCRIPTION

 Package: RMassBank
 Type: Package
 Title: Workflow to process tandem MS files and build MassBank records
-Version: 2.0.1
+Version: 2.0.2
 Authors@R: c(
     person(given = "RMassBank at Eawag", email = "massbank@eawag.ch",
     role=c("cre")),

NAMESPACE

 # Generated by roxygen2 (4.1.1): do not edit by hand
 
-S3method(c,msmsWSspecs)
 export(CTS.externalIdSubset)
 export(CTS.externalIdTypes)
 export(RmbDefaultSettings)
@@ -13,7 +12,6 @@ export(addProperty)
 export(aggregateSpectra)
 export(analyzeMsMs)
 export(analyzeMsMs.formula)
-export(analyzeMsMs.formula.optimized)
 export(analyzeMsMs.intensity)
 export(annotator.default)
 export(archiveResults)
@@ -41,7 +39,6 @@ export(findMsMsHR)
 export(findMsMsHR.direct)
 export(findMsMsHR.mass)
 export(findMsMsHR.ticms2)
-export(findMsMsHR.ticms2.d)
 export(findMsMsHRperxcms)
 export(findMsMsHRperxcms.direct)
 export(findMz)

man/c.msmsWSspecs.Rd

-% Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/leMsmsRaw.R
-\name{c.msmsWSspecs}
-\alias{c.msmsWSspecs}
-\title{Concatenation of raw spectra in msmsWorkspace}
-\usage{
-c.msmsWSspecs(w1, w2)
-}
-\arguments{
-\item{w1,w2}{The msmsWorkspaces of which the spectra should be concatenated}
-}
-\value{
-The \code{msmsWorkspace} with the spectra of two workspaces concatenated into one. Please note that the spectra from w2 will be concatenated to w1 and not vice versa.
-}
-\description{
-Concatenates the (at)specs spectra of msmsWorkspace according to cpdIDs
-}
-\examples{
-\dontrun{
-		c.msmsWSspecs(w1,w2)
-}
-}
-\author{
-Erik Mueller
-}
-\seealso{
-\code{\link{addPeaksManually}}
-}
-

man/checkIsotopes.Rd

@@ -22,7 +22,7 @@ checkIsotopes(w, mode = "pH", intensity_cutoff = 5000,
 \item{conflict}{Either "isotopic"(Peak formulas are always chosen if they fit the requirements for an isotopic peak)
 or "strict"(Peaks are only marked as isotopic when there hasn't been a formula assigned before.)}
 
-\item{isolationWindow}{The isolation window in Da}
+\item{isolationWindow}{The width of the isolation window in Da}
 
 \item{evalMode}{Currently no function yet, but planned}
 
@@ -32,7 +32,7 @@ or "strict"(Peaks are only marked as isotopic when there hasn't been a formula a
 \code{\link{loadRmbSettings}} et al. Refer to there for specific settings.}
 }
 \value{
-The \code{msmsWorkspace} with .
+The \code{msmsWorkspace} with annotated isolation peaks
 }
 \description{
 Checks for isotopes in a \code{msmsWorkspace}