Man pages for Sea2Data/Rstox
Running Stox functionality independently in R

abbrevWordsAbbreviates StoX project names.
abbrMatchGet subsequently plotting variables used in plotting...
addProcessesAdd processes to a project given as output from getParlist():
aggregateBySpeciesCategoryGenerate species matrix with biotic stations as rows and...
as.matrix_fullConvert list to matrix and generate missing values
baseline2ECAPrepare data from a project to the ECA model
bootstrapOneIterationRun one bootstrap iteration of biotic stations and acoustic...
bootstrapParallelBootstrap biotic stations and acoustic data
createProjectCreate, open or save a StoX project
data.frame2parStringConvert to and from parameter strings in StoX.
distributeAbundanceImpute unknown individual biological parameters from known...
downloadProjectZipDownload a zipped StoX project to a specified project path.
getAvailableFunctionsGet available StoX functions
getBioticAssignmentsGet joined table of trawl assignments, psu and stratum
getDataFrameConvert a storage object into a dataframe representation
getNASCDistrEstimate mean NASC distribution
getNMDinfoGet NMD API data and reference information
getowFunction for controling overwriting of prjects.
getParlistMerges a list and the following list elements given as "...".
getPlotsGet various plots and reports in Rstox
getPlottingUnitInterprets a unit key stings as a scaleing factor
getProcessGet process indices.
getProjectPathsFunctions to return various paths and file names.
getProjStringUtility functions for coordinate transformation between...
getPSUNASCGet and aggregate PSUNASC. Rows are reordered.
getResampledNASCDistrResample NASC distribution
getRstoxEnvSet up the RstoxEnv
getRstoxVersionGet the Rstox version and the version of the Java library...
getVarGet a specific variable of a list by its name, and issue an...
imputeByAgeImpute missing individual data by age
isURLAre the specified URLs acutally URLs to zip files?
JavaString2vectorConvert a Java string to R vector
jIntWrap basic R objects into Java objects
linkPSU2StratumBootstrap utils.
moveToTrashMove existing files to the trash directory in the directory...
NMDdecodeEncodes and decodes NMD API strings.
plotAbundancePlot abundance results to the graphics device or to a file
plotNASCDistributionPlot NASC distribution to file
pointToStoXFilesLink to the files in a stox project
polyAreaGet polygon area and convert to or from geographic and...
readBaselineFilesFunction for reading output files from StoX (Baseline or...
reportAbundanceCalculate a summary of the bootstrap iterations (possibly...
Rstox.initInitialize rJava
runBaselineRun a StoX baseline model
runBootstrapRun a bootstrap in StoX
runFunsRstoxGet various plots and reports in Rstox
sampleSortedSample a vector after sorting the vector and applying the...
searchNMDCruiseSearch for a cruise given the cruise number and ship name.
setAssignmentsSet NASC data and assignments to memory
setBaselineParametersSet, read, get or modify baseline parameters.
setJavaMemorySet the size of the Java memory
setPrecisionLevelFunctions for setting and getting the precision level of a...
setProjectDataSet, get, save or load project data.
surveyPlannerGet polygon area and convert to or from geographic and...
varianceEstimationParametric variance estimation
writeTransectsWrite transects generated by 'surveyPlanner' to various...
wtd.strata.estWeighted mean NASC by stratum
Sea2Data/Rstox documentation built on April 18, 2018, 11:11 p.m.