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 output from getParlist():
as.matrix_fullConvert list to matrix or data.frame and generate missing...
baseline2ECAPrepare data from a project to the ECA model
bootstrapOneIterationRun one bootstrap iteration of biotic stations and acoustic...
bootstrapParallelBootstrap biotic stations and acoustic data
checkAgeLengthchecks that agelenght is configured correctly
check_columns_presentchecks that column names are present on datamatrix
checkCovariateConsistencychecks that covariates are compatible between model and...
check_covariateschecks that specification of covariates are OK
checkLandingschecks that landings are specified correctly
check_landings_covchecks formatting on landing cov-matrices
check_none_missingcolumns does not have missing values
checkWeightLengthchecks that weightlenght is configured correctly
createProjectCreate, open or save a StoX project
data.frame2nestedListWrite biotic and acoustic XML files from data frames given a...
data.frame2parStringConvert to and from parameter strings in StoX.
diagnosticsCoverageRECAPaneled plots of cell coverage
diagnostics_model_configurationPlots diagnostics for model configuration. Whether all...
diagnosticsRECADiagonostics RECA
diagnosticsSamplesRECAPlot table showing coverage of gear, temporal and spatial...
distributeAbundanceImpute unknown individual biological parameters from known...
downloadProjectZipDownload a zipped StoX project to a specified project path.
formatPlotSaves plot to stox project location...
generateSpeciesMatrixGenerate species matrix with biotic stations as rows and...
getAvailableFunctionsGet available StoX functions
getBioticAssignmentsGet joined table of trawl assignments, psu and stratum
getCovariateValueFunction used for extracting the correct covariate value from...
getCovparamExtract the covaraite definitions
getDataFrameConvert a storage object into a dataframe representation
getDataMatrixANDCovariateMatrixFunction for extracting the DataMatrix for the given variable...
get_eq_tail_ciConstructs equal tailed credibility intervals. The...
get_fixed_effects_landingsGet aggregated landings for fixed effects
getGlobalParametersFunction for extracting the GlobalParameters object
get_g_s_a_frameget matrix of sample and landings from the subset of biotic...
get_gta_landingsExtracts all combinations of gear, temporal and spatial from...
getHardCodedFunction used for combining hard coded parameter values and...
getInfoFunction for extracting the CARNeighbours and info:
getLandingsFunction for extracting the Landings object
getLengthGivenAge_BioticFunction for converting to the input format required by ECA...
getMidSeasonFunction for setting getting appropriate value for the...
getModeFunction for getting the mode of a vector:
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...
getWeightGivenLength_BioticFunction for converting to the input format required by ECA...
hasAgeInSampleIdentifies whichindividuals are from catchsamples with some...
imputeByAgeImpute missing individual data by age
insertToProjectXMLModify a StoX project.xml file directly.
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.
papplyParallel version of lapply
plotAbundancePlot abundance results to the graphics device or to a file
plot_catch_at_age_ciPlot equal tailed credible intervals for a catch by age...
plot_catch_fractionsPlots composition in catchsamples of parameters that...
plot_cell_coveragePlot aggregated landings for different kind of sampling level...
plot_cell_landingsPlot aggregated landings for all cells, labeled with sampling...
plot_ciPlots means with error bars
plot_fixed_effect_coveragePlot table of coverage for fixed effects
plot_gear_temporal_areashow samples wrp common covariates gear, area and temporal
plot_length_at_agePlots mean length at age and sample range
plot_mission_typesComposition of mission types in the data
plotNASCDistributionPlot NASC distribution to file
plot_pred_boxPlot catch by age prediction as boxplots
plotRECAProduces plots for R report for RECA. Fails silently on...
plotRECAresultsGenerates plots and reports from RECA prediction
plot_RECA_results_panelPlots a panel of RECA results
plotSampleCompositionRECAPanelled plot of sample composition wrp potentially...
plot_sample_typesComposition of catch sample types in data
plotSamplingOverviewplotSamplingOverview
plot_station_typesComposition of station types (Stasjons: stasjonstype) in data
plot_weight_at_agePlots mean weight at age and sample range
pointToStoXFilesLink to the files in a stox project
polyAreaGet polygon area and convert to or from geographic and...
prepareDATRASGenerate DATRAS output for a specific StoX project or user...
prepareRECAPrepare data for RECA
readBaselineFilesFunction for reading output files from StoX (Baseline or...
reportAbundanceCalculate a summary of the bootstrap iterations (possibly...
reportRECAReport RECA.
rm.naSmall function for removing missing values if requested
Rstox.initInitialize rJava
Rstox-packageExtending the StoX survey estimation software into R
runBaselineRun a StoX baseline model
runBootstrapRun a bootstrap in StoX
runFunsRstoxGet various plots and reports in Rstox
runRECArun RECA
sampleSortedSample a vector after sorting the vector and applying the...
saveCatchMatrixSave catch at age matrix
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.
setJavaMemoryGet or set the size of the Java memory
setPrecisionLevelFunctions for setting and getting the precision level of a...
setProjectDataSet, get, save or load project data.
splitBioticCCSplits biotic frame by otolith type
splitPredCCSplits a prediction object from running coastal cod analysis...
surveyPlannerPlan an acoustic-trawl survey.
varianceEstimationParametric variance estimation
writeBioticXMLWrite biotic and acoustic XML files from data frames given a...
writeRecaConfigurationWrites RECA configuration
writeTransectsWrite transects generated by 'surveyPlanner' to various...
wtd.strata.estWeighted mean NASC by stratum
Sea2Data/Rstox documentation built on May 14, 2019, 8:58 a.m.