abbrevWords | Abbreviates StoX project names. |
abbrMatch | Get subsequently plotting variables used in plotting... |
addProcesses | Add processes to a project, given output from getParlist(): |
as.matrix_full | Convert list to matrix or data.frame and generate missing... |
baseline2ECA | Prepare data from a project to the ECA model |
bootstrapOneIteration | Run one bootstrap iteration of biotic stations and acoustic... |
bootstrapParallel | Bootstrap biotic stations and acoustic data |
checkAgeLength | checks that agelenght is configured correctly |
check_columns_present | checks that column names are present on datamatrix |
checkCovariateConsistency | checks that covariates are compatible between model and... |
check_covariates | checks that specification of covariates are OK |
checkLandings | checks that landings are specified correctly |
check_landings_cov | checks formatting on landing cov-matrices |
check_none_missing | columns does not have missing values |
checkWeightLength | checks that weightlenght is configured correctly |
createProject | Create, open or save a StoX project |
data.frame2nestedList | Write biotic and acoustic XML files from data frames given a... |
data.frame2parString | Convert to and from parameter strings in StoX. |
diagnosticsCoverageRECA | Paneled plots of cell coverage |
diagnostics_model_configuration | Plots diagnostics for model configuration. Whether all... |
diagnosticsRECA | Diagonostics RECA |
diagnosticsSamplesRECA | Plot table showing coverage of gear, temporal and spatial... |
distributeAbundance | Impute unknown individual biological parameters from known... |
downloadProjectZip | Download a zipped StoX project to a specified project path. |
formatPlot | Saves plot to stox project location... |
generateSpeciesMatrix | Generate species matrix with biotic stations as rows and... |
getAvailableFunctions | Get available StoX functions |
getBioticAssignments | Get joined table of trawl assignments, psu and stratum |
getCovariateValue | Function used for extracting the correct covariate value from... |
getCovparam | Extract the covaraite definitions |
getDataFrame | Convert a storage object into a dataframe representation |
getDataMatrixANDCovariateMatrix | Function for extracting the DataMatrix for the given variable... |
get_eq_tail_ci | Constructs equal tailed credibility intervals. The... |
get_fixed_effects_landings | Get aggregated landings for fixed effects |
getGlobalParameters | Function for extracting the GlobalParameters object |
get_g_s_a_frame | get matrix of sample and landings from the subset of biotic... |
get_gta_landings | Extracts all combinations of gear, temporal and spatial from... |
getHardCoded | Function used for combining hard coded parameter values and... |
getInfo | Function for extracting the CARNeighbours and info: |
getLandings | Function for extracting the Landings object |
getLengthGivenAge_Biotic | Function for converting to the input format required by ECA... |
getMidSeason | Function for setting getting appropriate value for the... |
getMode | Function for getting the mode of a vector: |
getNASCDistr | Estimate mean NASC distribution |
getNMDinfo | Get NMD API data and reference information |
getow | Function for controling overwriting of prjects. |
getParlist | Merges a list and the following list elements given as "...". |
getPlots | Get various plots and reports in Rstox |
getPlottingUnit | Interprets a unit key stings as a scaleing factor |
getProcess | Get process indices. |
getProjectPaths | Functions to return various paths and file names. |
getProjString | Utility functions for coordinate transformation between... |
getPSUNASC | Get and aggregate PSUNASC. Rows are reordered. |
getResampledNASCDistr | Resample NASC distribution |
getRstoxEnv | Set up the RstoxEnv |
getRstoxVersion | Get the Rstox version and the version of the Java library... |
getVar | Get a specific variable of a list by its name, and issue an... |
getWeightGivenLength_Biotic | Function for converting to the input format required by ECA... |
hasAgeInSample | Identifies whichindividuals are from catchsamples with some... |
imputeByAge | Impute missing individual data by age |
insertToProjectXML | Modify a StoX project.xml file directly. |
isURL | Are the specified URLs acutally URLs to zip files? |
JavaString2vector | Convert a Java string to R vector |
jInt | Wrap basic R objects into Java objects |
linkPSU2Stratum | Bootstrap utils. |
moveToTrash | Move existing files to the trash directory in the directory... |
NMDdecode | Encodes and decodes NMD API strings. |
papply | Parallel version of lapply |
plotAbundance | Plot abundance results to the graphics device or to a file |
plot_catch_at_age_ci | Plot equal tailed credible intervals for a catch by age... |
plot_catch_fractions | Plots composition in catchsamples of parameters that... |
plot_cell_coverage | Plot aggregated landings for different kind of sampling level... |
plot_cell_landings | Plot aggregated landings for all cells, labeled with sampling... |
plot_ci | Plots means with error bars |
plot_fixed_effect_coverage | Plot table of coverage for fixed effects |
plot_gear_temporal_area | show samples wrp common covariates gear, area and temporal |
plot_length_at_age | Plots mean length at age and sample range |
plot_mission_types | Composition of mission types in the data |
plotNASCDistribution | Plot NASC distribution to file |
plot_pred_box | Plot catch by age prediction as boxplots |
plotRECA | Produces plots for R report for RECA. Fails silently on... |
plotRECAresults | Generates plots and reports from RECA prediction |
plot_RECA_results_panel | Plots a panel of RECA results |
plotSampleCompositionRECA | Panelled plot of sample composition wrp potentially... |
plot_sample_types | Composition of catch sample types in data |
plotSamplingOverview | plotSamplingOverview |
plot_station_types | Composition of station types (Stasjons: stasjonstype) in data |
plot_weight_at_age | Plots mean weight at age and sample range |
pointToStoXFiles | Link to the files in a stox project |
polyArea | Get polygon area and convert to or from geographic and... |
prepareDATRAS | Generate DATRAS output for a specific StoX project or user... |
prepareRECA | Prepare data for RECA |
readBaselineFiles | Function for reading output files from StoX (Baseline or... |
reportAbundance | Calculate a summary of the bootstrap iterations (possibly... |
reportRECA | Report RECA. |
rm.na | Small function for removing missing values if requested |
Rstox.init | Initialize rJava |
Rstox-package | Extending the StoX survey estimation software into R |
runBaseline | Run a StoX baseline model |
runBootstrap | Run a bootstrap in StoX |
runFunsRstox | Get various plots and reports in Rstox |
runRECA | run RECA |
sampleSorted | Sample a vector after sorting the vector and applying the... |
saveCatchMatrix | Save catch at age matrix |
searchNMDCruise | Search for a cruise given the cruise number and ship name. |
setAssignments | Set NASC data and assignments to memory |
setBaselineParameters | Set, read, get or modify baseline parameters. |
setJavaMemory | Get or set the size of the Java memory |
setPrecisionLevel | Functions for setting and getting the precision level of a... |
setProjectData | Set, get, save or load project data. |
splitBioticCC | Splits biotic frame by otolith type |
splitPredCC | Splits a prediction object from running coastal cod analysis... |
surveyPlanner | Plan an acoustic-trawl survey. |
varianceEstimation | Parametric variance estimation |
writeBioticXML | Write biotic and acoustic XML files from data frames given a... |
writeRecaConfiguration | Writes RECA configuration |
writeTransects | Write transects generated by 'surveyPlanner' to various... |
wtd.strata.est | Weighted mean NASC by stratum |
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