Man pages for James-Thorson/FishStatsUtils
Utilities (shared code and data) for FishStats spatio-temporal modeling toolbox

bilinear_interpCalculate weights for bilinear interpolation
Calc_Anisotropic_MeshMake mesh for distances among points
calc_coherenceCalculate stability metrics
calc_covCalculate covariance
Calc_KmeansCalculate location for knots approximating spatial variation
Calc_Polygon_Areas_and_Polygons_FnCalculate areas and covariates for a given triangulated mesh
calc_synchronyCalculate synchrony among species or locations
calculate_proportionCalculate the compositional-expansion
CoherenceCalculate stability metrics
combine_extrapolation_infoCombines multiple extrapolation grids
combine_listsCombine lists
Convert_LL_to_EastNorth_FnConvert from Lat-Long to Eastings-Northings using WGS
Convert_LL_to_UTM_FnConvert from Lat-Long to UTM
convert_shapefileConvert shapefile to extrapolation-grid
convert_version_nameConvert string to semantic version number
Crossvalidate_FnK-fold crossvalidation
FishStatsUtilsFishStatsUtils
fit_modelFit VAST to data
format_covariatesFormat habitat covariate matrix
Geostat_SimSimulate data
get_latest_versionDetermine latest version of VAST
GOA_pcod_covariate_exampleData to demonstrate and test covariate effects
load_exampleLoad an example data set
make_covariatesFormat habitat covariate matrix
make_extrapolation_infoBuild extrapolation grid
make_map_infoGet information for adequate mapping for regions
make_settingsMake list of settings
make_spatial_infoBuild objects related to spatial information
map_hypervariancePlot variance of GMRF knots
plot_biomass_indexPlot index of abundance
plot_covPlot covariance matrix
plot_dataPlot location of sampling data
plot_encounter_diagnosticCheck predicted encounter probability against observed...
plot_factorsPlot factor-decomposition of covariance
plot.fit_modelPrint parameter estimates
plot_indexPlot an index
plot_loadingsPlotting loadings matrix
PlotLoadingsCopy of FishStatsUtils::plot_loadings
plot.make_extrapolation_infoPlot extrapolation-grid
plot.make_spatial_infoPlot spatial information
PlotMap_FnPlot maps with areal results
plot_mapsPlot standard maps
plot_overdispersionPlot estimated overdispersion
plot_quantile_diagnosticDiagnostic QQ function
plot_quantile_residualsPlot quantile residuals on map
plot_range_edgePlot shifts in range edges
plot_range_indexPlot shifts in distribution and area occupied
plot_residualsPlot Pearson residuals on map
plot_resultsPlot results
plot_variablePlot results on a multi-panel figure of maps
print.fit_modelPrint parameter estimates
print.make_extrapolation_infoExtract extrapolation-grid
print.make_spatial_infoPrint spatial information
project_coordinatesConvert from Lat-Long to UTM
Rerun_FnExplore counter-factual scenario
rotate_factorsRotate results
Rotate_FnCopy of FishStatsUtils::Rotate_Fn
sample_variableSample from predictive distribution of a variable
simulate_dataSimulate new dynamics and sampling data
smallPlotInset small plot within figure
stream_network_eel_exampleData to demonstrate and test stream-network options
summarize_covarianceExplore spatio-temporal covariance
summary.fit_modelExtract summary of spatial estimates
Vessel_FnPlot vessel effects
James-Thorson/FishStatsUtils documentation built on Aug. 12, 2020, 11:29 p.m.