Function reference • BIRDIE

All functions

addDuToitCounts(): Add DuToit's Pan data from Doug

addExtraSitesToSummary(): Add raw counts to CWAC SSM predictions

addSiteVarEETimeLimit(): Annotate site data with Google Earth Engine with a time limit

addSpOccDetCovt(): Add detection covariate to spOccupancy data list

barberspan: Barberspan CWAC data

combineAbuDiags(): Combine species abundance diagnostics into a single object

combineOccuDiags(): Combine species occupancy diagnostics into a single object

configPipeline(): Configure pipeline parameters

createCombinedExportFile(): Create a combined file for export to data mart

createLog(): Create pipeline event log

createOccuData(): Create data for fitting an occupancy model

createPredFromAbap(): Create prediction object directly from ABAP data

diagnoseGofJagsSsm(): Diagnose goodness-of-fit for JAGS state-space model

diagnoseGofSpOccu(): Conduct goodness-of-fit test for spOccupancy models

diagnoseRhatJagsSsm(): Diagnose convergence for JAGS state-space model

diagnoseRhatSpOccu(): Diagnose convergence for spOccupancy model

fitSpOccu(): Fit spOccupancy model

gatherYearFromVars(): Gather years from variables with year

logFitStatus(): Generate fit status messages

pipe_prll_fit(): Fit occupancy models in parallel

plotDetections(): Plot detection from occupancy data

plotJagsSsm2ss(): Plot state series of a JAGS state-space model with two seasons

plotOccuVars(): Plot occupancy covariates

postPredDistJagsSsm(): Prepare posterior predictive distribution for JAGS state-space model

ppl_create_data_ssm(): Prepare covariate data for abundance pipeline

ppl_create_indtr_file(): Create indicator storage files

ppl_create_site_visit(): Create site and visit occupancy files

ppl_diagnose_occu(): Run diagnostics for occupancy model fit

ppl_diagnose_ssm(): Run diagnostics for a state-space model fit

ppl_fit_occu_model(): Fit occupancy model

ppl_fit_ssm_model(): Fit state-space JAGS model

ppl_run_pipe_abu1(): Run abundance pipeline ABU1

ppl_run_pipe_dst1(): Run distribution indicators pipeline module 1

ppl_summarise_occu(): Summarise predictions from occupancy model

ppl_summarise_ssm(): Summarise predictions from state-space JAGS model

predictSpOccu(): Predict from spOccupancy model fit

prepGEECatchmData(): Prepare Google Earth Engine data for catchments

prepGEESiteData(): Prepare Google Earth Engine site data

prepGEEVisitData(): Prepare Google Earth Engine visit data

prepSpOccuData_multi(): Prepare spOccupancy data for multi-season model fitting

prepSpOccuData_single(): Prepare spOccupancy data for single-season model fitting

prepSsmData(): Prepare CWAC data to fit a state-space model

processJAGSoutput(): Process JAGS model outputs

scaleSpOccVars(): Scale covariates in spOccupancy-type data

selectSppFromDiag(): Select species based on model diagnostics

setSpOutFilePath(): Set a standard path for a pipeline output file associated with a species

simDetSpOccu(): Simulate detections from spOccupancy fit

summariseSpOccu(): Summarise spOccupancy occupancy estimates

summaryJags(): Summarise JAGS model fit

waterbirds: BIRDIE's waterbird masterlist