Package index • caribouMetrics

Overview

Overview of the package.

caribouMetrics caribouMetrics-package: caribouMetrics: Models and Metrics of Boreal Caribou Demography and Habitat Selection

Caribou demography

Functions for predicting boreal caribou demographic rates and projecting population growth

bayesianScenariosWorkflow(): Run the Bayesian population model for multiple parameter sets
bayesianTrajectoryWorkflow(): Bayesian population model for boreal caribou
betaNationalPriors(): Get prior parameters for Bayesian Beta demographic rate models
caribouPopGrowth(): Caribou demographic model
compareTrajectories(): Summarize results of Bayesian demographic model in tables
compositionBiasCorrection(): Calculate bias correction term for calf:cow composition survey.
dataFromSheets(): Demographic data from Google sheet
demographicProjectionApp(): Run the Bayesian caribou demographic projection app
estimateBayesianRates(): Create summary table of demographic rates from survival and recruitment surveys
estimateNationalRate() estimateNationalRates(): Sample demographic rates
getNationalCoefficients() sampleNationalCoefs() subsetNationalCoefs(): Sample demographic regression model coefficients
getScenarioDefaults(): Default parameters for simulation of example demographic trajectories.
plotCompareTrajectories(): Plot Bayesian population model results
plotSurvivalSeries(): Plot survival time series
plotTrajectories(): TO DO: document plotTrajectories
popGrowthTableJohnsonECCC: Population growth model table for Johnson models
simulateObservations(): Simulate observations
convertTrajectories() summarizeTrajectories() simulateTrajectoriesFromPosterior(): Format trajectory tables
trajectoriesFromBayesian(): Get trajectories from a Bayesian model result
trajectoriesFromNational(): Get a set of simulation results from the national demographic model
trajectoriesFromSummary(): Projections of population growth from demographic model summaries.
trajectoriesFromSummaryForApp(): Demographic projections for cases with no change in demographic rates over time. This is the method used (so far) in the demography app. TO DO: Consider removing and replacing with call to trajectoriesFromSummary.

Summarizing disturbance

Functions for determining the percentage of a landscape that has been disturbed

DisturbanceMetrics-class DisturbanceMetrics: Disturbance Metrics class
disturbanceMetrics(): Calculate metrics of natural and anthropogenic disturbance
loadSpatialInputs(): Load Spatial Input Data
rasterizeLineDensity(): Rasterize line density
reclassDist(): Reclassify natural disturbance and harvest layers
results(): Extract results
updateDisturbance(): Update an existing DisturbanceMetrics Object