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

bbouMakeSummaryTable(): Create summary table of demographic rates from survival and recruitment surveys

caribouBayesianPM(): Bayesian population model for boreal caribou

caribouPopGrowth(): Caribou demographic model

caribouPopSimMCMC() convertTrajectories() summarizeCaribouPopSim(): Get a set of simulation results from fitted demographic models in raw form Assumes that rec_pred and surv_pred each include the same years and populations.TO DO: check this.

compositionBiasCorrection(): Calculate bias correction term for calf:cow composition survey.

demographicCoefficients() getCoefs() sampleCoefs(): Sample demographic regression model coefficients

demographicProjectionApp(): Run the Bayesian caribou demographic projection app

demographicRates() sampleRates(): Sample expected survival and recruitment rates

doSim(): Do multiple caribouPopGrowth runs

getBBNationalInformativePriors(): Get informative priors for bboutools logistic models

getOutputTables(): Summarize results of Bayesian demographic model in tables

getPriors(): Get prior parameters for Bayesian beta population model

getScenarioDefaults(): Default parameters for simulation of example demographic trajectories.

getSimsInitial(): Get a set of simulation results from fitted demographic models (if bbouResults argument is provided) or from national demographic disturbance model.

getSimsNational(): Get a set of simulation results from the national demographic model

plotRes(): Plot Bayesian population model results

popGrowthTableJohnsonECCC: Population growth model table for Johnson models

runScnSet(): Run the Bayesian population model for multiple parameter sets

simulateObservations(): Simulate observations

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

reclassDist(): Reclassify natural disturbance and harvest layers

results(): Extract results

updateDisturbance(): Update an existing DisturbanceMetrics Object

Caribou habitiat

Functions for predicting boreal caribou habitat use in 13 Ontario caribou ranges

CaribouHabitat-class CaribouHabitat: Caribou Habitat class

calcBinaryUse(): Calculate binary use

caribouHabitat(): Calculate relative probability of caribou habitat use

coefTableHR: Model coefficients for caribou ranges

coefTableStd: Model coefficients from standardized data for caribou ranges

fnlcToResType: Lookup table for FNLC to resource type

loadSpatialInputs(): Load Spatial Input Data

plcToResType: Lookup table for PLC to resource type

rasterizeLineDensity(): Rasterize line density

reclassPLC(): Reclassify provincial land cover

resTypeCode: Lookup table for resource type codes

results(): Extract results

rfuToResType: Lookup table for RFU to resource type

threshTable: Binary habitat use thresholds table

updateCaribou(): Update an existing CaribouHabitat Object

plot(<CaribouHabitat>,<ANY>): Plot method for CaribouHabitat Objects