Skip to contents

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