Package index
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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
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bbouMakeSummaryTable()
- Create summary table of demographic rates from survival and recruitment surveys
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caribouBayesianPM()
- Bayesian population model for boreal caribou
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caribouPopGrowth()
- Caribou demographic model
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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.
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compositionBiasCorrection()
- Calculate bias correction term for calf:cow composition survey.
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demographicCoefficients()
getCoefs()
sampleCoefs()
- Sample demographic regression model coefficients
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demographicProjectionApp()
- Run the Bayesian caribou demographic projection app
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demographicRates()
sampleRates()
- Sample expected survival and recruitment rates
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doSim()
- Do multiple caribouPopGrowth runs
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getBBNationalInformativePriors()
- Get informative priors for bboutools logistic models
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getOutputTables()
- Summarize results of Bayesian demographic model in tables
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getPriors()
- Get prior parameters for Bayesian beta population model
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getScenarioDefaults()
- Default parameters for simulation of example demographic trajectories.
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getSimsInitial()
- Get a set of simulation results from fitted demographic models (if bbouResults argument is provided) or from national demographic disturbance model.
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getSimsNational()
- Get a set of simulation results from the national demographic model
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plotRes()
- Plot Bayesian population model results
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popGrowthTableJohnsonECCC
- Population growth model table for Johnson models
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runScnSet()
- Run the Bayesian population model for multiple parameter sets
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simulateObservations()
- Simulate observations
Summarizing disturbance
Functions for determining the percentage of a landscape that has been disturbed
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DisturbanceMetrics-class
DisturbanceMetrics
- Disturbance Metrics class
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disturbanceMetrics()
- Calculate metrics of natural and anthropogenic disturbance
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reclassDist()
- Reclassify natural disturbance and harvest layers
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results()
- Extract results
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updateDisturbance()
- Update an existing DisturbanceMetrics Object
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CaribouHabitat-class
CaribouHabitat
- Caribou Habitat class
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calcBinaryUse()
- Calculate binary use
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caribouHabitat()
- Calculate relative probability of caribou habitat use
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coefTableHR
- Model coefficients for caribou ranges
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coefTableStd
- Model coefficients from standardized data for caribou ranges
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fnlcToResType
- Lookup table for FNLC to resource type
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loadSpatialInputs()
- Load Spatial Input Data
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plcToResType
- Lookup table for PLC to resource type
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rasterizeLineDensity()
- Rasterize line density
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reclassPLC()
- Reclassify provincial land cover
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resTypeCode
- Lookup table for resource type codes
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results()
- Extract results
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rfuToResType
- Lookup table for RFU to resource type
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threshTable
- Binary habitat use thresholds table
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updateCaribou()
- Update an existing CaribouHabitat Object
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plot(<CaribouHabitat>,<ANY>)
- Plot method for
CaribouHabitat
Objects