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DESCRIPTION
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Package: caribouMetrics
Type: Package
Title: Models and Metrics of Boreal Caribou Demography and Habitat Selection
Version: 0.4.0
Authors@R: c(person("Josie", "Hughes", role = c("aut"), email = "[email protected]", comment = c(ORCID = "0000-0001-7875-9015")),
person("Sarah", "Endicott", email = "[email protected]",
role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9644-5343")),
person("Craig", "Simpkins", email = "[email protected]", role = "aut"),
person("Tati", "Michelleti", email = "[email protected]",
role = c("aut", "cph"), comment = c("Functions getCoefs and sampleRates are derived from code written by Tati Micheletti")),
person("Eliot", "McIntire", email = "[email protected]", role = "aut"),
person("Daniel", "Eacker", role = "cph", comment = c("Lead author of paper where code modified in caribouBayesianPM, plotRes, and getSumStats was published")),
person("Saralees", "Nadarajah", role = "cph", comment = c("Author of truncdist package, which function rtrunc and qtrunc were modified from")),
person("Frederick", "Novomestky", role = "cph", comment = c("Author of truncdist package, which function rtrunc and qtrunc were modified from")),
person(given="Her Majesty the Queen in Right of Canada, as represented by the Minister of Environment and Climate Change",
role = "cph"))
Description: caribouMetrics provides implementations of several different different models of Boreal woodland
caribou demography and habitat selection. A national two-stage demographic model with density
dependence and interannual variability follows [Johnson et. al. (2020)](doi:10.1111/1365-2664.13637)
with modifications described in [Dyson et al. (2022)](https://doi.org/10.1101/2022.06.01.494350).
Demographic rates vary with disturbance as estimated by [Johnson et. al. (2020)](doi:10.1111/1365-2664.13637).
The package also includes a Bayesian population model designed to integrate prior information
from Johnson et al's national analysis of demographic-disturbance relationships with available
local demographic data to reduce uncertainty in population viability projections. The Bayesian
population model is an extension of work by [Eacker et al. (2019)](https://doi.org/10.1002/wsb.950).
The national model can be used to simulate example population trajectories, and combined with a
simple observation model and the Bayesian population model to show how monitoring requirements
depend on landscape condition. Finally, caribouMetrics contains an implementation of
[Hornseth and Rempel's (2016)](https://doi.org/10.1139/cjz-2015-0101) Ontario boreal caribou resource
selection model described in [Dyson et al. (2022)](https://doi.org/10.1101/2022.06.01.494350).
Model implementation is intended to be modular and flexible, allowing reuse of components in a
variety of contexts including projections of the cumulative effects of disturbance and
climate change [(e.g. Stewart et al. 2023)](https://doi.org/10.1002/eap.2816) and a
[Shiny app](https://landscitech.github.io/BayesianCaribouDemographicProjection/) designed to
allow allow exploration of user-specified monitoring and disturbance scenarios.
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Imports:
dplyr,
data.table,
sf,
tidyr,
stringr,
purrr,
methods,
matrixStats,
simstudy,
rlang,
terra,
R2jags,
survival
Collate:
'AAAClassDefinitions.R'
'applyDist.R'
'betaSample.R'
'calcBinaryUse.R'
'calcRSP.R'
'caribouBayesianPM.R'
'caribouHabitat.R'
'caribouMetrics-package.R'
'caribouPopGrowth.R'
'checkInputs.R'
'combineLinFeat.R'
'compositionBiasCorrection.R'
'data.R'
'dataPrepFns.R'
'demographicCoefficients.R'
'demographicProjectionApp.R'
'demographicRates.R'
'disturbanceMetrics.R'
'getCoefs.R'
'getOutputTables.R'
'getPriors.R'
'getScenarioDefaults.R'
'getSimsNational.R'
'spatialAlignFns.R'
'inputData.R'
'inputDataDisturbance.R'
'internal_demog_fns.R'
'loadSpatialInputs.R'
'movingWindowAvg.R'
'plot.R'
'plotRes.R'
'popGrowthTableJohnsonECCC.R'
'processData.R'
'rasterizeLineDensity.R'
'reclassDist.R'
'reclassPLC.R'
'results.R'
'runScnSet.R'
'sampleCoefs.R'
'sampleRates.R'
'simulateObservations.R'
'tabAllRes.R'
'updateCaribou.R'
'updateDisturbance.R'
Suggests:
testthat (>= 2.1.0),
knitr,
rmarkdown,
tmap,
tmaptools,
ggplot2,
rsyncrosim,
pfocal,
BayesianCaribouDemographicProjection,
raster
Remotes: LandSciTech/pfocal,
LandSciTech/BayesianCaribouDemographicProjection
Additional_repositories: https://landscitech.github.io/drat
VignetteBuilder: knitr
Depends:
R (>= 3.5)
URL: https://landscitech.github.io/caribouMetrics, https://github.com/LandSciTech/caribouMetrics