Fit Models Derived from Point Processes to Species Distributions using 'inlabru'

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Documentation for package ‘PointedSDMs’ version 2.1.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

BBA	Dataset of setophaga caerulescens obtained from the Pennsylvania Atlas of Breeding Birds.
BBS	Dataset of setophaga caerulescens obtained from the North American Breeding Bird survey across Pennsylvania state.
BBSColinusVirginianus	Dataset of Colinus Virginianus obtained from the North American Breeding Bird survey across Alabama state.
blockedCV	_blockedCV_: run spatial blocked cross-validation on the integrated model.
blockedCV-class	Export class blockedCV
blockedCVpred-class	Export class blockedCVpred
bruSDM-class	Export bru_sdm class
bruSDM_predict-class	Export class predict_bru_sdm
changeCoords	_changeCoords_: function used to change coordinate names.
checkCoords	_checkCoords_: function used to check coordinate names.
checkVar	_checkVar_: Function used to check variable names.
data2ENV	_data2ENV_: function used to move objects from one environment to another.
dataOrganize	R6 class to assist in reformatting the data to be used in dataSDM.
dataSet	Internal function used to standardize datasets, as well as assign metadata.
datasetOut	_datasetOut_: function that removes a dataset out of the main model, and calculates some cross-validation score.
datasetOut-class	Export class bru_sdm_leave_one_out
eBird	data.frame object containing solitary tinamou observations from eBird
elev_raster	Raster object containing the elevation across Pennsylvania state.
fitISDM	_fitISDM_: function used to run the integrated model.
Gbif	data.frame object containing solitary tinamou observations from Gbif
intModel	_intModel_: Function used to initialize the integrated species distribution model.
Koala	Dataset of Eucalyptus globulus (common name: blue gum) sightings collected across the Koala conservation reserve on Phillip island (Australia) between 1993 and 2004. Two marks are considered from this dataset: "koala" which describes the number of koala visits to each tree, and "food" which is some index of the palatability of the leaves.
makeFormulaComps	_makeFormulaComps_: function to make components for the covariate and bias Formulas.
makeLhoods	_makeLhoods_: function to make likelihoods.
modISDM-class	Export modISDM class
modISDM_predict-class	Export class predict.modISDM
modMarks-class	Export modMarks class
modMarks_predict-class	Export class predict_modMarks
modSpecies-class	Export modSpecies class
modSpecies_predict-class	Export class predict_modSpecies
nameChanger	_nameChanger_: function to change a variable name.
nearestValue	nearestValue: Match species location data to environmental raster layers
NLCD_canopy_raster	Raster object containing the canopy cover across Pennsylvania state.
Parks	data.frame object containing solitary tinamou observations from Parks
plot.bruSDM_predict	Generic plot function for 'predict_bru_sdm'.
plot.modISDM_predict	Generic plot function for 'predict_bru_sdm'.
plot.modMarks_predict	Generic plot function for 'predict_bru_sdm'.
plot.modSpecies_predict	Generic plot function for 'predict_bru_sdm'.
predict.bruSDM	Generic predict function for 'bru_SDM' objects.
predict.modISDM	Generic predict function for 'bru_SDM' objects.
predict.modMarks	Generic predict function for 'bru_SDM' objects.
predict.modSpecies	Generic predict function for 'bru_SDM' objects.
print.blockedCV	Print function for 'blockedCV'.
print.blockedCVpred	Print function for 'blockedCV'.
print.bruSDM	Generic print function for 'bruSDM'.
print.bruSDM_predict	Generic print function for 'bru_sdm_predict'.
print.datasetOut	Generic print function for 'datasetOut'.
print.modISDM	Generic print function for 'modISDM'.
print.modMarks	Generic print function for 'modMarks'.
print.modSpecies	Generic print function for 'modSpecies'.
reduceComps	reduceComps: Reduce the components of the model.
region	sf object containing the boundary region for solitary tinamouc
removeFormula	removeFormula: Function to remove term from a formula.
runModel	_runModel_: function used to run the integrated model. Note that this function is depreciated, and will be removed in a later version of the package.
SetophagaData	List of all data objects used for the Setophaga vignette.
SolitaryTinamou	List of all data objects used for the solitary tinamou vignette.
SolTinCovariates	spatRaster object containing covariate values
specifyISDM	R6 class for creating a 'startISDM' object.
specifyMarks	R6 class for creating a 'specifyMarks' object.
specifySpecies	R6 class for creating a 'startSpecies' object.
startISDM	_startISDM_: Function used to initialize the integrated species distribution model.
startMarks	_startMarks_: Function used to initialize a marked-point process model.
startSpecies	_startSpecies_: Function used to initialize a multi-species integrated species distribution model.
summary.bruSDM	Generic summary function for 'bruSDM'.
summary.modISDM	Generic summary function for 'bruSDM'.
summary.modMarks	Generic summary function for 'bruSDM'.
summary.modSpecies	Generic summary function for 'bruSDM'.