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

## Documentation for package ‘PointedSDMs’ version 2.1.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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'.