Fit Models Derived from Point Processes to Species Distributions using 'inlabru'
startISDM: Function used to initialize the integrated species dist...
startMarks: Function used to initialize a marked-point process mod...
startSpecies: Function used to initialize a multi-species integrat...
Generic summary function for bruSDM.
R6 class for creating a startISDM object.
R6 class for creating a specifyMarks object.
R6 class for creating a startSpecies object.
Dataset of setophaga caerulescens obtained from the Pennsylvania Atlas...
Dataset of setophaga caerulescens obtained from the North American Bre...
Export class blockedCV
nameChanger: function to change a variable name.
Raster object containing the canopy cover across Pennsylvania state.
data.frame object containing solitary tinamou observations from Parks
blockedCV: run spatial blocked cross-validation on the integrated ...
Export class blockedCVpred
Export class predict_bru_sdm
Export bru_sdm class
changeCoords: function used to change coordinate names.
checkCoords: function used to check coordinate names.
checkVar: Function used to check variable names.
data2ENV: function used to move objects from one environment to an...
R6 class to assist in reformatting the data to be used in dataSDM.
Internal function used to standardize datasets, as well as assign meta...
Export class bru_sdm_leave_one_out
spatRaster object containing covariate values
datasetOut: function that removes a dataset out of the main model,...
data.frame object containing solitary tinamou observations from eBird
Raster object containing the elevation across Pennsylvania state.
fitISDM: function used to run the integrated model.
data.frame object containing solitary tinamou observations from Gbif
intModel: Function used to initialize the integrated species distr...
makeFormulaComps: function to make components for the covariate an...
makeLhoods: function to make likelihoods.
Export class predict.modISDM
Export modISDM class
Export class predict_modMarks
Export modMarks class
Export class predict_modSpecies
Export modSpecies class
Generic plot function for predict_bru_sdm.
Generic predict function for bru_SDM objects.
Print function for blockedCV.
Print function for blockedCV.
Generic print function for bru_sdm_predict.
Generic print function for bruSDM.
Generic print function for datasetOut.
Generic print function for modISDM.
Generic print function for modMarks.
Generic print function for modSpecies.
reduceComps: Reduce the components of the model.
sf object containing the boundary region for solitary tinamouc
removeFormula: Function to remove term from a formula.
runModel: function used to run the integrated model. Note that thi...
Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models. Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking. We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them. There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions. An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Useful links