Package: PointedSDMs 2.1.2

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

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>.

Authors:Philip Mostert [aut, cre], Bob O'hara [aut]

PointedSDMs_2.1.2.tar.gz
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PointedSDMs.pdf |PointedSDMs.html✨
PointedSDMs/json (API)
NEWS

# Install 'PointedSDMs' in R:
install.packages('PointedSDMs', repos = c('https://philipmostert.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/philipmostert/pointedsdms/issues

Datasets:
  • BBSColinusVirginianus - Dataset of Colinus Virginianus obtained from the North American Breeding Bird survey across Alabama state.
  • 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.
  • SetophagaData - List of all data objects used for the Setophaga vignette.
  • SolitaryTinamou - List of all data objects used for the solitary tinamou vignette.

On CRAN:

14 exports 23 stars 3.39 score 56 dependencies 2 dependents 41 scripts 369 downloads

Last updated 21 days agofrom:a30a030546. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-winNOTEAug 28 2024
R-4.5-linuxOKAug 28 2024
R-4.4-winOKAug 28 2024
R-4.4-macOKAug 28 2024
R-4.3-winNOTEAug 28 2024
R-4.3-macOKAug 28 2024

Exports:blockedCVdataOrganizedataSetdatasetOutfitISDMintModelnearestValuerunModelspecifyISDMspecifyMarksspecifySpeciesstartISDMstartMarksstartSpecies

Dependencies:base64encblockCVclassclassIntclicolorspaceDBIdplyre1071fansifarverfmesherFNNgenericsggplot2gluegtableinlabruisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmgcvmunsellnlmepillarpkgconfigplyrproxyR.devicesR.methodsS3R.ooR.utilsR6rasterRColorBrewerRcpprlangs2scalessfspterratibbletidyselectunitsutf8vctrsviridisLitewithrwk

Example of PointedSDMs for the solitary tinamou

Rendered fromSolitary_tinamou.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2024-06-06
Started: 2022-04-07

Marked Point Process

Philip Mostert

Rendered fromMarked_Point_Process.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2024-06-13
Started: 2023-01-16

Setophaga example

Philip Mostert

Rendered fromSetophaga.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2024-07-09
Started: 2022-06-08

Spatiotemporal example

Philip Mostert

Rendered fromSpatiotemporal_example.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2024-06-13
Started: 2022-08-16

Readme and manuals

Help Manual

Help pageTopics
Dataset of setophaga caerulescens obtained from the Pennsylvania Atlas of Breeding Birds.BBA
Dataset of setophaga caerulescens obtained from the North American Breeding Bird survey across Pennsylvania state.BBS
Dataset of Colinus Virginianus obtained from the North American Breeding Bird survey across Alabama state.BBSColinusVirginianus
_blockedCV_: run spatial blocked cross-validation on the integrated model.blockedCV
Export class blockedCVblockedCV-class
Export class blockedCVpredblockedCVpred-class
Export class predict_bru_sdmbruSDM_predict-class
Export bru_sdm classbruSDM-class
_changeCoords_: function used to change coordinate names.changeCoords
_checkCoords_: function used to check coordinate names.checkCoords
_checkVar_: Function used to check variable names.checkVar
_data2ENV_: function used to move objects from one environment to another.data2ENV
R6 class to assist in reformatting the data to be used in dataSDM.dataOrganize
Internal function used to standardize datasets, as well as assign metadata.dataSet
_datasetOut_: function that removes a dataset out of the main model, and calculates some cross-validation score.datasetOut
Export class bru_sdm_leave_one_outdatasetOut-class
data.frame object containing solitary tinamou observations from eBirdeBird
Raster object containing the elevation across Pennsylvania state.elev_raster
_fitISDM_: function used to run the integrated model.fitISDM
data.frame object containing solitary tinamou observations from GbifGbif
_intModel_: Function used to initialize the integrated species distribution model.intModel
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.Koala
_makeFormulaComps_: function to make components for the covariate and bias Formulas.makeFormulaComps
_makeLhoods_: function to make likelihoods.makeLhoods
Export class predict.modISDMmodISDM_predict-class
Export modISDM classmodISDM-class
Export class predict_modMarksmodMarks_predict-class
Export modMarks classmodMarks-class
Export class predict_modSpeciesmodSpecies_predict-class
Export modSpecies classmodSpecies-class
_nameChanger_: function to change a variable name.nameChanger
nearestValue: Match species location data to environmental raster layersnearestValue
Raster object containing the canopy cover across Pennsylvania state.NLCD_canopy_raster
data.frame object containing solitary tinamou observations from ParksParks
Generic plot function for 'predict_bru_sdm'.plot.bruSDM_predict plot.modISDM_predict plot.modMarks_predict plot.modSpecies_predict
Generic predict function for 'bru_SDM' objects.predict.bruSDM predict.modISDM predict.modMarks predict.modSpecies
Print function for 'blockedCV'.print.blockedCV
Print function for 'blockedCV'.print.blockedCVpred
Generic print function for 'bruSDM'.print.bruSDM
Generic print function for 'bru_sdm_predict'.print.bruSDM_predict
Generic print function for 'datasetOut'.print.datasetOut
Generic print function for 'modISDM'.print.modISDM
Generic print function for 'modMarks'.print.modMarks
Generic print function for 'modSpecies'.print.modSpecies
reduceComps: Reduce the components of the model.reduceComps
sf object containing the boundary region for solitary tinamoucregion
removeFormula: Function to remove term from a formula.removeFormula
_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.runModel
List of all data objects used for the Setophaga vignette.SetophagaData
List of all data objects used for the solitary tinamou vignette.SolitaryTinamou
spatRaster object containing covariate valuesSolTinCovariates
R6 class for creating a 'startISDM' object.specifyISDM
R6 class for creating a 'specifyMarks' object.specifyMarks
R6 class for creating a 'startSpecies' object.specifySpecies
_startISDM_: Function used to initialize the integrated species distribution model.startISDM
_startMarks_: Function used to initialize a marked-point process model.startMarks
_startSpecies_: Function used to initialize a multi-species integrated species distribution model.startSpecies
Generic summary function for 'bruSDM'.summary.bruSDM summary.modISDM summary.modMarks summary.modSpecies