Package: IsoriX 0.9.3.9000

IsoriX: Isoscape Computation and Inference of Spatial Origins using Mixed Models

Building isoscapes using mixed models and inferring the geographic origin of samples based on their isotopic ratios. This package is essentially a simplified interface to several other packages which implements a new statistical framework based on mixed models. It uses 'spaMM' for fitting and predicting isoscapes, and assigning an organism's origin depending on its isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for plotting the maps produced with 'terra' using 'lattice'.

Authors:Alexandre Courtiol [aut, cre], François Rousset [aut], Marie-Sophie Rohwaeder [aut], Stephanie Kramer-Schadt [aut]

IsoriX_0.9.3.9000.tar.gz
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IsoriX.pdf |IsoriX.html✨
IsoriX/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/courtiol/isorix/issues

Datasets:

On CRAN:

39 exports 12 stars 2.34 score 39 dependencies 1 mentions 55 scripts 920 downloads

Last updated 7 days agofrom:59a66074ad. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 11 2024
R-4.5-winOKSep 11 2024
R-4.5-linuxOKSep 11 2024
R-4.4-winOKSep 11 2024
R-4.4-macOKSep 11 2024
R-4.3-winOKSep 11 2024
R-4.3-macOKSep 11 2024

Exports:calibfitcellSizecreate_alienscrscrs<-downloadfileextext<-extractget_ranParsgetelevgetOption_IsoriXgetprecipgpargrid.textisofindisofitisomultifitisomultiscapeisoscapelayerlevelplotlpolygonoptions_IsoriXplotpointspolysprepcipitatepreprasterprepsourcesrastRdBuThemereadRDSsaveRDSsaveRDS_IsoriXshiftvaluesvectxyplot

Dependencies:abindbackportsbootcheckmatecrayondeldirgeometrygmphexbininterpjpeglatticelatticeExtralinproglpSolvemagicMASSMatrixminqanlmenloptrnumDerivpbapplypngproxyrasterrasterVisRColorBrewerRcppRcppEigenRcppProgressregistryROIslamspspaMMterraviridisLitezoo

Readme and manuals

Help Manual

Help pageTopics
Isoscape Computation and Inference of Spatial Origins using Mixed ModelsIsoriX-package IsoriX
Simulated assignment datasetAssignDataAlien
Assignment datasets for bat speciesAssignDataBat AssignDataBatRev
Assignment datasets for bat speciesAssignDataBat2 AssignDataBat2Rev
Simulated calibration datasetCalibDataAlien
Calibration datasets for bat speciesCalibDataBat CalibDataBatRev
Calibration datasets for bat speciesCalibDataBat2 CalibDataBat2Rev
Fit the calibration model (or load parameters from calibration done outside IsoriX)calibfit print.CALIBFIT summary.CALIBFIT
Class CALIBFITCALIBFIT-class
Borders of world CountryBordersCountryBorders
Simulate datasets for calibrations or assignmentscreate_aliens
Download files and check their binary integritydownloadfile
The raster of elevation for GermanyElevRasterDE
Download an elevation raster from internetgetelev
Download rasters of monthly precipitation from internetgetprecip
Hydrogen delta values in precipitation water, GermanyGNIPDataDE
Hydrogen delta values in precipitation water (aggregated per location)GNIPDataALLagg GNIPDataEUagg
Infer spatial originsisofind print.ISOFIND summary.ISOFIND
Class ISOFINDISOFIND-class
Fit the isoscape modelsisofit print.ISOFIT summary.ISOFIT
Fit isoscape models per strata (typically time interval such as months)isomultifit
Predicts the average spatial distribution of isotopic values over months, years...isomultiscape
Colour palettes for plottingisopalette1 isopalette2
Defunct and deprecated functionsCalibfit GetElev Isofit Isorix IsoriX-defunct Isoscape Isosim prepdata prepelev prepiso QueryGNIP queryGNIP RElevate relevate
Predicts the spatial distribution of source isotopic valuesisoscape print.isoscape summary.isoscape
Class ISOSCAPEISOSCAPE-class
Mask of world oceansOceanMask
Setting and displaying the options of the packagegetOption_IsoriX options options_IsoriX
Plotting functions for IsoriXplot.CALIBFIT plot.ISOFIND plot.ISOFIT plot.ISOSCAPE plot.SpatRaster plots points.CALIBFIT
The precipitation monthly amounts for GermanyPrecipBrickDE
Prepare the raster brick containing the precipitation dataprepcipitate
Prepare the structural rasterprepraster
Filter and aggregate the raw source datasetprepsources
Save and read objects produced by IsoriX using RDS filesreadRDS readRDS,character-method readRDS.character saveRDS saveRDS,CALIBFIT-method saveRDS,ISOFIND-method saveRDS,ISOSCAPE-method saveRDS.CALIBFIT saveRDS.ISOFIND saveRDS.ISOSCAPE saveRDS_IsoriX serialise serialize