├── .Rbuildignore ├── .Rproj.user ├── 27B36B43 │ └── sources │ │ └── prop │ │ └── INDEX └── shared │ └── notebooks │ └── patch-chunk-names ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── .Rhistory ├── DC_detProbMM.R ├── DC_loglikFun.R ├── ExtractCovarsAtNodes.R ├── GPsimFFT3.R ├── MakeAAstack.R ├── MakeDCStack.R ├── MakePAstack.R ├── MakePPPstack.R ├── MakeSpatialRegion.R ├── PopEstimate.R ├── Pub_drawPosteriorSamps7.R ├── checkDesignMatrix1.R ├── checkInput.R ├── checkMesh.R ├── combineFormulae.R ├── createOffsets.R ├── estimatePisDoubleCount.R ├── isdm.model.matrix.R ├── isdm_onGrid.R ├── makeBoundary.R ├── makeCombinedStack.R ├── makeControl.R ├── makeFamLink.R ├── makeLoglWts.R ├── makeMesh.R ├── makePopEstiControl.R ├── plot.isdm.R ├── predFromObj.R ├── predict.isdm.R ├── prepareDCdata.R ├── prepareSingleSurvey.R ├── print.summary.isdm.R ├── remove.holes.R ├── removeParsingChars.R ├── residuals.isdm.R ├── set.sim.control.R ├── setPriors.R ├── simulate.R ├── standardiseThatDesMatrix.R ├── summary.isdm.R └── uniqueVarNames.R ├── README.html ├── README.md ├── README.rmd ├── RISDM.Rproj ├── inst ├── CITATION └── extdata │ ├── ACT_DemoData.grd │ ├── ACT_DemoData.grd.aux.xml │ ├── ACT_DemoData.gri │ ├── GambaExample_SMRZ_23Mar28.tif │ ├── GambaExample_sqrtACC_23Mar28.tif │ ├── GambaExample_sqrtDEM_23Mar28.tif │ ├── Gamba_PA_23Mar28.RDS │ └── Gamba_PO_23Mar28.RDS ├── man ├── .Rhistory ├── PopEstimate.rd ├── checkMesh.rd ├── isdm.rd ├── makeMesh.rd ├── plot.isdm.rd ├── predict.isdm.rd ├── residuals.isdm.rd ├── simulateData.isdm.rd └── summary.isdm.rd ├── tests ├── testthat.R └── testthat │ ├── test_PopEstimate.R │ ├── test_checkMesh.R │ ├── test_isdm.R │ ├── test_makeMesh.R │ ├── test_plot.R │ ├── test_predict.isdm.R │ ├── test_residuals.isdm.R │ ├── test_simulateData.isdm.R │ └── test_summary.isdm.R └── vignettes ├── RISDM-concordance.tex ├── RISDM.bib ├── RISDM.bib.bak ├── RISDM.rnw └── figure ├── checkMesh1-1.pdf ├── interp-1.pdf ├── 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