Files in spaMM

Mixed-Effect Models, with or without Spatial Random Effects

R/RcppExports.R R/LevenbergMstep.R R/glm.nodev.fit.R R/preprocess_MV.R R/corrPars.R R/corrHLfit.R R/corrHLfit_body.R R/corrHLfit-internals.R R/combinepar.R R/sXaug_sparsePrecisions.R R/predict_mv.R R/update.HL.R R/safe_opt.R R/Matern_family.R R/corMatern.R R/multinomial.R R/calc_LRT.R R/drop1.R R/LevM_v_h_spprec.R R/hatvalues.R R/save.R R/predictor.R R/bloc_lambda.R R/HLfit.R R/GLM.fit.R R/COMPoisson.R R/LMLTslots.R R/simulate.HL.R R/sparseX.R R/correlationFns.R R/terms.R R/plot.HLfit.R R/LevM_internals.R R/fitme_body.R R/postfit_internals.R R/Beta.R R/HLFactorList.R R/geo_info.R R/poisson.R R/llm.fit.R R/get_cPredVar.R R/spaMM.data.R R/corrFamilies.R R/augZXy_obj.R R/multiFRK.R R/sXaug_Matrix_QRP_CHM.R R/sXaug_Matrix_CHM_Hess.R R/precision_internals.R R/HLfit_Internals.R R/fit_as_sparsePrecision.R R/predict.R R/dispGammaGLM.R R/HLfit_body_NOT_loopenv.R R/LevM_v_h.R R/LLM.R R/constructors_IMRFs.R R/makeLowerUpper.R R/generateName.R R/predict_marg.R R/fit_as_ZX.R R/numInfo.R R/corrMM.LRT.R R/betabin.R R/fitmv_internals.R R/negbin2.R R/HLfit_loop.R R/extractors.R R/get_inits_by_glm.R R/spaMM_boot.R R/HLframes.R R/negbin1.R R/dofuture.R R/fitme.R R/cov_new_fix.R R/fam2LLfam.R R/HLCor_body.R R/confint.R R/step_HLfit.R R/determine_spprec.R R/ZAL_class.R R/fitmv_body.R R/CanonizeRanPars.R R/antisym.R R/locoptim.R R/profile.R R/spaMM_error.R R/MakeCovEst.R R/HLCor.R R/sXaug_EigenDense_QRP_Chol_scaled.R R/preprocess.R R/betaresp.R R/fitme_fitmv_internals.R R/HLfit_body_augZXy.R R/IRLS_internals.R R/HLfit_body.R R/preprocess_internals.R R/LR.R R/separator.R R/fitmecorrHLfit_body_internals.R R/X.GCA.R R/corrFamily.R R/summary.HL.R R/mapMM.R R/calc_logdisp_cov.R R/plot_effects.R R/utils.R R/expandSlash.R R/SEM.R R/HLfit_b_internals.R R/glm.reformat.R R/inverse.Gamma.R R/newPLS.R tests/plot2.pdf tests/plot1.pdf tests/test-all.R tests/testthat/test-pdep-effects.R tests/testthat/test-IMRF.R tests/testthat/test-extractors-spprec.R tests/testthat/test-salamander.R tests/testthat/test-random-slope.R tests/testthat/test-Rasch.R tests/testthat/test-ANOVA-&-lmerTest.R tests/testthat/test-ranCoefs.R tests/testthat/test-predVar-Matern-corrMatrix.R tests/testthat/test-X.GCA.R tests/testthat/test-Nugget.R tests/testthat/test_outer.R tests/testthat/test-fixedLRT.R tests/testthat/test-IsoriX-new.R tests/testthat/test-obsInfo.R tests/testthat/test-multinomial.R tests/testthat/test-corrFamily-doc-examples.R tests/testthat/test-distMatrix.R tests/testthat/test-LLM.R tests/testthat/test-spaMM.R tests/testthat/test-DHARMa.R tests/testthat/test_init_NaN.R tests/testthat/test-LRT-boot.R tests/testthat/test-numInfo.R tests/testthat/test-predVar.R tests/testthat/test-COMPoisson.R tests/testthat/test-poly.R tests/testthat/test-composite.R tests/testthat/test-Infusion.R tests/testthat/test-confint-spprec.R tests/testthat/test-rank.R tests/testthat/test-spaMM.filled.contour.R tests/testthat/test-simulate.R tests/testthat/test-corMatern.R tests/testthat/test-AR1.R tests/testthat/test-augZXy.R tests/testthat/test-GxE_variance_stability.R tests/testthat/test-separation.R tests/testthat/test-HLCor.R tests/testthat/test-confint.R tests/testthat/test-CAR.R tests/testthat/test-corrFamilies.R tests/testthat/test-cloglog.R tests/testthat/test-nested-geostat.R tests/testthat/test-dhglm.R tests/testthat/test-filled.mapMM.R tests/testthat/test-adjacency-long.R tests/testthat/test-inverse.Gamma.R tests/testthat/test-pedigree.R tests/testthat/test-cAIC.R tests/testthat/test-adjacency-corrMatrix.R tests/testthat/test-MSFDR.R tests/testthat/test-more-predict.R tests/testthat/test-HLfit.R tests/testthat/test-spaMM_glm.R tests/testthat/test-blackbox.R tests/testthat/test-mv.R tests/testthat/test-truncated.R tests/testthat/test-negbin1.R tests/testthat/nestedFiles/isoscape.R tests/testthat/nestedFiles/calibfit.R tests/testthat/extralong/test-mv-corrFamily.R tests/testthat/extralong/test-mv-extra.R tests/testthat/extralong/test-composite-extra.R man/MaternIMRF.Rd man/rankinfo.Rd man/mv.Rd man/residuals.HLfit.Rd man/ARp.Rd man/setNbThreads.Rd man/corrHLfit.Rd man/pedigree.Rd man/wrap_parallel.Rd man/numInfo.Rd man/predict.Rd man/dofuture.Rd man/multinomial.Rd man/spaMM-conventions.Rd man/random-effects.Rd man/convergence.Rd man/diallel_fixed.Rd man/COMPoisson.Rd man/IMRF.Rd man/get_cPredVar.Rd man/drop1.HLfit.Rd man/seeds.Rd man/HLCor.Rd man/phi-resid.model.Rd man/Loaloa.Rd man/residVar.Rd man/plot_effect.Rd man/AIC.Rd man/is_separated.Rd man/freight.Rd man/spaMM_boot.Rd man/get_RLRSim_args.Rd man/DoF.Rd man/spaMMcolors.Rd man/update.Rd man/confint.Rd man/mapMM.Rd man/blackcap.Rd man/verbose.Rd man/summary.HL.Rd man/control.HLfit.Rd man/negbin1.Rd man/resid.model.Rd man/algebra.Rd man/eval_replicate.Rd man/lev2bool.Rd man/Gryphon.Rd man/fitmv.Rd man/vcov.Rd man/wafers.Rd man/method.Rd man/dopar.Rd man/corrFamily-design.Rd man/poisson.Rd man/PLS-internals.Rd man/as_LMLT.Rd man/corrFamily.Rd man/fix_predVar.Rd man/good-practice.Rd man/hatvalues.HLfit.Rd man/adjlg.Rd man/get_fittedPars.Rd man/div_info.Rd man/fixed.Rd man/stripHLfit.Rd man/corMatern.Rd man/GLM.fit.Rd man/clinics.Rd man/register_cF.Rd man/covStruct.Rd man/get_inits_from_fit.Rd man/spaMM-S3.Rd man/corrMatrix.Rd man/R2.Rd man/fixed.LRT.Rd man/predVar.Rd man/plot.HL.Rd man/get_matrix.Rd man/diallel.Rd man/welding.Rd man/anova.HLfit.Rd man/inits.Rd man/spaMM.filled.contour.Rd man/simulate.Rd man/spaMM.Rd man/extractors.Rd man/corrFamily-definition.Rd man/MaternCorr.Rd man/corr_family.Rd man/CauchyCorr.Rd man/spaMM-internal.Rd man/autoregressive.Rd man/how.Rd man/beta_resp.Rd man/make.scaled.dist.Rd man/WinterWheat.Rd man/seaMask.Rd man/post-fit.Rd man/negbin.Rd man/libraries.Rd man/composite_ranef.Rd man/arabidopsis.Rd man/llm.fit.Rd man/inverse.Gamma.Rd man/options.Rd man/mat_sqrt.Rd man/ZAXlist.Rd man/betabin.Rd man/MSFDR.Rd man/fitme.Rd man/salamander.Rd man/extreme_eig.Rd man/scotlip.Rd man/HLfit.Rd man/Leuca.Rd