Files in sdmTMB

Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

MD5

NEWS.md

NAMESPACE

DESCRIPTION

R/rtmb-prepare.R R/covariate-diffusion.R R/tidy.R R/fit.R R/mesh.R R/print.R R/methods.R R/get-range-edge.R R/plot-pc-matern.R R/check.R R/family-capabilities.R R/priors.R R/zero-one-map.R R/rtmb-effects.R R/enum.R R/rtmb-priors.R R/emmeans.R R/rtmb-diffusion.R R/families.R R/family-response.R R/analysis-rows.R R/data.R R/predict.R R/rtmb-predictors.R R/gather-spread.R R/index.R R/rtmb-precision.R R/rtmb-report.R R/stacking.R R/areal.R R/prior-diagnostics.R R/plot.R R/smoothers.R R/caic.R R/backend.R R/rtmb-obs-families.R R/extra-optimization.R R/compare-deviance.R R/residuals.R R/get-index-sims.R R/tmb-sim.R R/rtmb-objective.R R/parsing.R R/visreg.R R/zzz.R R/predict-prepare.R R/model-matrix.R R/cross-val.R R/crs.R R/rtmb-observations.R R/censored-betabinomial.R R/family-prediction.R R/dharma.R R/family-spec.R R/project.R R/utils.R

src/sdmTMB.cpp

src/Makevars

src/covariate-diffusion.h

src/utils.h

inst/COPYRIGHTS

inst/CITATION

inst/WORDLIST

inst/doc/model-description.html

inst/doc/model-description.Rmd inst/doc/model-description.R

build/vignette.rds

build/partial.rdb

tests/testthat.R tests/testthat/test-rtmb-custom-priors.R tests/testthat/test-areal-domain.R tests/testthat/test-make-category-svc.R tests/testthat/test-rsr.R tests/testthat/test-2-print-anisotropy.R tests/testthat/test-rtmb-diffusion.R tests/testthat/test-betabinomial.R tests/testthat/test-zero-one-map.R tests/testthat/test-reml.R tests/testthat/test-threshold-models.R tests/testthat/test-rtmb-index.R tests/testthat/helper-covariate-diffusion.R tests/testthat/test-deviance.R tests/testthat/test-mcmc-resid.R tests/testthat/test-5-residuals.R tests/testthat/test-6-tmb-simulation.R tests/testthat/test-factor-levels.R tests/testthat/test-nonstationary.R tests/testthat/test-delta-population-predictions.R tests/testthat/test-methods.R tests/testthat/test-rtmb-fields.R tests/testthat/test-1-visreg.R tests/testthat/helper-rtmb.R tests/testthat/test-waywiser.R tests/testthat/test-smooths.R tests/testthat/test-offset.R tests/testthat/test-index.R tests/testthat/test-covariate-diffusion-grid.R tests/testthat/test-mesh.R tests/testthat/test-rtmb-families.R tests/testthat/test-prediction-missing-years.R tests/testthat/helper-fits.R tests/testthat/test-extra-time.R tests/testthat/test-predict-routing.R tests/testthat/test-family-response.R tests/testthat/test-forecasting.R tests/testthat/test-dispformula.R tests/testthat/test-rtmb-delta.R tests/testthat/test-emmeans.R tests/testthat/test-projection.R tests/testthat/test-covariate-diffusion-predict.R tests/testthat/test-tinyVAST.R tests/testthat/test-plots.R tests/testthat/test-se-fit.R tests/testthat/test-covariate-diffusion-parse.R tests/testthat/test-3-families.R tests/testthat/test-random-intercepts.R tests/testthat/test-without-spatial.R tests/testthat/test-areal-ohio-regression.R tests/testthat/test-covariate-diffusion-output.R tests/testthat/test-1-fit-basic.R tests/testthat/test-priors.R tests/testthat/test-rtmb-postfit.R tests/testthat/test-mix.R tests/testthat/test-ordbeta.R tests/testthat/test-rtmb-backend.R tests/testthat/test-deprecated-args.R tests/testthat/test-model-fixes.R tests/testthat/test-random-effects.R tests/testthat/test-2-fit-less-basic.R tests/testthat/test-extra-optimization.R tests/testthat/test-delta.R tests/testthat/test-tmb-simulation.R tests/testthat/test-covariate-diffusion-fit.R tests/testthat/test-range-edge.R tests/testthat/test-multi-family-core.R tests/testthat/test-rtmb-effects.R tests/testthat/test-sanity.R tests/testthat/test-covariate-diffusion-regression.R tests/testthat/test-covariate-diffusion-plumbing.R tests/testthat/test-utm-conversions.R tests/testthat/test-cAIC.R tests/testthat/test-cross-validation.R tests/testthat/test-response-means.R tests/testthat/test-8-delta2.R tests/testthat/test-aniso-plots.R tests/testthat/test-bayesian-predict.R tests/testthat/test-parameter-bounds.R tests/testthat/test-collapse.R tests/testthat/test-9-mvn-simulation.R tests/testthat/test-link-prediction.R tests/testthat/test-2-tidy.R tests/testthat/test-covariate-diffusion-simulation.R tests/testthat/test-dharma.R tests/testthat/test-predict-design-specs.R tests/testthat/test-links.R tests/testthat/test-share-range.R tests/testthat/helper-backend.R tests/testthat/test-sdmTMB-simulate.R tests/testthat/test-time-varying.R tests/testthat/test-ggeffect.R tests/testthat/test-poisson-link.R tests/testthat/test-covariate-diffusion-projection.R tests/testthat/test-3-spatial-varying.R tests/testthat/test-covariate-diffusion-plot.R tests/testthat/test-truncated-dists.R

vignettes/refs.bib

vignettes/model-description.Rmd

vignettes/mee.csl

data/hbll_s_grid.rda

data/ohio_sf.rda

data/pcod.rda

data/dogfish.rda

data/qcs_grid.rda

data/ohio_df.rda

data/yelloweye.rda

data/pcod_2011.rda

data/wcvi_grid.rda

data/pcod_mesh_2011.rda

man/Effect.sdmTMB.Rd man/residuals.sdmTMB.Rd man/reexports.Rd man/make_zero_one_map.Rd man/simulate.sdmTMB.Rd man/get_index_sims.Rd man/get_range_edge.Rd man/coef.sdmTMB.Rd man/plot_anisotropy.Rd man/surveydata.Rd man/cAIC.Rd man/sdmTMBcontrol.Rd man/cv_to_waywiser.Rd man/priors.Rd man/gather_sims.Rd man/get_pars.Rd man/make_mesh.Rd man/sdmTMB.Rd man/plot_pc_matern.Rd man/dharma_residuals.Rd man/make_areal_domain.Rd man/sdmTMB_stacking.Rd man/ohio_sf.Rd man/nonlocal_formula_plots.Rd man/sdmTMB_cv.Rd man/elpd.sdmTMB_cv.Rd man/replicate_df.Rd man/add_utm_columns.Rd man/project.Rd man/ggplot2_installed.Rd man/sanity.Rd man/make_category_svc.Rd man/run_extra_optimization.Rd man/emmeans.sdmTMB.Rd man/visreg_delta.Rd man/get_prior_parameters.Rd man/plot_smooth.Rd man/tidy.sdmTMB.Rd man/sigma.sdmTMB.Rd man/get_censored_upper.Rd man/update.sdmTMB.Rd man/nonlocal_terms.Rd man/get_index.Rd man/compare_deviance.Rd man/predict.sdmTMB.Rd man/set_delta_model.Rd man/simulate_new.Rd man/families.Rd

man/figures/lifecycle-stable.svg

man/figures/lifecycle-superseded.svg

man/figures/lifecycle-questioning.svg

man/figures/lifecycle-archived.svg

man/figures/lifecycle-defunct.svg

man/figures/lifecycle-experimental.svg

man/figures/lifecycle-deprecated.svg

man/figures/lifecycle-maturing.svg

sdmTMB documentation built on Oct. 17, 2026, 1:07 a.m.