Files in pbs-assess/sdmTMB

Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check-HTML5.yaml

.github/workflows/R-CMD-check-valgrind2.yaml

.github/workflows/R-CMD-check.yaml

.github/workflows/pkgdown.yaml

.github/workflows/rhub-manual.yaml

.github/workflows/rhub.yaml

.github/workflows/test-coverage.yaml

.gitignore

DESCRIPTION

Makefile

NAMESPACE

NEWS.md

R/.gitignore

R/check.R R/cross-val.R R/crs.R R/data.R R/deprecated.R R/dharma.R R/emmeans.R R/enum.R R/extra-optimization.R R/families.R R/fit.R R/gather-spread.R R/get-index-sims.R R/index.R R/mesh.R R/methods.R R/plot-pc-matern.R R/plot.R R/predict.R R/print.R R/priors.R R/residuals.R R/smoothers.R R/stacking.R R/tidy.R R/tmb-sim.R R/utils.R R/visreg.R R/zzz.R README.Rmd README.md

_pkgdown.yml

codecov.yml

cran-comments.md data-raw/bc_coast.R data-raw/pcod.R

data/dogfish.rda

data/hbll_s_grid.rda

data/pcod.rda

data/pcod_2011.rda

data/pcod_mesh_2011.rda

data/qcs_grid.rda

data/wcvi_grid.rda

data/yelloweye.rda

header.md

inst/CITATION

inst/COPYRIGHTS

man/Effect.sdmTMB.Rd man/add_barrier_mesh.Rd man/add_utm_columns.Rd man/dharma_residuals.Rd man/emmeans.sdmTMB.Rd man/extract_mcmc.Rd man/families.Rd

man/figures/README-inla-mesh-1.png

man/figures/README-plot-cog-1.png

man/figures/README-plot-dharma-1.png

man/figures/README-plot-index-1.png

man/figures/README-plot-mvn-1.png

man/figures/README-plot-pc-matern-1.png

man/figures/README-plot-pred-mvn-1.png

man/figures/README-plot-predictions-1.png

man/figures/README-plot-quant-resid-1.png

man/figures/README-plot-sim-dat-1.png

man/figures/README-plot-smooth-1.png

man/figures/README-plot-visreg-link-1.png

man/figures/README-plot-visreg-response-1.png

man/figures/README-plot-zeta-1.png

man/figures/lifecycle-archived.svg

man/figures/lifecycle-defunct.svg

man/figures/lifecycle-deprecated.svg

man/figures/lifecycle-experimental.svg

man/figures/lifecycle-maturing.svg

man/figures/lifecycle-questioning.svg

man/figures/lifecycle-stable.svg

man/figures/lifecycle-superseded.svg

man/figures/logo-sdmTMB.png

man/gather_sims.Rd man/get_index.Rd man/get_index_sims.Rd man/get_pars.Rd man/ggplot2_installed.Rd man/make_mesh.Rd man/plot_anisotropy.Rd man/plot_pc_matern.Rd man/plot_smooth.Rd man/predict.sdmTMB.Rd man/priors.Rd man/reexports.Rd man/replicate_df.Rd man/residuals.sdmTMB.Rd man/run_extra_optimization.Rd man/sanity.Rd man/sdmTMB.Rd man/sdmTMB_cv.Rd man/sdmTMB_simulate.Rd man/sdmTMB_stacking.Rd man/sdmTMBcontrol.Rd man/set_delta_model.Rd man/simulate.sdmTMB.Rd man/surveydata.Rd man/tidy.sdmTMB.Rd man/visreg_delta.Rd

scratch/.gitignore

scratch/aniso-tests.R scratch/barrier-mgcv.R scratch/barrier-vignette.R scratch/barrier-vignette2.R scratch/binary-search.R scratch/censored.R scratch/collapse.R scratch/delta-experiments.R scratch/dharma.R scratch/faster-index-calcs.R scratch/gg-mesh.R scratch/how-many-knots.Rmd scratch/jacobian-pcprior-tests.R scratch/jacobian-pcprior-tests2.R scratch/jacobian-tests.R scratch/julia-vignettes/forecasting.Rmd scratch/julia-vignettes/presence-only.Rmd scratch/julia-vignettes/test-1-vast.R

scratch/lm.cpp

scratch/lm_limits.cpp

scratch/lm_prior_jb.cpp

scratch/lm_prior_nojb.cpp

scratch/logo.R scratch/make_enum.R scratch/memory-tweedie.R scratch/osa.R scratch/pc-experiments.R scratch/pc-experiments2.R

scratch/pc_matern.cpp

scratch/pc_matern_prior.cpp

scratch/pc_matern_prior_jacobian.cpp

scratch/pc_matern_prior_jacobian2.cpp

scratch/poisson-link-debugging.R scratch/poisson-link.R scratch/profile.R

scratch/r2-glmm.qmd

scratch/r2.R scratch/rw-field-sparseness.Rmd scratch/rw.R scratch/sim-stan-experiments.R scratch/sim-test-ar1.Rmd scratch/sim-test-car.R scratch/sim-tmb.R scratch/smoother-tests.R scratch/stan-testing.R scratch/stan.R

scratch/symbols.csv

scratch/test-ar1.R scratch/test-cog.R scratch/test-fit-bias-epsilon.R scratch/test-fit-bias-families.R scratch/test-fit-bias-index.R scratch/test-fit-bias-st.R scratch/test-fit-bias.R scratch/test-fit-bias2.R scratch/test-interpolate-index.R scratch/test-lm.R scratch/test-open-mp.R scratch/test-random-intercepts.R scratch/test-range.R scratch/test-species.R scratch/test-temp-real-data.R scratch/test-tweedie.R scratch/test-valgrind.R scratch/test-versions.R

scratch/test_range.cpp

scratch/tmb-simulate-st.R scratch/tmb-simulate.R scratch/update-test.R scratch/upr_censoring.R

scratch/upr_censoring_test_df.csv

scratch/vast-compare.R scratch/westcoast.R

sdmTMB.Rproj

src/Makevars

src/sdmTMB.cpp

src/utils.h

tests/testthat.R tests/testthat/test-1-fit-basic.R tests/testthat/test-1-visreg.R tests/testthat/test-2-fit-less-basic.R tests/testthat/test-2-print-anisotropy.R tests/testthat/test-3-families.R tests/testthat/test-3-spatial-varying.R tests/testthat/test-4-index-calculation.R tests/testthat/test-5-residuals.R tests/testthat/test-6-tmb-simulation.R tests/testthat/test-8-delta2.R tests/testthat/test-9-mvn-simulation.R tests/testthat/test-aniso-plots.R tests/testthat/test-cross-validation.R tests/testthat/test-delta-population-predictions.R tests/testthat/test-delta.R tests/testthat/test-deprecated-args.R tests/testthat/test-dharma.R tests/testthat/test-extra-optimization.R tests/testthat/test-extra-time.R tests/testthat/test-factor-levels.R tests/testthat/test-forecasting.R tests/testthat/test-ggeffect.R tests/testthat/test-index.R tests/testthat/test-link-prediction.R tests/testthat/test-links.R tests/testthat/test-mcmc-resid.R tests/testthat/test-methods.R tests/testthat/test-mix.R tests/testthat/test-nonstationary.R tests/testthat/test-offset.R tests/testthat/test-parameter-bounds.R tests/testthat/test-plots.R tests/testthat/test-prediction-missing-years.R tests/testthat/test-priors.R tests/testthat/test-random-intercepts.R tests/testthat/test-reml.R tests/testthat/test-sanity.R tests/testthat/test-sdmTMB-simulate.R tests/testthat/test-share-range.R tests/testthat/test-smooths.R tests/testthat/test-threshold-models.R tests/testthat/test-tidy.R tests/testthat/test-time-varying.R tests/testthat/test-tmb-simulation.R tests/testthat/test-utm-conversions.R tests/testthat/test-varying-epsilon.R tests/testthat/test-without-spatial.R

vignettes/.gitignore

vignettes/mee.csl

vignettes/model-description.Rmd

vignettes/refs.bib

vignettes/web_only/basic-intro.Rmd vignettes/web_only/bayesian.Rmd vignettes/web_only/cross-validation.Rmd vignettes/web_only/delta-models.Rmd vignettes/web_only/ggeffects.Rmd vignettes/web_only/index-standardization.Rmd vignettes/web_only/poisson-link.Rmd vignettes/web_only/pretty-plots.Rmd vignettes/web_only/residual-checking.Rmd vignettes/web_only/spatial-trend-models.Rmd vignettes/web_only/threshold-models.Rmd vignettes/web_only/visreg.Rmd

pbs-assess/sdmTMB documentation built on April 22, 2024, 3:26 p.m.