Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

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Documentation for package ‘sdmTMB’ version 1.2.0

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A B C D E F G H L M N O P Q R S T U V W Y

-- A --

add_utm_columns Add UTM coordinates to a data frame

-- B --

Beta Additional families
betabinomial Additional families

-- C --

cAIC Calculate conditional AIC
censored_betabinomial Additional families
censored_binomial Additional families
censored_nbinom1 Additional families
censored_nbinom2 Additional families
censored_poisson Additional families
coef.sdmTMB Get fixed-effect coefficients
compare_deviance Compare deviance between two models
cv_to_waywiser Convert 'sdmTMB_cv()' objects to 'sf' format for spatial assessment with 'waywiser'

-- D --

delta_beta Additional families
delta_gamma Additional families
delta_gamma_mix Additional families
delta_gengamma Additional families
delta_lognormal Additional families
delta_lognormal_mix Additional families
delta_truncated_nbinom1 Additional families
delta_truncated_nbinom2 Additional families
dharma_residuals DHARMa residual diagnostics
diffusion Non-local covariate terms
dogfish Example fish survey data

-- E --

Effect.sdmTMB Calculate effects
elpd.sdmTMB_cv Expected log predictive density from cross validation for 'loo'
emmeans.sdmTMB Estimated marginal means with the 'emmeans' package with 'sdmTMB'

-- F --

Families Additional families

-- G --

gamma_cv Prior distributions
gamma_mix Additional families
gather_sims Extract parameter simulations from the joint precision matrix
gengamma Additional families
get_censored_upper Calculate an upper bound on catch counts for the censored Poisson family
get_cog Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
get_crs Add UTM coordinates to a data frame
get_eao Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
get_index Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
get_index_sims Calculate a population index via simulation from the joint precision matrix
get_index_split Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
get_pars Get TMB parameter list
get_prior_densities Inspect custom priors
get_prior_parameters Inspect custom priors
get_range_edge Calculate range edges via simulation from the joint precision matrix
get_weighted_average Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average

-- H --

halfnormal Prior distributions
hbll_s_grid Example fish survey data

-- L --

lognormal Additional families
lognormal_mix Additional families
lognormal_prior Prior distributions

-- M --

make_areal_domain Create an areal spatial domain for SAR/CAR models
make_category_svc Set up spatially varying coefficients for category composition models
make_mesh Construct an SPDE mesh for sdmTMB
make_zero_one_map Fix factor-level intercepts for groups with all zeros or ones
mvnormal Prior distributions

-- N --

nbinom1 Additional families
nbinom2 Additional families
nbinom2_mix Additional families
nonlocal_terms Non-local covariate terms
normal Prior distributions

-- O --

ohio_df Ohio lung cancer mortality data, reshaped for spatiotemporal examples
ohio_sf Ohio lung cancer mortality data, reshaped for spatiotemporal examples
ordbeta Additional families

-- P --

pcod Example fish survey data
pcod_2011 Example fish survey data
pcod_mesh_2011 Example fish survey data
pc_matern Prior distributions
plot.sdmTMBmesh Construct an SPDE mesh for sdmTMB
plot_anisotropy Plot anisotropy from an sdmTMB model
plot_anisotropy2 Plot anisotropy from an sdmTMB model
plot_nonlocal_covariate Plot Covariate-Diffusion Diagnostics
plot_nonlocal_kernel Plot Covariate-Diffusion Diagnostics
plot_pc_matern Plot PC Matérn priors
plot_smooth Plot a smooth term from an sdmTMB model
predict.sdmTMB Predict from an sdmTMB model
project Project from an 'sdmTMB' model using simulation

-- Q --

qcs_grid Example fish survey data

-- R --

replicate_df Replicate a prediction data frame over time
residuals.sdmTMB Residuals method for sdmTMB models
run_extra_optimization Run extra optimization on an already fitted object

-- S --

sanity Sanity check of an sdmTMB model
sdmTMB Fit a spatial or spatiotemporal GLMM with TMB
sdmTMBcontrol Optimization control options
sdmTMBpriors Prior distributions
sdmTMB_cv Cross validation with sdmTMB models
sdmTMB_simulate Simulate from a spatial/spatiotemporal model
sdmTMB_stacking Perform stacking with log scores on 'sdmTMB_cv()' output
set_delta_model Set delta model for 'ggeffects::ggpredict()'
sigma.sdmTMB Extract residual standard deviation or dispersion parameter
simulate.sdmTMB Simulate from a fitted sdmTMB model
simulate_new Simulate from a spatial/spatiotemporal model
spread_sims Extract parameter simulations from the joint precision matrix
student Additional families

-- T --

tidy.sdmTMB Turn sdmTMB model output into a tidy data frame
tidy.sdmTMB_cv Turn sdmTMB model output into a tidy data frame
time_lag Non-local covariate terms
truncated_nbinom1 Additional families
truncated_nbinom2 Additional families
tweedie Additional families

-- U --

update.sdmTMB Update an sdmTMB model

-- V --

visreg2d_delta Plot sdmTMB models with the 'visreg' package
visreg_delta Plot sdmTMB models with the 'visreg' package

-- W --

wcvi_grid Example fish survey data

-- Y --

yelloweye Example fish survey data