sdmTMB0.7.0 package

Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

add_barrier_mesh

Transform a mesh object into a mesh with correlation barriers

gather_sims

Extract parameter simulations from the joint precision matrix

get_index_sims

Calculate a population index via simulation from the joint precision m...

get_index

Extract a relative biomass/abundance index, center of gravity, or effe...

get_pars

Get TMB parameter list

ggplot2_installed

Check if ggplot2 installed

run_extra_optimization

Run extra optimization on an already fitted object

sanity

Sanity check of an sdmTMB model

sdmTMB_cv

Cross validation with sdmTMB models

sdmTMB_simulate

Simulate from a spatial/spatiotemporal model

visreg_delta

Plot sdmTMB models with the visreg package

replicate_df

Replicate a prediction data frame over time

residuals.sdmTMB

Residuals method for sdmTMB models

add_utm_columns

Add UTM coordinates to a data frame

cAIC

Calculate conditional AIC

coef.sdmTMB

Get fixed-effect coefficients

dharma_residuals

DHARMa residuals

Effect.sdmTMB

Calculate effects

emmeans.sdmTMB

Estimated marginal means with the emmeans package with sdmTMB

extract_mcmc

Extract MCMC samples from a model fit with tmbstan.

families

Additional families

make_mesh

Construct an SPDE mesh for sdmTMB

plot_anisotropy

Plot anisotropy from an sdmTMB model

plot_pc_matern

Plot PC Matérn priors

plot_smooth

Plot a smooth term from an sdmTMB model

predict.sdmTMB

Predict from an sdmTMB model

priors

Prior distributions

project

Project from an sdmTMB model using simulation

reexports

Objects exported from other packages

sdmTMB_stacking

Perform stacking with log scores on sdmTMB_cv() output

sdmTMB

Fit a spatial or spatiotemporal GLMM with TMB

sdmTMBcontrol

Optimization control options

set_delta_model

Set delta model for ggeffects::ggpredict()

simulate.sdmTMB

Simulate from a fitted sdmTMB model

surveydata

Example fish survey data

tidy.sdmTMB

Turn sdmTMB model output into a tidy data frame

Implements spatial and spatiotemporal GLMMs (Generalized Linear Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial Differential Equation) Gaussian Markov random field approximation to Gaussian random fields. One common application is for spatially explicit species distribution models (SDMs). See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.

  • Maintainer: Sean C. Anderson
  • License: GPL-3
  • Last published: 2025-04-01