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_pkgdown.yml
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url: https://pbs-assess.github.io/sdmTMB/
template:
bootstrap: 5
reference:
- title: internal
contents:
- pcod
- pcod_2011
- pcod_mesh_2011
- qcs_grid
- dogfish
- yelloweye
- hbll_s_grid
- wcvi_grid
- get_pars
- delta_poisson_link_gamma
- delta_poisson_link_lognormal
- title: 'Mesh construction'
desc: |
Tools for converting coordinates into UTMs, constructing SPDE meshes prior
to model fitting, and adding correlation barriers.
contents:
- add_utm_columns
- get_crs
- make_mesh
- add_barrier_mesh
- title: 'Fitting and predicting'
desc: |
Core tools for model fitting, prediction, and inspection.
contents:
- sdmTMB
- sanity
- tidy.sdmTMB
- predict.sdmTMB
- residuals.sdmTMB
- dharma_residuals
- sdmTMBcontrol
- run_extra_optimization
- replicate_df
- set_delta_model
- coef.sdmTMB
- cAIC
- title: 'Families'
desc: |
Additional families beyond the standard R families.
contents:
- Beta
- lognormal
- nbinom2
- nbinom1
- student
- tweedie
- censored_poisson
- truncated_nbinom1
- truncated_nbinom2
- delta_gamma
- delta_lognormal
- delta_truncated_nbinom1
- delta_truncated_nbinom2
- gamma_mix
- lognormal_mix
- nbinom2_mix
- delta_gamma_mix
- delta_lognormal_mix
- title: 'Priors'
desc: |
Optional priors or penalties on parameters.
contents:
- sdmTMBpriors
- pc_matern
- plot_pc_matern
- normal
- halfnormal
- mvnormal
- title: 'Simulation'
desc: |
Simulating new data with an sdmTMB model.
contents:
- simulate.sdmTMB
- sdmTMB_simulate
- project
- title: 'Plotting'
desc: |
Functions for plotting.
contents:
- plot_anisotropy
- plot_smooth
- plot_pc_matern
- visreg_delta
- visreg2d_delta
- title: 'Cross validation'
desc: |
Functions related to cross validation.
contents:
- sdmTMB_cv
- sdmTMB_stacking
- title: 'Derived quantities'
desc: |
Derived quantities that can be calculated from sdmTMB models.
contents:
- get_index
- get_index_sims
- get_cog
- title: 'Miscellaneous parameter extraction'
desc: |
Functions for calculating effect sizes or extracting parameter samples.
contents:
- Effect.sdmTMB
- emmeans.sdmTMB
- spread_sims
- gather_sims