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Extract structured-effect metadata

Source: R/methods.R
structured_effects.Rd

structured_effects() returns the structured random-effect markers that drmTMB parsed and fitted. It gives downstream tools a stable post-fit metadata table so they do not need to grep or re-parse formula text.

Usage

structured_effects(object, ...)

# Default S3 method
structured_effects(object, ...)

# S3 method for class 'drmTMB'
structured_effects(object, ...)

Arguments

object

A drmTMB fit.

...

Reserved for future extractor options.

Value

A data frame with one row per fitted structured-effect marker. The args, dpars, coef_names, endpoint_members, member_levels, provider_levels, observed_levels, endpoint_blocks, and endpoint_covariance_labels columns are list columns. Empty fits return the same columns with zero rows.

Details

The current fitted marker grammar is:

  • phylo(1 | species, tree = tree)

  • spatial(1 | site, coords = coords)

  • animal(1 | id, pedigree = pedigree), animal(1 | id, A = A), or animal(1 | id, Ainv = Ainv)

  • relmat(1 | id, K = K) or relmat(1 | id, Q = Q)

  • phylo_interaction(1 | plant:pollinator, tree1 = plant_tree, tree2 = pollinator_tree)

Some Gaussian routes also fit matching location-scale, bivariate, or one-slope structured blocks. Those routes still return one row per parsed structured marker, with dpars and coef_names stored as list columns.

Examples

dat <- data.frame(
  y = c(0.1, 0.4, 0.8, 1.1),
  x = c(-1, 0, 1, 2)
)
fit <- drmTMB(bf(y ~ x, sigma ~ 1), data = dat)
structured_effects(fit)
#>  [1] marker                     provider                  
#>  [3] grouping_variable          matrix_attachment         
#>  [5] matrix_id                  matrix_slot               
#>  [7] matrix_source              matrix_role               
#>  [9] matrix_digest              input_scale               
#> [11] level_alignment            missing_level_policy      
#> [13] bridge_marshalling         provenance_contract       
#> [15] structure                  group1                    
#> [17] group2                     label                     
#> [19] block                      block_label               
#> [21] covariance_layout          endpoint_set              
#> [23] coefficient_set            endpoint_member_set       
#> [25] endpoint_member_count      q                         
#> [27] n_re                       member_count              
#> [29] provider_level_count       observed_level_count      
#> [31] random_effect_block        correlation_level         
#> [33] dpars                      coef_names                
#> [35] endpoint_members           member_levels             
#> [37] provider_levels            observed_levels           
#> [39] endpoint_blocks            endpoint_covariance_labels
#> [41] args                      
#> <0 rows> (or 0-length row.names)