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Extract parameter simulations from the joint precision matrix

Source: R/gather-spread.R
gather_sims.Rd

spread_sims() returns a wide-format data frame. gather_sims() returns a long-format data frame. The format matches the format in the tidybayes spread_draws() and gather_draws() functions.

Usage

spread_sims(object, nsim = 200, n_sims = deprecated())

gather_sims(object, nsim = 200, n_sims = deprecated())

Arguments

object

Output from sdmTMB().

nsim

The number of simulation draws.

n_sims

Deprecated: please use nsim.

Value

A data frame. gather_sims() returns a long-format data frame:

  • .iteration: the sample ID

  • .variable: the parameter name

  • .value: the parameter sample value

spread_sims() returns a wide-format data frame:

  • .iteration: the sample ID

  • columns for each parameter with a sample per row

Examples

m <- sdmTMB(density ~ depth_scaled,
  data = pcod_2011, mesh = pcod_mesh_2011, family = tweedie())
head(spread_sims(m, nsim = 10))
#>   .iteration X.Intercept. depth_scaled    range      phi tweedie_p  sigma_O
#> 1          1     2.266213   -0.7238414 60.55531 14.53894  1.607782 1.751851
#> 2          2     2.753081   -0.6773062 38.69599 16.34944  1.595390 1.712716
#> 3          3     2.804002   -0.8767018 23.69324 16.09331  1.569319 2.801673
#> 4          4     2.850459   -0.7198302 33.79501 15.90992  1.591263 1.703641
#> 5          5     3.053531   -0.4808541 41.66564 15.91765  1.565976 1.897514
#> 6          6     2.935834   -0.4422661 35.64105 16.55391  1.557440 2.352120
head(gather_sims(m, nsim = 10))
#>   .iteration    .variable   .value
#> 1          1 X.Intercept. 3.190661
#> 2          2 X.Intercept. 2.980947
#> 3          3 X.Intercept. 2.845583
#> 4          4 X.Intercept. 2.647753
#> 5          5 X.Intercept. 2.042331
#> 6          6 X.Intercept. 2.632511
samps <- gather_sims(m, nsim = 1000)

if (require("ggplot2", quietly = TRUE)) {
  ggplot(samps, aes(.value)) + geom_histogram() +
    facet_wrap(~.variable, scales = "free_x")
}
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.