Fix print() method for model_parameters.stanmvreg()
#173
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most likely related to easystats/bayestestR#31. |
strengejacke
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model_parameters fails with Bayesian multivariate glmer modelmodel_parameters.stanmvreg()
set.seed(123)
library(rstanarm)
pbcLong$ybern <- as.integer(pbcLong$logBili >= mean(pbcLong$logBili))
# model
mod <-
rstanarm::stan_mvmer(
formula = list(
ybern ~ year + (1 | id),
albumin ~ sex + year + (year | id)
),
data = pbcLong,
family = list(binomial, gaussian),
chains = 1, cores = 1, seed = 12345, iter = 1000
)
# summary
parameters::model_parameters(mod)
#> Parameter | Median | CI | 89% CI | pd | Rhat | ESS | Prior | Prior_Response
#> ------------------------------------------------------------------------------------------------------------
#> | -0.15 | 89.00 | [-1.99, 1.63] | 55.60% | 1.027 | 81 | NA ( +- ) |
#> | 0.41 | 89.00 | [ 0.28, 0.56] | 100% | 0.998 | 1251 | NA ( +- ) |
#> | 3.46 | 89.00 | [ 3.06, 3.79] | 100% | 1.018 | 142 | NA ( +- ) |
#> | 0.07 | 89.00 | [-0.27, 0.45] | 62.60% | 1.005 | 214 | NA ( +- ) |
#> | -0.13 | 89.00 | [-0.16, -0.10] | 100% | 1.011 | 183 | NA ( +- ) |
#> (Intercept) | | | | | | | Normal (0 +- 10.00) | y1
#> (Intercept) | | | | | | | Normal (0 +- 0.70) | y1
#> sexf | | | | | | | Normal (0 +- 1.39) | y2
#> year | | | | | | | Normal (0 +- 5.57) | y2
#> year | | | | | | | Normal (0 +- 0.39) | y2Created on 2019-12-26 by the reprex package (v0.3.0) |
# setup
set.seed(123)
library(rstanarm)
#> Loading required package: Rcpp
#> Registered S3 method overwritten by 'xts':
#> method from
#> as.zoo.xts zoo
#> rstanarm (Version 2.19.2, packaged: 2019-10-01 20:20:33 UTC)
#> - Do not expect the default priors to remain the same in future rstanarm versions.
#> Thus, R scripts should specify priors explicitly, even if they are just the defaults.
#> - For execution on a local, multicore CPU with excess RAM we recommend calling
#> options(mc.cores = parallel::detectCores())
#> - bayesplot theme set to bayesplot::theme_default()
#> * Does _not_ affect other ggplot2 plots
#> * See ?bayesplot_theme_set for details on theme setting
pbcLong$ybern <- as.integer(pbcLong$logBili >= mean(pbcLong$logBili))
# model
mod <-
rstanarm::stan_mvmer(
formula = list(
ybern ~ year + (1 | id),
albumin ~ sex + year + (year | id)
),
data = pbcLong,
family = list(binomial, gaussian),
chains = 1, cores = 1, seed = 12345, iter = 1000
)
#> Fitting a multivariate glmer model.
#>
#> Please note the warmup may be much slower than later iterations!
#>
#> SAMPLING FOR MODEL 'mvmer' NOW (CHAIN 1).
#> Chain 1:
#> Chain 1: Gradient evaluation took 0 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1:
#> Chain 1:
#> Chain 1: Iteration: 1 / 1000 [ 0%] (Warmup)
#> Chain 1: Iteration: 100 / 1000 [ 10%] (Warmup)
#> Chain 1: Iteration: 200 / 1000 [ 20%] (Warmup)
#> Chain 1: Iteration: 300 / 1000 [ 30%] (Warmup)
#> Chain 1: Iteration: 400 / 1000 [ 40%] (Warmup)
#> Chain 1: Iteration: 500 / 1000 [ 50%] (Warmup)
#> Chain 1: Iteration: 501 / 1000 [ 50%] (Sampling)
#> Chain 1: Iteration: 600 / 1000 [ 60%] (Sampling)
#> Chain 1: Iteration: 700 / 1000 [ 70%] (Sampling)
#> Chain 1: Iteration: 800 / 1000 [ 80%] (Sampling)
#> Chain 1: Iteration: 900 / 1000 [ 90%] (Sampling)
#> Chain 1: Iteration: 1000 / 1000 [100%] (Sampling)
#> Chain 1:
#> Chain 1: Elapsed Time: 5.158 seconds (Warm-up)
#> Chain 1: 2.81 seconds (Sampling)
#> Chain 1: 7.968 seconds (Total)
#> Chain 1:
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
library(parameters)
model_parameters(mod)
#> # y1 response
#>
#> Parameter | Median | 89% CI | pd | Rhat | ESS | Prior
#> ----------------------------------------------------------------------------------
#> (Intercept) | -0.15 | [-1.99, 1.63] | 55.60% | 1.027 | 81 | Normal (0 +- 10.00)
#> year | 0.41 | [ 0.28, 0.56] | 100% | 0.998 | 1251 | Normal (0 +- 0.70)
#>
#> # y2 response
#>
#> Parameter | Median | 89% CI | pd | Rhat | ESS | Prior
#> ---------------------------------------------------------------------------------
#> (Intercept) | 3.46 | [ 3.06, 3.79] | 100% | 1.018 | 142 | Normal (0 +- 5.57)
#> sexf | 0.07 | [-0.27, 0.45] | 62.60% | 1.005 | 214 | Normal (0 +- 1.39)
#> year | -0.13 | [-0.16, -0.10] | 100% | 1.011 | 183 | Normal (0 +- 0.39)Created on 2019-12-30 by the reprex package (v0.3.0) |
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Created on 2019-12-24 by the reprex package (v0.3.0)
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