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including prior information in model_parameters
output for metaBMA
objects
#347
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library(parameters)
library(metaBMA)
#> Loading required package: Rcpp
data(towels)
set.seed(123)
mr <- meta_random(logOR, SE, study, data = towels,
d = prior("norm", c(mean=0, sd=.3), lower = 0),
tau = prior("invgamma", c(shape = 1, scale = 0.15)),
rel.tol=.Machine$double.eps^.15, iter=1000)
mr2 <- meta_fixed(logOR, SE, study, data = towels)
model_parameters(mr)
#> # Studies
#>
#> Parameter | Coefficient | SE | 95% CI | Weight
#> -------------------------------------------------------------------------------------------------
#> Goldstein, Cialdini, & Griskevicius (2008), Exp. 1 | 0.38 | 0.20 | [-0.01, 0.77] | 25.59
#> Goldstein, Cialdini, & Griskevicius (2008), Exp. 2 | 0.30 | 0.14 | [ 0.04, 0.57] | 53.97
#> Schultz, Khazian, & Zaleski (2008), Exp. 2 | 0.21 | 0.19 | [-0.17, 0.58] | 27.24
#> Schultz, Khazian, & Zaleski (2008), Exp. 3 | 0.25 | 0.17 | [-0.08, 0.58] | 34.57
#> Mair & Bergin-Seers (2010), Exp. 1 | 0.29 | 0.82 | [-1.33, 1.90] | 1.47
#> Bohner & Schluter (2014), Exp. 1 | -0.12 | 0.25 | [-0.61, 0.36] | 16.25
#> Bohner & Schluter (2014), Exp. 2 | -1.46 | 0.76 | [-2.95, 0.03] | 1.73
#>
#> # Meta-Parameters
#>
#> Parameter | Coefficient | SE | 95% CI | BF | Rhat | ESS | Prior
#> ---------------------------------------------------------------------------------------------
#> Overall | 0.19 | 0.09 | [0.02, 0.35] | 3.81 | 1.001 | 1077.40 | Norm (0 +- 0.30)
#> tau | 0.13 | 0.09 | [0.02, 0.32] | | 1.002 | 928.20 | Invgamma (1 +- 0.15)
#> Using highest density intervals as credible intervals.
model_parameters(mr2)
#> # Studies
#>
#> Parameter | Coefficient | SE | 95% CI | Weight
#> -------------------------------------------------------------------------------------------------
#> Goldstein, Cialdini, & Griskevicius (2008), Exp. 1 | 0.38 | 0.20 | [-0.01, 0.77] | 25.59
#> Goldstein, Cialdini, & Griskevicius (2008), Exp. 2 | 0.30 | 0.14 | [ 0.04, 0.57] | 53.97
#> Schultz, Khazian, & Zaleski (2008), Exp. 2 | 0.21 | 0.19 | [-0.17, 0.58] | 27.24
#> Schultz, Khazian, & Zaleski (2008), Exp. 3 | 0.25 | 0.17 | [-0.08, 0.58] | 34.57
#> Mair & Bergin-Seers (2010), Exp. 1 | 0.29 | 0.82 | [-1.33, 1.90] | 1.47
#> Bohner & Schluter (2014), Exp. 1 | -0.12 | 0.25 | [-0.61, 0.36] | 16.25
#> Bohner & Schluter (2014), Exp. 2 | -1.46 | 0.76 | [-2.95, 0.03] | 1.73
#>
#> # Meta-Parameters
#>
#> Parameter | Coefficient | SE | 95% CI | BF | Prior
#> ------------------------------------------------------------------------
#> Overall | 0.21 | 0.08 | [0.06, 0.36] | 11.97 | Norm (0 +- 0.30)
#> Using highest density intervals as credible intervals. Created on 2020-11-24 by the reprex package (v0.3.0) |
I think there is something wrong here. The prior information doesn't match with prior information in the model object. I would have expected the prior here to be 0.707. # setup
set.seed(123)
library(metaBMA)
#> Loading required package: Rcpp
# creating a dataframe
df1 <-
structure(
.Data = list(
term = c("1", "2", "3", "4", "5"),
estimate = c(
0.382047603321706,
0.780783111514665,
0.425607573765058,
0.558365541235078,
0.956473848429961
),
std.error = c(
0.0465576338644502,
0.0330218199731529,
0.0362834986178494,
0.0480571500648261,
0.062215818388157
)
),
row.names = c(NA, -5L),
class = c("tbl_df", "tbl", "data.frame")
)
# model
set.seed(123)
mod <-
meta_random(
y = df1$estimate,
SE = df1$std.error,
iter = 1000,
summarize = "integrate"
)
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
mod$jzs
#> $rscale_contin
#> [1] 0.5
#>
#> $rscale_discrete
#> [1] 0.7071068
#>
#> $centering
#> [1] TRUE
insight::get_priors(mod)
#> Parameter Distribution Location Scale
#> 1 (Intercept) norm 0 0.30
#> 2 tau invgamma 1 0.15 Created on 2020-11-24 by the reprex package (v0.3.0.9001) |
I think we had this discussion before. mod
#> ### Bayesian Random-Effects Meta-Analysis ###
#> Prior on d: 'norm' (mean=0, sd=0.3) with support on the interval [-Inf,Inf].
#> Prior on tau: 'invgamma' (shape=1, scale=0.15) with support on the interval [0,Inf].
#>
#> # Bayes factors:
#> (denominator)
#> (numerator) random_H0 random_H1
#> random_H0 1.0 0.0354
#> random_H1 28.2 1.0000
#>
#> # Posterior summary statistics of random-effects model:
#> mean sd 2.5% 50% 97.5% hpd95_lower hpd95_upper n_eff Rhat
#> d 0.518 0.140 0.180 0.536 0.743 0.219 0.766 NA NA
#> tau 0.288 0.141 0.134 0.253 0.653 0.106 0.553 NA NA Created on 2020-11-24 by the reprex package (v0.3.0) |
Hmm, I see. Okay, I will still be curious to hear from @danheck about what's the official take on this. |
Sorry for the confusion - the internal numbers However, one could argue that the default prior |
Thanks a lot, @danheck! This is really helpful and clears up the confusion on my side. I would also vote for defaulting to |
Created on 2020-11-24 by the reprex package (v0.3.0.9001)
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