extr_outs {ProbBreed} | R Documentation |
stanfit
objects obtained from bayes_metExtracts outputs of the Bayesian model fitted
using bayes_met()
, and provides some diagnostics.
extr_outs(model, probs = c(0.025, 0.975), verbose = FALSE)
model |
An object of class |
probs |
A vector with two elements representing the probabilities (in decimal scale) that will be considered for computing the quantiles. |
verbose |
A logical value. If |
More details about the usage of extr_outs
and other functions of
the ProbBreed
package can be found at https://saulo-chaves.github.io/ProbBreed_site/.
The function returns an object of class extr
, which is a list with:
variances
: a data frame containing the variance components of
the model effects, their standard deviation, naive standard error and highest
posterior density interval.
post
: a list with the posterior of the effects, and the data
generated by the model.
map
: a list with the maximum posterior values of each effect
ppcheck
: a matrix containing the p-values of maximum, minimum,
median, mean and standard deviation; effective number of parameters, WAIC2
value, Rhat and effective sample size.
rstan::stan_diag, ggplot2::ggplot, rstan::check_hmc_diagnostics, plot.extr
mod = bayes_met(data = maize,
gen = "Hybrid",
loc = "Location",
repl = c("Rep","Block"),
trait = "GY",
reg = "Region",
year = NULL,
res.het = TRUE,
iter = 2000, cores = 2, chain = 4)
outs = extr_outs(model = mod,
probs = c(0.05, 0.95),
verbose = TRUE)