swh:1:snp:2c68a6c5a8af2f06ac2c0225927f25b54fd1f9d0
Tip revision: 428249f43a9c6fd0c425b28deb5fee51a9525d69 authored by Dominique Makowski on 18 September 2022, 01:46:03 UTC
version 0.13.0
version 0.13.0
Tip revision: 428249f
describe_posterior.R
#' Describe Posterior Distributions
#'
#' Compute indices relevant to describe and characterize the posterior distributions.
#'
#' @param posteriors A vector, data frame or model of posterior draws.
#' **bayestestR** supports a wide range of models (see `methods("describe_posterior")`)
#' and not all of those are documented in the 'Usage' section, because methods
#' for other classes mostly resemble the arguments of the `.numeric` method.
#' @param ci_method The type of index used for Credible Interval. Can be
#' `"ETI"` (default, see [bayestestR::eti()]), `"HDI"`
#' (see [bayestestR::hdi()]), `"BCI"` (see
#' [bayestestR::bci()]), `"SPI"` (see [bayestestR::spi()]), or
#' `"SI"` (see [bayestestR::si()]).
#' @param test The indices of effect existence to compute. Character (vector) or
#' list with one or more of these options: `"p_direction"` (or `"pd"`),
#' `"rope"`, `"p_map"`, `"equivalence_test"` (or `"equitest"`),
#' `"bayesfactor"` (or `"bf"`) or `"all"` to compute all tests.
#' For each "test", the corresponding \pkg{bayestestR} function is called
#' (e.g. [bayestestR::rope()] or [bayestestR::p_direction()]) and its results
#' included in the summary output.
#' @param rope_range ROPE's lower and higher bounds. Should be a list of two
#' values (e.g., `c(-0.1, 0.1)`) or `"default"`. If `"default"`,
#' the bounds are set to `x +- 0.1*SD(response)`.
#' @param rope_ci The Credible Interval (CI) probability, corresponding to the
#' proportion of HDI, to use for the percentage in ROPE.
#' @param keep_iterations If `TRUE`, will keep all iterations (draws) of
#' bootstrapped or Bayesian models. They will be added as additional columns
#' named `iter_1, iter_2, ...`. You can reshape them to a long format by
#' running [bayestestR::reshape_iterations()].
#' @param bf_prior Distribution representing a prior for the computation of
#' Bayes factors / SI. Used if the input is a posterior, otherwise (in the
#' case of models) ignored.
#' @param priors Add the prior used for each parameter.
#'
#' @inheritParams point_estimate
#' @inheritParams ci
#' @inheritParams si
#'
#' @details
#' One or more components of point estimates (like posterior mean or median),
#' intervals and tests can be omitted from the summary output by setting the
#' related argument to `NULL`. For example, `test = NULL` and `centrality =
#' NULL` would only return the HDI (or CI).
#'
#' @references
#' - Makowski, D., Ben-Shachar, M. S., Chen, S. H. A., and Lüdecke, D. (2019).
#' *Indices of Effect Existence and Significance in the Bayesian Framework*.
#' Frontiers in Psychology 2019;10:2767. \doi{10.3389/fpsyg.2019.02767}
#' - [Region of Practical Equivalence (ROPE)](https://easystats.github.io/bayestestR/articles/region_of_practical_equivalence.html)
#' - [Bayes factors](https://easystats.github.io/bayestestR/articles/bayes_factors.html)
#'
#' @examples
#' library(bayestestR)
#'
#' if (require("logspline")) {
#' x <- rnorm(1000)
#' describe_posterior(x)
#' describe_posterior(x, centrality = "all", dispersion = TRUE, test = "all")
#' describe_posterior(x, ci = c(0.80, 0.90))
#'
#' df <- data.frame(replicate(4, rnorm(100)))
#' describe_posterior(df)
#' describe_posterior(df, centrality = "all", dispersion = TRUE, test = "all")
#' describe_posterior(df, ci = c(0.80, 0.90))
#'
#' df <- data.frame(replicate(4, rnorm(20)))
#' head(reshape_iterations(describe_posterior(df, keep_iterations = TRUE)))
#' }
#' \dontrun{
#' # rstanarm models
#' # -----------------------------------------------
#' if (require("rstanarm") && require("emmeans")) {
#' model <- stan_glm(mpg ~ wt + gear, data = mtcars, chains = 2, iter = 200, refresh = 0)
#' describe_posterior(model)
#' describe_posterior(model, centrality = "all", dispersion = TRUE, test = "all")
#' describe_posterior(model, ci = c(0.80, 0.90))
#'
#' # emmeans estimates
#' # -----------------------------------------------
#' describe_posterior(emtrends(model, ~1, "wt"))
#' }
#'
#' # brms models
#' # -----------------------------------------------
#' if (require("brms")) {
#' model <- brms::brm(mpg ~ wt + cyl, data = mtcars)
#' describe_posterior(model)
#' describe_posterior(model, centrality = "all", dispersion = TRUE, test = "all")
#' describe_posterior(model, ci = c(0.80, 0.90))
#' }
#'
#' # BayesFactor objects
#' # -----------------------------------------------
#' if (require("BayesFactor")) {
#' bf <- ttestBF(x = rnorm(100, 1, 1))
#' describe_posterior(bf)
#' describe_posterior(bf, centrality = "all", dispersion = TRUE, test = "all")
#' describe_posterior(bf, ci = c(0.80, 0.90))
#' }
#' }
#' @export
describe_posterior <- function(posteriors, ...) {
UseMethod("describe_posterior")
}
#' @export
describe_posterior.default <- function(posteriors, ...) {
stop(insight::format_message(
paste0("`describe_posterior()` is not yet implemented for objects of class `", class(posteriors)[1], "`.")
), call. = FALSE)
}
#' @keywords internal
.describe_posterior <- function(x,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
bf_prior = NULL,
BF = 1,
...) {
if (is.null(x)) {
warning("Could not extract posterior samples.", call. = FALSE)
return(NULL)
}
if (!is.data.frame(x) && !is.numeric(x)) {
is_stanmvreg <- inherits(x, "stanmvreg")
cleaned_parameters <- insight::clean_parameters(x)
# rename to use `x` in bayes factor later
x_df <- insight::get_parameters(x, ...)
} else {
cleaned_parameters <- NULL
x_df <- x
}
# Arguments fixes
if (!is.null(centrality) && length(centrality) == 1 && (centrality == "none" || centrality == FALSE)) centrality <- NULL
if (!is.null(ci) && length(ci) == 1 && (is.na(ci) || ci == FALSE)) ci <- NULL
if (!is.null(test) && length(test) == 1 && (test == "none" || test == FALSE)) test <- NULL
# Point-estimates
if (!is.null(centrality)) {
estimates <- .prepare_output(
point_estimate(x_df, centrality = centrality, dispersion = dispersion, ...),
cleaned_parameters,
is_stanmvreg
)
if (!"Parameter" %in% names(estimates)) {
estimates <- cbind(data.frame("Parameter" = "Posterior"), estimates)
}
} else {
estimates <- data.frame("Parameter" = NA)
}
# Uncertainty
if (!is.null(ci)) {
ci_method <- match.arg(tolower(ci_method), c("hdi", "spi", "quantile", "ci", "eti", "si", "bci", "bcai"))
# not sure why "si" requires the model object
if (ci_method == "si") {
uncertainty <- ci(x, BF = BF, method = ci_method, prior = bf_prior, ...)
} else {
uncertainty <- ci(x_df, ci = ci, method = ci_method, ...)
}
uncertainty <- .prepare_output(
uncertainty,
cleaned_parameters,
is_stanmvreg
)
if (!"Parameter" %in% names(uncertainty)) {
uncertainty <- cbind(data.frame("Parameter" = "Posterior"), uncertainty)
}
} else {
uncertainty <- data.frame("Parameter" = NA)
}
# Effect Existence
if (!is.null(test)) {
test <- .check_test_values(test)
if ("all" %in% test) {
test <- c("pd", "p_map", "p_rope", "p_significance", "rope", "equivalence", "bf")
}
## TODO no BF for arm::sim
if (inherits(x_df, c("sim", "sim.merMod", "mcmc", "stanfit"))) {
test <- setdiff(test, "bf")
}
## TODO enable once "rope()" works for multi-response models
# no ROPE for multi-response models
if (insight::is_multivariate(x_df)) {
test <- setdiff(test, c("rope", "p_rope"))
warning(insight::format_message(
"Multivariate response models are not yet supported for tests `rope` and `p_rope`."
), call. = FALSE)
}
# MAP-based p-value
if (any(c("p_map", "p_pointnull") %in% test)) {
test_pmap <- .prepare_output(
p_map(x_df, ...),
cleaned_parameters,
is_stanmvreg
)
if (!is.data.frame(test_pmap)) test_pmap <- data.frame("Parameter" = "Posterior", "p_map" = test_pmap)
} else {
test_pmap <- data.frame("Parameter" = NA)
}
# Probability of direction
if (any(c("pd", "p_direction", "pdir", "mpe") %in% test)) {
test_pd <- .prepare_output(
p_direction(x_df, ...),
cleaned_parameters,
is_stanmvreg
)
if (!is.data.frame(test_pd)) test_pd <- data.frame("Parameter" = "Posterior", "pd" = test_pd)
} else {
test_pd <- data.frame("Parameter" = NA)
}
# Probability of rope
if (any(c("p_rope") %in% test)) {
test_prope <- .prepare_output(
p_rope(x_df, range = rope_range, ...),
cleaned_parameters,
is_stanmvreg
)
if (!"Parameter" %in% names(test_prope)) {
test_prope <- cbind(data.frame("Parameter" = "Posterior"), test_prope)
}
} else {
test_prope <- data.frame("Parameter" = NA)
}
# Probability of significance
if (any(c("ps", "p_sig", "p_significance") %in% test)) {
test_psig <- .prepare_output(
p_significance(x_df, threshold = rope_range, ...),
cleaned_parameters,
is_stanmvreg
)
if (!is.data.frame(test_psig)) test_psig <- data.frame("Parameter" = "Posterior", "ps" = test_psig)
} else {
test_psig <- data.frame("Parameter" = NA)
}
# ROPE
if (any(c("rope") %in% test)) {
test_rope <- .prepare_output(
rope(x_df, range = rope_range, ci = rope_ci, ...),
cleaned_parameters,
is_stanmvreg
)
if (!"Parameter" %in% names(test_rope)) {
test_rope <- cbind(data.frame("Parameter" = "Posterior"), test_rope)
}
names(test_rope)[names(test_rope) == "CI"] <- "ROPE_CI"
} else {
test_rope <- data.frame("Parameter" = NA)
}
# Equivalence test
if (any(c("equivalence", "equivalence_test", "equitest") %in% test)) {
if (any("rope" %in% test)) {
equi_warnings <- FALSE
} else {
equi_warnings <- TRUE
}
test_equi <- .prepare_output(
equivalence_test(x_df,
range = rope_range,
ci = rope_ci,
verbose = equi_warnings,
...
),
cleaned_parameters,
is_stanmvreg
)
test_equi$Cleaned_Parameter <- NULL
if (!"Parameter" %in% names(test_equi)) {
test_equi <- cbind(data.frame("Parameter" = "Posterior"), test_equi)
}
names(test_equi)[names(test_equi) == "CI"] <- "ROPE_CI"
test_rope <- merge(test_rope, test_equi, all = TRUE)
test_rope <- test_rope[!names(test_rope) %in% c("HDI_low", "HDI_high")]
}
# Bayes Factors
if (any(c("bf", "bayesfactor", "bayes_factor") %in% test)) {
test_bf <- tryCatch(
.prepare_output(
bayesfactor_parameters(x, prior = bf_prior, ...),
cleaned_parameters,
is_stanmvreg
),
error = function(e) data.frame("Parameter" = NA)
)
if (!"Parameter" %in% names(test_bf)) {
test_bf <- cbind(data.frame("Parameter" = "Posterior"), test_bf)
}
} else {
test_bf <- data.frame("Parameter" = NA)
}
} else {
test_pd <- data.frame(
"Parameter" = NA,
"Effects" = NA,
"Component" = NA,
"Response" = NA
)
test_rope <- data.frame(
"Parameter" = NA,
"Effects" = NA,
"Component" = NA,
"Response" = NA
)
test_prope <- data.frame(
"Parameter" = NA,
"Effects" = NA,
"Component" = NA,
"Response" = NA
)
test_psig <- data.frame(
"Parameter" = NA,
"Effects" = NA,
"Component" = NA,
"Response" = NA
)
test_bf <- data.frame(
"Parameter" = NA,
"Effects" = NA,
"Component" = NA,
"Response" = NA
)
test_pmap <- data.frame(
"Parameter" = NA,
"Effects" = NA,
"Component" = NA,
"Response" = NA
)
}
# for data frames or numeric, and even for some models, we don't
# have the "Effects" or "Component" column for all data frames.
# To make "merge()" work, we add those columns to all data frames,
# filled with NA, and remove the columns later if necessary
estimates <- .add_effects_component_column(estimates)
uncertainty <- .add_effects_component_column(uncertainty)
test_pmap <- .add_effects_component_column(test_pmap)
test_pd <- .add_effects_component_column(test_pd)
test_prope <- .add_effects_component_column(test_prope)
test_psig <- .add_effects_component_column(test_psig)
test_rope <- .add_effects_component_column(test_rope)
test_bf <- .add_effects_component_column(test_bf)
# at least one "valid" data frame needs a row id, to restore
# row-order after merging
if (!all(is.na(estimates$Parameter))) {
estimates$.rowid <- seq_len(nrow(estimates))
} else if (!all(is.na(test_pmap$Parameter))) {
test_pmap$.rowid <- seq_len(nrow(test_pmap))
} else if (!all(is.na(test_pd$Parameter))) {
test_pd$.rowid <- seq_len(nrow(test_pd))
} else if (!all(is.na(test_prope$Parameter))) {
test_prope$.rowid <- seq_len(nrow(test_prope))
} else if (!all(is.na(test_psig$Parameter))) {
test_psig$.rowid <- seq_len(nrow(test_psig))
} else if (!all(is.na(test_rope$Parameter))) {
test_rope$.rowid <- seq_len(nrow(test_rope))
} else if (!all(is.na(test_bf$Parameter))) {
test_bf$.rowid <- seq_len(nrow(test_bf))
} else {
estimates$.rowid <- seq_len(nrow(estimates))
}
# remove duplicated columns
if (all(c("rope", "p_rope") %in% test)) {
test_prope$ROPE_low <- NULL
test_prope$ROPE_high <- NULL
}
# merge all data frames
merge_by <- c("Parameter", "Effects", "Component", "Response")
# merge_by <- intersect(merge_by, colnames(estimates))
out <- merge(estimates, uncertainty, by = merge_by, all = TRUE)
out <- merge(out, test_pmap, by = merge_by, all = TRUE)
out <- merge(out, test_pd, by = merge_by, all = TRUE)
out <- merge(out, test_prope, by = merge_by, all = TRUE)
out <- merge(out, test_psig, by = merge_by, all = TRUE)
out <- merge(out, test_rope, by = merge_by, all = TRUE)
out <- merge(out, test_bf, by = merge_by, all = TRUE)
out <- out[!is.na(out$Parameter), ]
# check which columns can be removed at the end. In any case, we don't
# need .rowid in the returned data frame, and when the Effects or Component
# column consist only of missing values, we remove those columns as well
remove_columns <- ".rowid"
if (insight::n_unique(out$Effects, na.rm = TRUE) < 2) remove_columns <- c(remove_columns, "Effects")
if (insight::n_unique(out$Component, na.rm = TRUE) < 2) remove_columns <- c(remove_columns, "Component")
if (insight::n_unique(out$Response, na.rm = TRUE) < 2) remove_columns <- c(remove_columns, "Response")
# Restore columns order
out <- datawizard::data_remove(out[order(out$.rowid), ], remove_columns, verbose = FALSE)
# Add iterations
if (keep_iterations == TRUE) {
row_order <- out$Parameter
iter <- as.data.frame(t(as.data.frame(x_df, ...)))
names(iter) <- paste0("iter_", seq_len(ncol(iter)))
iter$Parameter <- row.names(iter)
out <- merge(out, iter, all.x = TRUE, by = "Parameter")
out <- out[match(row_order, out$Parameter), ]
row.names(out) <- NULL
}
# Prepare output
attr(out, "ci_method") <- ci_method
out
}
#' @keywords internal
.add_effects_component_column <- function(x) {
if (!"Effects" %in% names(x)) x <- cbind(x, data.frame("Effects" = NA))
if (!"Component" %in% names(x)) x <- cbind(x, data.frame("Component" = NA))
if (!"Response" %in% names(x)) x <- cbind(x, data.frame("Response" = NA))
x
}
# Models based on simple data frame of posteriors ---------------------
#' @rdname describe_posterior
#' @export
describe_posterior.numeric <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
bf_prior = NULL,
BF = 1,
...) {
out <- .describe_posterior(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
bf_prior = bf_prior,
BF = BF,
...
)
class(out) <- unique(c("describe_posterior", "see_describe_posterior", class(out)))
out
}
#' @export
describe_posterior.double <- describe_posterior.numeric
#' @export
describe_posterior.data.frame <- describe_posterior.numeric
#' @export
describe_posterior.sim.merMod <- describe_posterior.numeric
#' @export
describe_posterior.sim <- describe_posterior.numeric
#' @export
describe_posterior.bayesQR <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
parameters = NULL,
...) {
out <- .describe_posterior(
insight::get_parameters(posteriors),
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
effects = "fixed",
parameters = parameters,
...
)
attr(out, "ci_method") <- ci_method
attr(out, "object_name") <- insight::safe_deparse(substitute(posteriors))
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
out
}
#' @export
describe_posterior.blrm <- describe_posterior.bayesQR
#' @export
describe_posterior.mcmc <- describe_posterior.bayesQR
#' @export
describe_posterior.mcmc.list <- describe_posterior.bayesQR
#' @export
describe_posterior.BGGM <- describe_posterior.bayesQR
#' @export
describe_posterior.draws <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
bf_prior = NULL,
BF = 1,
...) {
out <- .describe_posterior(
.posterior_draws_to_df(posteriors),
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
bf_prior = bf_prior,
BF = BF,
...
)
class(out) <- unique(c("describe_posterior", "see_describe_posterior", class(out)))
out
}
#' @export
describe_posterior.rvar <- describe_posterior.draws
# easystats methods ------------------------
#' @export
describe_posterior.effectsize_std_params <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
bf_prior = NULL,
BF = 1,
...) {
class(posteriors) <- "data.frame"
no_unique <- sapply(posteriors, function(col) {
length(unique(col)) == 1
})
if (any(no_unique)) {
no_unique <- which(no_unique)
out <- describe_posterior.data.frame(
posteriors[, -no_unique],
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
bf_prior = bf_prior,
BF = BF,
...
)
out_int <- data.frame(Parameter = colnames(posteriors)[no_unique])
col_diff <- setdiff(colnames(out), colnames(out_int))
out_int[, col_diff] <- NA
out <- rbind(out_int, out)
out <- out[order(match(out$Parameter, colnames(posteriors))), ]
return(out)
}
describe_posterior.data.frame(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
bf_prior = bf_prior,
BF = BF,
...
)
}
#' @export
describe_posterior.get_predicted <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = NULL,
...) {
if ("iterations" %in% names(attributes(posteriors))) {
describe_posterior(
as.data.frame(t(attributes(posteriors)$iterations)),
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
...
)
} else {
stop("No iterations present in the output.", call. = FALSE)
}
}
# emmeans ---------------------------
#' @export
describe_posterior.emmGrid <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
bf_prior = NULL,
BF = 1,
...) {
if (any(c("all", "bf", "bayesfactor", "bayes_factor") %in% tolower(test)) ||
"si" %in% tolower(ci_method)) {
samps <- .clean_priors_and_posteriors(posteriors, bf_prior)
bf_prior <- samps$prior
posteriors <- samps$posterior
} else {
posteriors <- insight::get_parameters(posteriors)
}
out <- .describe_posterior(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
bf_prior = bf_prior,
BF = BF,
...
)
row.names(out) <- NULL # Reset row names
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
attr(out, "ci_method") <- ci_method
attr(out, "object_name") <- insight::safe_deparse(substitute(posteriors))
out
}
#' @export
describe_posterior.emm_list <- describe_posterior.emmGrid
# Stan ------------------------------
#' @inheritParams insight::get_parameters
#' @inheritParams diagnostic_posterior
#' @rdname describe_posterior
#' @export
describe_posterior.stanreg <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
bf_prior = NULL,
diagnostic = c("ESS", "Rhat"),
priors = FALSE,
effects = c("fixed", "random", "all"),
component = c("location", "all", "conditional", "smooth_terms", "sigma", "distributional", "auxiliary"),
parameters = NULL,
BF = 1,
...) {
if ((any(c("all", "bf", "bayesfactor", "bayes_factor") %in% tolower(test)) ||
"si" %in% tolower(ci_method)) && is.null(bf_prior)) {
bf_prior <- suppressMessages(unupdate(posteriors))
}
effects <- match.arg(effects)
component <- match.arg(component)
out <- .describe_posterior(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
bf_prior = bf_prior,
BF = BF,
effects = effects,
component = component,
parameters = parameters,
...
)
diagnostic <- diagnostic_posterior(
posteriors,
diagnostic,
effects = effects,
component = component,
parameters = parameters,
...
)
out <- .merge_and_sort(out, diagnostic, by = "Parameter", all = TRUE)
if (isTRUE(priors)) {
priors_data <- describe_prior(posteriors, parameters = out$Parameter, ...)
out <- .merge_and_sort(out, priors_data, by = "Parameter", all = TRUE)
}
out <- .add_clean_parameters_attribute(out, posteriors)
attr(out, "ci_method") <- ci_method
attr(out, "object_name") <- insight::safe_deparse(substitute(posteriors))
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
out
}
#' @inheritParams insight::get_parameters
#' @inheritParams diagnostic_posterior
#' @export
describe_posterior.stanmvreg <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = "p_direction",
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
bf_prior = NULL,
diagnostic = c("ESS", "Rhat"),
priors = FALSE,
effects = c("fixed", "random", "all"),
component = c("location", "all", "conditional", "smooth_terms", "sigma", "distributional", "auxiliary"),
parameters = NULL,
...) {
effects <- match.arg(effects)
component <- match.arg(component)
out <- .describe_posterior(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
bf_prior = bf_prior,
effects = effects,
parameters = parameters,
...
)
if (is.null(out$Response)) {
out$Response <- gsub("(b\\[)*(.*)\\|(.*)", "\\2", out$Parameter)
}
diagnostic <- diagnostic_posterior(
posteriors,
diagnostic,
effects = effects,
parameters = parameters,
...
)
out <- .merge_and_sort(out, diagnostic, by = c("Parameter", "Response"), all = TRUE)
if (isTRUE(priors)) {
priors_data <- describe_prior(posteriors, parameters = NULL, ...)
priors_data$Parameter <- gsub("^(.*)\\|(.*)", replacement = "\\2", priors_data$Parameter)
out <- .merge_and_sort(out, priors_data, by = c("Parameter", "Response"), all = TRUE)
}
out <- .add_clean_parameters_attribute(out, posteriors)
attr(out, "ci_method") <- ci_method
attr(out, "object_name") <- insight::safe_deparse(substitute(posteriors))
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
out
}
#' @inheritParams insight::get_parameters
#' @inheritParams diagnostic_posterior
#' @export
describe_posterior.stanfit <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
diagnostic = c("ESS", "Rhat"),
effects = c("fixed", "random", "all"),
parameters = NULL,
priors = FALSE,
...) {
effects <- match.arg(effects)
out <- .describe_posterior(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
effects = effects,
parameters = parameters,
...
)
diagnostic <- diagnostic_posterior(
posteriors,
diagnostic,
effects = effects,
parameters = parameters,
...
)
out <- .merge_and_sort(out, diagnostic, by = "Parameter", all = TRUE)
if (isTRUE(priors)) {
priors_data <- describe_prior(posteriors, parameters = out$Parameter, ...)
out <- .merge_and_sort(out, priors_data, by = "Parameter", all = TRUE)
}
attr(out, "ci_method") <- ci_method
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
out
}
#' @inheritParams describe_posterior.stanreg
#' @rdname describe_posterior
#' @export
describe_posterior.brmsfit <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
bf_prior = NULL,
diagnostic = c("ESS", "Rhat"),
effects = c("fixed", "random", "all"),
component = c("conditional", "zi", "zero_inflated", "all", "location", "distributional", "auxiliary"),
parameters = NULL,
BF = 1,
priors = FALSE,
...) {
effects <- match.arg(effects)
component <- match.arg(component)
if ((any(c("all", "bf", "bayesfactor", "bayes_factor") %in% tolower(test)) ||
"si" %in% tolower(ci_method)) && is.null(bf_prior)) {
bf_prior <- suppressMessages(unupdate(posteriors))
}
out <- .describe_posterior(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
bf_prior = bf_prior,
BF = BF,
effects = effects,
component = component,
parameters = parameters,
...
)
if (!is.null(diagnostic)) {
diagnostic <- diagnostic_posterior(
posteriors,
diagnostic,
effects = effects,
component = component,
parameters = parameters,
...
)
out <- .merge_and_sort(out, diagnostic, by = "Parameter", all = TRUE)
}
if (isTRUE(priors)) {
priors_data <- describe_prior(posteriors, parameters = out$Parameter, ...)
out <- .merge_and_sort(out, priors_data, by = "Parameter", all = TRUE)
}
out <- .add_clean_parameters_attribute(out, posteriors)
attr(out, "ci_method") <- ci_method
attr(out, "object_name") <- insight::safe_deparse(substitute(posteriors))
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
out
}
#' @export
describe_posterior.blavaan <- describe_posterior.stanfit
# other models --------------------------------
#' @inheritParams describe_posterior.stanreg
#' @export
describe_posterior.MCMCglmm <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
diagnostic = "ESS",
parameters = NULL,
...) {
out <- .describe_posterior(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
effects = "fixed",
parameters = parameters,
...
)
if (!is.null(diagnostic) && diagnostic == "ESS") {
diagnostic <- effective_sample(posteriors, effects = "fixed", parameters = parameters, ...)
out <- .merge_and_sort(out, diagnostic, by = "Parameter", all = TRUE)
}
out
}
#' @export
describe_posterior.bcplm <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
priors = TRUE,
parameters = NULL,
...) {
out <- .describe_posterior(
insight::get_parameters(posteriors),
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
effects = "fixed",
parameters = parameters,
...
)
if (isTRUE(priors)) {
priors_data <- describe_prior(posteriors, parameters = out$Parameter, ...)
out <- .merge_and_sort(out, priors_data, by = "Parameter", all = TRUE)
}
attr(out, "ci_method") <- ci_method
attr(out, "object_name") <- insight::safe_deparse(substitute(posteriors))
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
out
}
#' @export
describe_posterior.bamlss <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
component = c("all", "conditional", "location"),
parameters = NULL,
...) {
component <- match.arg(component)
out <- .describe_posterior(
posteriors,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
component = component,
parameters = parameters,
...
)
attr(out, "ci_method") <- ci_method
attr(out, "object_name") <- insight::safe_deparse(substitute(posteriors))
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
out
}
# BayesFactor --------------------
#' @export
describe_posterior.BFBayesFactor <- function(posteriors,
centrality = "median",
dispersion = FALSE,
ci = 0.95,
ci_method = "eti",
test = c("p_direction", "rope", "bf"),
rope_range = "default",
rope_ci = 0.95,
keep_iterations = FALSE,
priors = TRUE,
verbose = TRUE,
...) {
# Match test args to catch BFs
if (!is.null(test)) {
test <- .check_test_values(test)
if ("all" %in% test) {
test <- c("pd", "p_map", "p_rope", "p_significance", "rope", "equivalence", "bf")
}
}
# Remove BF from list
if (any(c("bf", "bayesfactor", "bayes_factor") %in% test)) {
test <- test[!test %in% c("bf", "bayesfactor", "bayes_factor")]
if (length(test) == 0L) test <- NULL
compute_bf <- TRUE
} else {
compute_bf <- FALSE
}
draws <- insight::get_parameters(posteriors)
if (all(rope_range == "default")) {
rope_range <- rope_range(posteriors, verbose = verbose)
}
# Describe posterior
out <- .describe_posterior(
draws,
centrality = centrality,
dispersion = dispersion,
ci = ci,
ci_method = ci_method,
test = test,
rope_range = rope_range,
rope_ci = rope_ci,
keep_iterations = keep_iterations,
...
)
if (is.null(out)) {
return(NULL)
}
# Compute and read BF a posteriori
if (compute_bf) {
tryCatch(
{
out$log_BF <- as.data.frame(bayesfactor_models(posteriors[1], ...))[-1, ]$log_BF
out$BF <- exp(out$log_BF)
},
error = function(e) {
NULL
}
)
}
# Add priors
if (priors) {
priors_data <- describe_prior(posteriors, ...)
out <- .merge_and_sort(out, priors_data, by = intersect(names(out), names(priors_data)), all = TRUE)
}
attr(out, "ci_method") <- ci_method
attr(out, "object_name") <- insight::safe_deparse(substitute(posteriors))
class(out) <- c("describe_posterior", "see_describe_posterior", class(out))
out
}
# Helpers -----------------------------------------------------------------
#' @keywords internal
.check_test_values <- function(test) {
match.arg(tolower(test), c(
"pd", "p_direction", "pdir", "mpe", "ps", "psig", "p_significance",
"p_rope", "rope", "equivalence", "equivalence_test", "equitest",
"bf", "bayesfactor", "bayes_factor", "p_map", "all"
), several.ok = TRUE)
}