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# .zeroinfl, .hurdle, .zerocount
# model parameters -----------------
#' @export
model_parameters.zeroinfl <- model_parameters.zcpglm
#' @export
model_parameters.hurdle <- model_parameters.zcpglm
#' @export
model_parameters.zerocount <- model_parameters.zcpglm
# ci -----------------
#' @export
ci.zeroinfl <- function(x,
ci = 0.95,
dof = NULL,
method = "wald",
component = "all",
verbose = TRUE,
...) {
method <- tolower(method)
method <- insight::validate_argument(
method,
c("wald", "normal", "residual", "robust")
)
component <- insight::validate_argument(
component,
c("all", "conditional", "zi", "zero_inflated")
)
if (is.null(.check_component(x, component, verbose = verbose))) {
return(NULL)
}
# all other
.ci_generic(model = x, ci = ci, dof = dof, method = method, component = component, ...)
}
#' @export
ci.hurdle <- ci.zeroinfl
#' @export
ci.zerocount <- ci.zeroinfl
# standard error -----------------
#' @export
standard_error.zeroinfl <- function(model,
component = "all",
method = NULL,
verbose = TRUE,
...) {
component <- insight::validate_argument(
component,
c("all", "conditional", "zi", "zero_inflated")
)
if (is.null(.check_component(model, component, verbose = verbose))) {
return(NULL)
}
robust <- !is.null(method) && method == "robust"
if (.check_vcov_args(robust, ...)) {
return(standard_error.default(model, component = component, ...))
}
cs <- insight::compact_list(stats::coef(summary(model)))
x <- lapply(names(cs), function(i) {
if (i == "count") {
comp <- "conditional"
} else {
comp <- "zi"
}
stats <- cs[[i]]
# remove log(theta)
theta <- grepl("Log(theta)", rownames(stats), fixed = TRUE)
if (any(theta)) {
stats <- stats[!theta, ]
}
.data_frame(
Parameter = insight::find_parameters(model, effects = "fixed", component = comp, flatten = TRUE),
SE = as.vector(stats[, 2]),
Component = comp
)
})
se <- do.call(rbind, x)
se$Component <- .rename_values(se$Component, "cond", "conditional")
se$Component <- .rename_values(se$Component, "zi", "zero_inflated")
.filter_component(se, component)
}
#' @export
standard_error.hurdle <- standard_error.zeroinfl
#' @export
standard_error.zerocount <- standard_error.zeroinfl
# p values -----------------------
#' @export
p_value.zeroinfl <- function(model, component = "all", method = NULL, verbose = TRUE, ...) {
component <- insight::validate_argument(
component,
c("all", "conditional", "zi", "zero_inflated")
)
if (is.null(.check_component(model, component, verbose = verbose))) {
return(NULL)
}
robust <- !is.null(method) && method == "robust"
if (.check_vcov_args(robust, ...)) {
return(p_value.default(model, component = component, ...))
}
cs <- insight::compact_list(stats::coef(summary(model)))
x <- lapply(names(cs), function(i) {
if (i == "count") {
comp <- "conditional"
} else {
comp <- "zi"
}
stats <- cs[[i]]
# remove log(theta)
theta <- grepl("Log(theta)", rownames(stats), fixed = TRUE)
if (any(theta)) {
stats <- stats[!theta, ]
}
.data_frame(
Parameter = insight::find_parameters(model, effects = "fixed", component = comp, flatten = TRUE),
p = as.vector(stats[, 4]),
Component = comp
)
})
p <- do.call(rbind, x)
p$Component <- .rename_values(p$Component, "cond", "conditional")
p$Component <- .rename_values(p$Component, "zi", "zero_inflated")
.filter_component(p, component)
}
#' @export
p_value.hurdle <- p_value.zeroinfl
#' @export
p_value.zerocount <- p_value.zeroinfl
# simulate model -----------------
#' @export
simulate_model.zeroinfl <- simulate_model.glmmTMB
#' @export
simulate_model.hurdle <- simulate_model.zeroinfl
#' @export
simulate_model.zerocount <- simulate_model.zeroinfl
# simulate paramaters -----------------
#' @export
simulate_parameters.zeroinfl <- function(model,
iterations = 1000,
centrality = "median",
ci = 0.95,
ci_method = "quantile",
test = "p-value",
...) {
data <- simulate_model(model, iterations = iterations, ...)
out <-
.summary_bootstrap(
data = data,
test = test,
centrality = centrality,
ci = ci,
ci_method = ci_method,
...
)
params <- insight::get_parameters(model)
if ("Effects" %in% colnames(params) && insight::n_unique(params$Effects) > 1) {
out$Effects <- params$Effects
}
if ("Component" %in% colnames(params) && insight::n_unique(params$Component) > 1) {
out$Component <- params$Component
}
if (inherits(model, c("zeroinfl", "hurdle", "zerocount"))) {
out$Parameter <- gsub("^(count_|zero_)", "", out$Parameter)
}
class(out) <- c("parameters_simulate", "see_parameters_simulate", class(out))
attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(model))
attr(out, "iterations") <- iterations
attr(out, "ci") <- ci
attr(out, "ci_method") <- ci_method
attr(out, "centrality") <- centrality
out
}
#' @export
simulate_parameters.hurdle <- simulate_parameters.zeroinfl
#' @export
simulate_parameters.zerocount <- simulate_parameters.zeroinfl
|
