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.ci_profiled <- function(model, ci) {
glm_ci <- tryCatch(
{
out <- as.data.frame(
suppressWarnings(stats::confint(model, level = ci)),
stringsAsFactors = FALSE
)
names(out) <- c("CI_low", "CI_high")
out$CI <- ci
out$Parameter <- insight::get_parameters(model,
effects = "fixed",
component = "conditional",
verbose = FALSE
)$Parameter
out <- out[c("Parameter", "CI", "CI_low", "CI_high")]
rownames(out) <- NULL
out
},
error = function(e) {
NULL
}
)
if (is.null(glm_ci)) {
glm_ci <- .ci_generic(model, ci = ci)
}
glm_ci
}
# we need this function for models where confint and get_parameters return
# different length (e.g. as for "polr" models)
.ci_profiled2 <- function(model, ci) {
glm_ci <- tryCatch(
{
out <- as.data.frame(stats::confint(model, level = ci), stringsAsFactors = FALSE)
names(out) <- c("CI_low", "CI_high")
out$CI <- ci
out$Parameter <- .remove_backticks_from_string(rownames(out))
out <- out[c("Parameter", "CI", "CI_low", "CI_high")]
rownames(out) <- NULL
out
},
error = function(e) {
NULL
}
)
if (is.null(glm_ci)) {
glm_ci <- .ci_generic(model, ci = ci)
}
glm_ci
}
#' @keywords internal
.ci_profile_merMod <- function(x, ci, profiled, ...) {
out <- as.data.frame(suppressWarnings(stats::confint(profiled, level = ci, ...)))
rownames(out) <- gsub("`", "", rownames(out), fixed = TRUE)
out <- out[rownames(out) %in% insight::find_parameters(x, effects = "fixed")$conditional, ]
names(out) <- c("CI_low", "CI_high")
# Clean up
out$Parameter <- row.names(out)
out$CI <- ci
out <- out[c("Parameter", "CI", "CI_low", "CI_high")]
row.names(out) <- NULL
out
}
#' @keywords internal
.ci_profile_glmmTMB <- function(x, ci, profiled, component, ...) {
# make sure "..." doesn't pass invalid arguments to package TMB
dot_args <- .check_profile_uniroot_args(...)
if (is.null(profiled)) {
fun_args <- list(x, method = "profile", level = ci, dot_args)
out <- as.data.frame(do.call(stats::confint, fun_args))
} else {
fun_args <- list(profiled, level = ci, dot_args)
out <- .safe(as.data.frame(do.call(stats::confint, fun_args)))
if (is.null(out)) {
fun_args <- list(x, method = "profile", level = ci, dot_args)
out <- as.data.frame(do.call(stats::confint, fun_args))
}
}
.process_glmmTMB_CI(x, out, ci, component)
}
#' @keywords internal
.ci_uniroot_glmmTMB <- function(x, ci, component, ...) {
# make sure "..." doesn't pass invalid arguments to package TMB
dot_args <- .check_profile_uniroot_args(...)
fun_args <- list(x, level = ci, method = "uniroot", dot_args)
out <- as.data.frame(do.call(stats::confint, fun_args))
.process_glmmTMB_CI(x, out, ci, component)
}
.check_profile_uniroot_args <- function(...) {
.profile_formals <- c(
"cl", "fitted", "h", "level_max", "lincomb", "maxit", "name",
"ncpus", "npts", "obj", "parallel", "parm", "parm.range", "slice",
"stderr", "stepfac", "trace", "ystep", "ytol"
)
dots <- list(...)
dot_args <- intersect(names(dots), .profile_formals)
out <- dots[dot_args]
if (!length(out)) {
return(NULL)
}
out
}
.process_glmmTMB_CI <- function(x, out, ci, component) {
rownames(out) <- gsub("`", "", rownames(out), fixed = TRUE)
pars <- insight::get_parameters(x,
effects = "fixed",
component = component,
verbose = FALSE
)
param_names <- switch(component,
conditional = pars$Parameter,
zi = ,
zero_inflated = paste0("zi~", pars$Parameter),
c(
pars$Parameter[pars$Component == "conditional"],
paste0("zi~", pars$Parameter[pars$Component == "zero_inflated"])
)
)
out <- out[rownames(out) %in% param_names, ]
names(out) <- c("CI_low", "CI_high")
# Clean up
out$Parameter <- pars$Parameter
out$CI <- ci
out <- out[c("Parameter", "CI", "CI_low", "CI_high")]
out$Component <- pars$Component
row.names(out) <- NULL
out
}
#' @keywords internal
.ci_boot_merMod <- function(x, ci, iterations = 500, effects = "fixed", ...) {
insight::check_if_installed("lme4")
# Compute
out <- suppressWarnings(suppressMessages(as.data.frame(
lme4::confint.merMod(x, level = ci, method = "boot", nsim = iterations, ...)
)))
rownames(out) <- gsub("`", "", rownames(out), fixed = TRUE)
out <- out[rownames(out) %in% insight::find_parameters(x, effects = "fixed")$conditional, ]
names(out) <- c("CI_low", "CI_high")
# Clean up
out$Parameter <- row.names(out)
out$CI <- ci
out <- out[c("Parameter", "CI", "CI_low", "CI_high")]
row.names(out) <- NULL
out
}
|
