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#' @export
model_parameters.mjoint <- function(model,
ci = 0.95,
effects = "fixed",
component = "all",
exponentiate = FALSE,
p_adjust = NULL,
keep = NULL,
drop = NULL,
verbose = TRUE,
...) {
effects <- insight::validate_argument(effects, c("fixed", "random", "all"))
component <- insight::validate_argument(component, c("all", "conditional", "survival"))
params <- params_variance <- NULL
if (effects %in% c("fixed", "all")) {
# Processing
params <- .extract_parameters_generic(
model,
ci = ci,
component = component,
standardize = FALSE,
p_adjust = p_adjust,
keep_parameters = keep,
drop_parameters = drop,
...
)
# exponentiate coefficients and SE/CI, if requested
params <- .exponentiate_parameters(params, model, exponentiate)
params$Effects <- "fixed"
}
if (effects %in% c("random", "all")) {
params_variance <- .extract_random_variances(
model,
ci = ci,
effects = effects,
ci_method = NULL,
ci_random = FALSE,
verbose = verbose
)
params_variance$Component <- "conditional"
}
# merge random and fixed effects, if necessary
if (!is.null(params) && !is.null(params_variance)) {
params$Level <- NA
params$Group <- ""
# add component column
if (!"Component" %in% colnames(params)) {
params$Component <- "conditional"
}
# reorder
params <- params[match(colnames(params_variance), colnames(params))]
}
params <- rbind(params, params_variance)
# remove empty column
if (!is.null(params$Level) && all(is.na(params$Level))) {
params$Level <- NULL
}
params <- .add_model_parameters_attributes(
params,
model,
ci = ifelse(effects == "random", NA, ci),
exponentiate,
ci_method = NULL,
p_adjust = p_adjust,
verbose = verbose,
group_level = FALSE,
...
)
attr(params, "object_name") <- insight::safe_deparse_symbol(substitute(model))
class(params) <- c("parameters_model", "see_parameters_model", class(params))
params
}
#' @export
p_value.mjoint <- function(model, component = c("all", "conditional", "survival"), ...) {
component <- match.arg(component)
s <- summary(model)
params <- rbind(
data.frame(
Parameter = rownames(s$coefs.long),
p = unname(s$coefs.long[, 4]),
Component = "conditional",
stringsAsFactors = FALSE,
row.names = NULL
),
data.frame(
Parameter = rownames(s$coefs.surv),
p = unname(s$coefs.surv[, 4]),
Component = "survival",
stringsAsFactors = FALSE,
row.names = NULL
)
)
if (component != "all") {
params <- params[params$Component == component, , drop = FALSE]
}
params
}
#' @export
ci.mjoint <- function(x, ci = 0.95, ...) {
.ci_generic(model = x, ci = ci, dof = Inf, ...)
}
#' @export
standard_error.mjoint <- function(model, component = c("all", "conditional", "survival"), ...) {
component <- match.arg(component)
s <- summary(model)
params <- rbind(
data.frame(
Parameter = rownames(s$coefs.long),
SE = unname(s$coefs.long[, 2]),
Component = "conditional",
stringsAsFactors = FALSE,
row.names = NULL
),
data.frame(
Parameter = rownames(s$coefs.surv),
SE = unname(s$coefs.surv[, 2]),
Component = "survival",
stringsAsFactors = FALSE,
row.names = NULL
)
)
if (component != "all") {
params <- params[params$Component == component, , drop = FALSE]
}
params
}
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