R/methods_mmrm.R

In parameters: Processing of Model Parameters

# model_parameters --------------------

#' @export
model_parameters.mmrm <- function(model,
                                  ci = 0.95,
                                  ci_method = NULL,
                                  bootstrap = FALSE,
                                  iterations = 1000,
                                  standardize = NULL,
                                  exponentiate = FALSE,
                                  p_adjust = NULL,
                                  summary = getOption("parameters_summary", FALSE),
                                  keep = NULL,
                                  drop = NULL,
                                  verbose = TRUE,
                                  ...) {
  ci_method <- switch(model$method,
    Satterthwaite = "satterthwaite",
    "kenward"
  )

  # extract model parameters table, as data frame
  out <- tryCatch(
    {
      .model_parameters_generic(
        model = model,
        ci = ci,
        ci_method = ci_method,
        bootstrap = bootstrap,
        iterations = iterations,
        merge_by = "Parameter",
        standardize = standardize,
        exponentiate = exponentiate,
        p_adjust = p_adjust,
        summary = summary,
        keep_parameters = keep,
        drop_parameters = drop,
        vcov = NULL,
        vcov_args = NULL,
        verbose = verbose,
        ...
      )
    },
    error = function(e) {
      fail <- NA
      attr(fail, "error") <- gsub("  ", " ", gsub("\\n", "", e$message), fixed = TRUE)
      fail
    }
  )

  # tell user if something went wrong...
  if (length(out) == 1 && isTRUE(is.na(out))) {
    insight::format_error(
      paste0(
        "Sorry, `model_parameters()` failed with the following error (possible class `",
        class(model)[1],
        "` not supported):\n"
      ),
      attr(out, "error")
    )
  }

  attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(model))
  out
}

#' @export
model_parameters.mmrm_fit <- model_parameters.mmrm

#' @export
model_parameters.mmrm_tmb <- model_parameters.mmrm


# ci --------------------

#' @export
ci.mmrm <- function(x, ci = 0.95, method = "residual", ...) {
  .ci_generic(model = x, ci = ci, method = "residual", ...)
}

#' @export
ci.mmrm_fit <- ci.mmrm

#' @export
ci.mmrm_tmb <- ci.mmrm


# p --------------------

#' @export
p_value.mmrm <- function(model,
                         dof = NULL,
                         method = NULL,
                         component = "all",
                         vcov = NULL,
                         vcov_args = NULL,
                         verbose = TRUE,
                         ...) {
  p_value.default(
    model,
    dof = NULL,
    method = NULL,
    component = "all",
    vcov = NULL,
    vcov_args = NULL,
    verbose = verbose,
    ...
  )
}

#' @export
p_value.mmrm_fit <- p_value.mmrm

#' @export
p_value.mmrm_tmb <- p_value.mmrm


# SE --------------------

#' @export
standard_error.mmrm <- function(model, ...) {
  se <- .get_se_from_summary(model)
  .data_frame(Parameter = names(se), SE = as.vector(se))
}

#' @export
standard_error.mmrm_fit <- standard_error.mmrm

#' @export
standard_error.mmrm_tmb <- standard_error.mmrm


# degrees of freedom ------------------

#' @export
degrees_of_freedom.mmrm <- function(model, ...) {
  summary_table <- stats::coef(summary(model))
  unname(summary_table[, "df"])
}

#' @export
degrees_of_freedom.mmrm_fit <- degrees_of_freedom.mmrm

#' @export
degrees_of_freedom.mmrm_tmb <- degrees_of_freedom.mmrm