From 2dd09fdf5ceae24e300b8c2f7a562013a4b6a589 Mon Sep 17 00:00:00 2001 From: Daniel Date: Tue, 19 Nov 2024 14:01:26 +0100 Subject: [PATCH] docs --- R/4_standard_error.R | 1 + R/methods_lme4.R | 1 - man/standard_error.Rd | 33 ++++++++------------------------- 3 files changed, 9 insertions(+), 26 deletions(-) diff --git a/R/4_standard_error.R b/R/4_standard_error.R index d4985305f..07a7c9c46 100644 --- a/R/4_standard_error.R +++ b/R/4_standard_error.R @@ -76,6 +76,7 @@ standard_error <- function(model, ...) { #' @rdname standard_error #' @export standard_error.default <- function(model, + effects = "fixed", component = "all", vcov = NULL, vcov_args = NULL, diff --git a/R/methods_lme4.R b/R/methods_lme4.R index cbe6f9dc2..fc8ad47f4 100644 --- a/R/methods_lme4.R +++ b/R/methods_lme4.R @@ -223,7 +223,6 @@ ci.merMod <- function(x, } -#' @rdname standard_error #' @export standard_error.merMod <- function(model, effects = "fixed", diff --git a/man/standard_error.Rd b/man/standard_error.Rd index 3a864e342..b598205b2 100644 --- a/man/standard_error.Rd +++ b/man/standard_error.Rd @@ -1,18 +1,18 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/4_standard_error.R, R/methods_base.R, -% R/methods_glmmTMB.R, R/methods_lme4.R +% R/methods_glmmTMB.R \name{standard_error} \alias{standard_error} \alias{standard_error.default} \alias{standard_error.factor} \alias{standard_error.glmmTMB} -\alias{standard_error.merMod} \title{Standard Errors} \usage{ standard_error(model, ...) \method{standard_error}{default}( model, + effects = "fixed", component = "all", vcov = NULL, vcov_args = NULL, @@ -29,21 +29,18 @@ standard_error(model, ...) verbose = TRUE, ... ) - -\method{standard_error}{merMod}( - model, - effects = "fixed", - method = NULL, - vcov = NULL, - vcov_args = NULL, - ... -) } \arguments{ \item{model}{A model.} \item{...}{Arguments passed to or from other methods.} +\item{effects}{Should standard errors for fixed effects (\code{"fixed"}), random +effects (\code{"random"}), or both (\code{"all"}) be returned? Only applies +to mixed models. May be abbreviated. When standard errors for random +effects are requested, for each grouping factor a list of standard errors +(per group level) for random intercepts and slopes is returned.} + \item{component}{Model component for which standard errors should be shown. See the documentation for your object's class in \code{\link[=model_parameters]{model_parameters()}} or \code{\link[=p_value]{p_value()}} for further details.} @@ -84,20 +81,6 @@ values to calculate the standard error, with the lowest level being the value \code{1} (unless the factor has numeric levels, which are converted to the corresponding numeric value). By default, \code{NA} is returned for factors or character vectors.} - -\item{effects}{Should standard errors for fixed effects (\code{"fixed"}), random -effects (\code{"random"}), or both (\code{"all"}) be returned? Only applies -to mixed models. May be abbreviated. When standard errors for random -effects are requested, for each grouping factor a list of standard errors -(per group level) for random intercepts and slopes is returned.} - -\item{method}{Method for computing degrees of freedom for confidence -intervals (CI) and the related p-values. Allowed are following options (which -vary depending on the model class): \code{"residual"}, \code{"normal"}, \code{"likelihood"}, -\code{"satterthwaite"}, \code{"kenward"}, \code{"wald"}, \code{"profile"}, \code{"boot"}, \code{"uniroot"}, -\code{"ml1"}, \code{"betwithin"}, \code{"hdi"}, \code{"quantile"}, \code{"ci"}, \code{"eti"}, \code{"si"}, -\code{"bci"}, or \code{"bcai"}. See section \emph{Confidence intervals and approximation of -degrees of freedom} in \code{\link[=model_parameters]{model_parameters()}} for further details.} } \value{ A data frame with at least two columns: the parameter names and the