brokenstick-package.R

#' \pkg{brokenstick}: A package for irregular longitudinal data.
#'
#' The broken stick model describes a set of individual curves
#' by a linear mixed model using second-order linear B-splines. The
#' main use of the model is to align irregularly observed data to a
#' user-specified grid of break ages.
#'
#' The \pkg{brokenstick} package contains functions for
#' fitting a broken stick model to data, for predicting broken
#' stick curves for new data, and for plotting the results.
#'
#' @section brokenstick functions:
#' The main functions are:
#' \tabular{ll}{
#'   \code{brokenstick()} \tab Fit a broken stick model to irregular data\cr
#'   \code{plot()} \tab Plot observed and fitted trajectories by group \cr
#'   \code{predict()} \tab Obtain predictions on new data\cr
#'   \code{summary()} \tab Extract object summaries\cr
#' }
#'
#' The following functions are user-oriented helpers:
#' \tabular{ll}{
#'   \code{coef()} \tab Extract estimated parameters\cr
#'   \code{fitted()} \tab Calculate fitted values\cr
#'   \code{get_knots()} \tab Obtain the knots from a broken stick model\cr
#'   \code{get_omega()} \tab Extract variance-covariance of random effects\cr
#'   \code{get_r2()} \tab Obtain proportion of explained variance \cr
#'   \code{model.frame()} \tab Extract model frame\cr
#'   \code{model.matrix()} \tab Extract design matrix\cr
#'   \code{residuals()} \tab Extract residuals from broken stick model\cr
#' }
#'
#' The following functions perform calculations:
#' \tabular{ll}{
#'    \code{set_control()}\tab Set controls to steer calculations\cr
#'    \code{control_kr()}\tab Set controls for the \code{kr} method\cr
#' }
#'
#' @docType package
#' @name brokenstick-pkg
#' @seealso \code{\link{brokenstick}},
#' \code{\link{EB}}, \code{\link{predict.brokenstick}}
#' @note
#' This work was supported by the Bill & Melinda Gates Foundation. The contents
#' are the sole responsibility of the authors and may not necessarily represent
#' the official views of the Bill & Melinda Gates Foundation or other agencies
#' that may have supported the primary data studies used in the present study.
#' @references
#' van Buuren, S. (2023). Broken Stick Model for Irregular Longitudinal Data.
#' \emph{Journal of Statistical Software}, 106(7), 1--51.
#' <doi:10.18637/jss.v106.i07>
#'
#' van Buuren, S. (2018). \emph{Flexible Imputation of Missing Data. Second Edition}.
#' Chapman & Hall/CRC. Chapter 11.
#' \url{https://stefvanbuuren.name/fimd/sec-rastering.html#sec:brokenstick}
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