R/sitar-package.R

In statist7/sitar: Super Imposition by Translation and Rotation Growth Curve Analysis

#' SITAR (SuperImposition by Translation And Rotation) growth curve analysis
#'
#' SITAR is a method of growth curve analysis, based on \pkg{nlme}, that
#' estimates a single mean growth curve as a regression B-spline, plus a set of
#' up to four fixed and random effects (a, b, c and d) (d was added in version 1.2.0)
#' defining how individual
#' growth curves differ from the mean curve. SITAR stands for SuperImposition
#' by Translation And Rotation.
#'
#' The package also contains some utility functions for the LMS method, as used
#' to construct growth reference centiles (see \pkg{gamlss}).
#'
#' \tabular{ll}{ Package: \tab sitar\cr Type: \tab Package\cr Version: \tab
#' 1.0\cr Date: \tab 2013-09-23\cr License: \tab GPL-2\cr } Effect a (or alpha)
#' measures size, and is a random intercept relative to the spline curve
#' intercept. Effect b (or beta) measures tempo, the timing of the growth
#' process, and reflects a shift on the x scale relative to the mean. Effect c
#' (or gamma) is velocity, and indicates how the x scale is stretched or shrunk
#' reflecting the rate at which 'time' passes for individuals. Effect d is a
#' rotation in the plane. The aim is for
#' individual curves, adjusted for {abcd} to lie on top of (i.e. be
#' superimposed on) the mean curve.
#'
#' The package creates an object of class \code{sitar}, based on \pkg{nlme},
#' representing the nonlinear mixed-effects model fit. Generic functions such
#' as \code{print}, \code{plot} and \code{summary} have methods to show the
#' results of the fit, along with \code{resid}, \code{coef}, \code{fitted},
#' \code{fixed.effects} and \code{random.effects} to extract some of its
#' components. The functions \code{AICadj}, \code{BICadj} and \code{varexp}
#' compare respectively the AIC, BIC and variance explained of a series of
#' models, taking into account any transformations of the y variable. Functions
#' \code{plotclean}, \code{velout}, \code{codeplot} and \code{zapvelout} are
#' useful to clean the data file.
#'
#' @name sitar-package
#' @docType package
#' @author Tim Cole \email{tim.cole@@ucl.ac.uk}
#' @references The idea of SITAR growth curve analysis arose from the paper by
#' Beath (2007) and was first described in Cole et al (2010). The other
#' references describe applications of SITAR to a variety of data forms.
#'
#' Beath KJ. Infant growth modelling using a shape invariant model with random
#' efffects. Stat Med 2007;26:2547-64.
#'
#' Cole TJ, Cortina Borja M, Sandhu J, et al. Nonlinear growth generates age
#' changes in the moments of the frequency distribution: the example of height
#' in puberty. Biostatistics 2008;9:159-71.
#'
#' Cole TJ, Donaldson MD, Ben-Shlomo Y. SITAR--a useful instrument for growth
#' curve analysis. Int J Epidemiol 2010;39:1558-66.
#'
#' Gault EJ, Perry RJ, Cole TJ, et al. Effect of oxandrolone and timing of
#' pubertal induction on final height in Turner's syndrome: randomised, double
#' blind, placebo controlled trial. BMJ 2011;\-342:d1980.
#'
#' Johnson L, Llewellyn CH, van Jaarsveld CHM, et al. Genetic and environmental
#' influences on infant growth: prospective analysis of the Gemini twin birth
#' cohort. PLoS ONE 2011;6:e19918.
#'
#' Prentice A, Dibba B, Sawo Y, et al. The effect of prepubertal calcium
#' carbonate supplementation on the age of peak height velocity in Gambian
#' adolescents. Am J Clin Nutr 2012;96:1042-50.
#'
#' Dean MC, Cole TJ. Human life history evolution explains dissociation between
#' the timing of tooth eruption and peak rates of root growth. PLoS ONE
#' 2013;8:e54534.
#'
#' Cole TJ, Statnikov Y, Santhakumaran S, et al. Birth weight and longitudinal
#' growth in infants born below 32 weeks gestation: a UK population study. Arch
#' Dis Child Fetal Neonatal Ed 2014;99:F34-F40.
#'
#' Cole TJ, Rousham EK, Hawley NL, et al. Ethnic and sex differences in
#' skeletal maturation among the Birth to Twenty cohort in South Africa. Arch
#' Dis Child 2014;100:138-43.
#'
#' Cole TJ, Pan H, Butler GE. A mixed effects model to estimate timing and
#' intensity of pubertal growth from height and secondary sexual
#' characteristics. Ann Hum Biol 2014;41:7683.
#'
#' Johnson L, van Jaarsveld CHM, Llewellyn CH, et al. Associations between
#' infant feeding and the size, tempo and velocity of infant weight gain: SITAR
#' analysis of the Gemini twin birth cohort. Int J Obes 2014;38:980-7.
#'
#' Pizzi C, Cole TJ, Richiardi L, et al. Prenatal influences on size, velocity
#' and tempo of iInfant growth: findings from three contemporary cohorts. PLoS
#' ONE 2014;9:e90291.
#'
#' Ward KA, Cole TJ, Laskey MA, et al. The Effect of Prepubertal Calcium
#' Carbonate Supplementation on Skeletal Development in Gambian Boys-A 12-Year
#' Follow-Up Study. J C E M 2014;99:3169-76.
#' @keywords package
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