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#' The Xpose Package
#'
#' Xpose is an R-based model building aid for population analysis using NONMEM.
#' It facilitates data set checkout, exploration and visualization, model
#' diagnostics, candidate covariate identification and model comparison.
#'
#' Xpose takes output from NONMEM output and/or PsN output and generates graphs
#' or other analyses. It is assumed that each NONMEM run can be uniquely
#' identified by a run number (see section below for how to generate the
#' appropriate input to Xpose). Xpose is implemented using the lattice graphics
#' library.
#'
#' The Xpose package can be divided up into six subsections (functions
#' associated with each of the different subsections are linked in the "See
#' Also" section):
#' \describe{
#' \item{Data Functions}{Functions for managing the
#' input data and manipulating the Xpose database.}
#' \item{Generic Functions}{Generic wrapper functions around the lattice
#' functions. These functions can be invoked by the user but require quite
#' detailed instructions to generate the desired output.}
#' \item{Specific Functions}{These functions are single purpose functions
#' that generate specific output given only the Xpose database as input. The
#' behavior can, to some extent, be influenced by the user.}
#' \item{Classic Functions}{Xpose has a text based menu interface to make it
#' simple for the user to invoke the Xpose specific functions. This interface is
#' called Xpose Classic. Given the limitations a text based interface imposes,
#' Xpose Classic is not very flexible but may be useful for quick assessment of
#' a model and for learning to use Xpose.}
#' \item{PsN Functions}{These functions are the interface between Xpose and
#' PsN, i.e. they do not post-process NONMEM output but rather PsN output.}
#' \item{GAM Functions}{Functions take an Xpose object and performs a generalized additive model
#' (GAM) stepwise search for influential covariates on a single model parameter.}
#' }
#'
#' @name xpose4-package
#' @aliases xpose4-package xpose
#' @docType package
#' @section How to make NONMEM generate input to Xpose: Xpose recognizes NONMEM
#' runs, and files associated to a particular run, though the run number.
#' This is a number that is used in the name of NONMEM model files, output
#' files and table files. The fundamental input to Xpose is one or more
#' NONMEM table files. These table files should be named as below followed by
#' the run number, for example xptab1 for run number 1. Xpose looks for files
#' according to the following pattern, where * is your run number:
#'
#' \bold{sdtab*} Standard table file, containing ID, IDV, DV, PRED, IPRED,
#' WRES, IWRES, RES, IRES, etc.
#'
#' \bold{patab*} Parameter table, containing model parameters - THETAs, ETAs
#' and EPSes
#'
#' \bold{catab*} Categorical covariates, e.g. SEX, RACE
#'
#' \bold{cotab*} Continuous covariates, e.g. WT, AGE
#'
#' \bold{extra*, mutab*, mytab*, xptab*, cwtab*} Other variables you might
#' need to have available to Xpose
#'
#' \bold{run*.mod} Model specification file
#'
#' \bold{run*.lst} NONMEM output
#'
#' Strictly, only one table file is needed for xpose (for example sdtab* or
#' xptab*). However, using patab*, cotab*, catab* will influence the way that
#' Xpose interprets the data and are recommended to get full benefit from
#' Xpose.
#'
#' You can use code in NONMEM similar to the following to generate the tables
#' you need. NONMEM automatically appends DV, PRED, WRES and RES unless
#' NOAPPEND is specified. Don't forget to leave at least one blank line at
#' the end of the NONMEM model specification file.
#'
#' \code{$TABLE ID TIME IPRED IWRES EVID MDV NOPRINT ONEHEADER FILE=sdtab1}
#' \code{$TABLE ID CL V2 KA K SLP KENZ NOPRINT ONEHEADER FILE=patab1}
#' \code{$TABLE ID WT HT AGE BMI PKG NOPRINT ONEHEADER FILE=cotab1}
#' \code{$TABLE ID SEX SMOK ALC NOPRINT ONEHEADER FILE=catab1}
#' @author E. Niclas Jonsson, Mats Karlsson, Justin Wilkins and Andrew Hooker
#' @references \href{https://uupharmacometrics.github.io/PsN/}{PsN}
#' @keywords methods package
#' @examples
#'
#' \dontrun{
#' # run the classic interface
#' library(xpose4)
#' xpose4()
#'
#' # command line interface
#' library(xpose4)
#' xpdb <- xpose.data(5)
#' basic.gof(xpdb)
#' }
#'
#' @family data functions
#' @family generic functions
#' @family specific functions
#' @family classic functions
#' @family PsN functions
#' @family GAM functions
#'
#' @import lattice
#' @import grid
#' @import gam
#' @import methods
#'
#' @importFrom stats aggregate anova as.formula coefficients
#' density dfbetas dnorm formula lm
#' lm.influence loess median predict preplot
#' qchisq quantile quasi reorder reshape
#' residuals sd summary.glm update
#' @importFrom grDevices bmp dev.cur dev.new dev.off jpeg pdf png postscript rgb tiff
#' @importFrom graphics hist par
#' @importFrom utils capture.output citation count.fields
#' data head installed.packages menu
#' packageDescription packageVersion read.csv
#' read.table setTxtProgressBar tail txtProgressBar
#' write.table
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