R/Gmisc.R

In raredd/Gmisc0: Collection of functions for plotting relations, generating tables, and more.

#' Collection of functions for plotting relations, generating tables, and more.
#'
#' This is a collection of functions that I've found useful in my research.
#' The package is inspired by Frank Harrell's \pkg{Hmisc} package. The main focus
#' is on tables, plots, and \pkg{knitr}-integration.
#'
#' @section Awesome tables:
#'
#' For tables you'll find the convenient \code{\link{htmlTable}} that I have used
#' for advanced table layout. A major focus has been to have
#' it compatible with LibreOffice (you can copy/past from there into word)
#' as I generally want to be able to send my documents to a
#' journal in .doc/.docx format. \bold{Note:} it is now in
#' \href{http://www.rstudio.com}{RStudio} possible to copy->paste
#' directly from the viewer into a MS Word document with minimal
#' layout loss.
#'
#' The \code{\link{getDescriptionStatsBy}} is a straight forward function that
#' aims at helping you to generate descriptive table stratified by different
#' variables. In other words, the function returns everything you need for generating
#' a \emph{Table 1} ready for publication. This function is accompanied by the
#' \code{\link{describeMean}}, \code{\link{describeMedian}}, \code{\link{describeProp}},
#' and \code{\link{describeFactors}} functions.
#'
#' @section Convenient knitr-helpers:
#'
#' One of the main priorities of this package is to make the preparation of
#' publication-ready manuscripts through the
#' \pkg{\href{http://yihui.name/knitr/}{knitr}}-package. The \code{\link{figCapNo}}
#' can be used for automated figure counting. The \code{\link{pvalueFormatter}}
#' tries to simplify rounding of p-values, e.g. you may be ok with just
#' 0.0005 as a p-value but when you come close to the "magic" 0.05 value
#' you may want to have two significant digits, i.e. 0.048 instead of just 0.05.
#' The \code{\link{outputInt}} simply transforms a large integer digit
#' to proper formatting.
#'
#' @section Some fancy plots:
#'
#' The forest plot function, \code{\link{forestplot2}}, is a more general
#' version of the original \pkg{rmeta}-packages \code{\link[rmeta]{forestplot}}
#' implementation. The aim is at using forest plots for more than
#' just meta-analyses.
#'
#' The transition plot function, \code{\link{transitionPlot}}, is for
#' descriptive purposes. It tries to illustrate the size of change
#' between one state and the next, i.e. a transition. This is
#' basically a graph of based upon \code{table(var1, var2)}.
#'
#' The \href{http://en.wikipedia.org/wiki/Singular_value_decomposition}{Singular value decomposition}
#' is a common method for reducing the number of variables. Unfortunately
#' this compression can reduce the interpretability of the model. The \code{\link{getSvdMostInfluential}}
#' function tries to remedy that by identifying the most influential
#' elements from the \code{V}-matrix.
#'
#' The \code{\link{getTicks}} tries to format ticks for plots in a nicer way.
#' The major use is for exponentials where ticks are generated using the
#' \eqn{2^n}{2^n} since a doubling is a concept easy to grasp even for
#' non-statisticians.
#'
#' @section Other stuff:
#'
#' The \code{\link{insertRowAndKeepAttr}} simply adds a row while remembering
#' all the attributes previously set by using the \code{\link{copyAllNewAttributes}}.
#' The \code{\link{mergeLists}} tries to merge lists that do not have identical
#' elements.
#'
#' @name Gmisc-package
#' @docType package
NULL