500 CHAPTER 21 Creating a package

Although the list provides all the information required, you’d rarely access the components directly. Instead, you can create generic print(), summary(), and plot() functions to present this information in more concise and meaningful ways. These generic functions are considered next.

21.2.2Printing the results

Most analytic functions of any breadth come with generic print() and summary() functions. print() provides basic or raw information about an object, and summary() provides more detailed or processed (summarized) information. A plot()function is frequently included when a plot makes sense in the given context.

Following the S3 OOP guidelines described in section 20.3.1, if an object has the class attribute "foo", then print(x) executes print.foo(x) if it exists or print.default(x) otherwise. The same goes for summary() and plot(). Because the oneway() function returns an object of class "oneway", you need to define print

.oneway(), summary.oneway(), and plot.oneway() functions. The print.oneway() function is given in listing 21.3.

For the life data, print(results) produces basic information about the multiple comparisons:

data: hlef by region

Multiple Comparisons (Wilcoxon Rank Sum Tests)

Probability Adjustment = holm

An informative header is printed, followed by Wilcoxon statistics and adjusted p-values for each pair of groups (Group.1 with Group.2).

Listing 21.3 Contents of the print.R file

#' @title Print multiple comparisons #'

#' @description

#' \code{print.oneway} prints pairwise group comparisons. #'

#' @details

#' This function prints Wilcoxon pairwise multiple comparisons created #' by the \code{\link{oneway}} function.

The header contains comments starting with #' that will be used by the roxygen2 package to create package documentation (see section 21.3). The inherits() function is used to make sure the submitted object has class "oneway" b. A set of cat() functions prints a description of the analysis c. (This could have been written as a single cat() function, but I thought the current code was easier to read.) Finally, print.default() is called to print the multiple comparisons d. The summary

.oneway() function is considered next.

21.2.3Summarizing the results

The summary() function produces more comprehensive and processed output than the print() function. For the healthy life-expectancy data, the summary(results) statement produces the following:

data: hlef on region

Omnibus Test

Kruskal-Wallis chi-squared = 17.8749, df = 3, p-value = 0.0004668

Multiple Comparisons (Wilcoxon Rank Sum Tests)

Probability Adjustment = holm

The output includes the results of the Kruskal–Wallis test, descriptive statistics (sample sizes, median, and median absolute deviations) for each group, and the multiple comparisons. In addition, the multiple-comparison table is annotated with stars to highlight significant results. The code for the summary.oneway() function is given in the following listing.

Listing 21.4 Contents of the summary.R file

#' @title Summarize oneway nonparametric analyses #'

#' @description

#' \code{summary.oneway} summarizes the results of a oneway #' nonparametric analysis.

#'

#' @details

#' This function prints a summary of analyses produced by

#' the \code{\link{oneway}} function. This includes descriptive #' statistics by group, an omnibus Kruskal-Wallis test, and

#' Wilcoxon pairwise multiple comparisons. #'

#' @param object an object of class \code{oneway}. #' @param ... additional parameters.

#' @method summary oneway #' @export

#' @return the input object is returned silently.

#' @author Rob Kabacoff <rkabacoff@@statmethods.net> #' @examples

#' results <- oneway(hlef ~ region, life) #' summary(results)

summary.oneway <- function(object, ...){ if (!inherits(object, "oneway"))

stop("Object must be of class 'oneway'") if(!exists("digits")) digits <- 4L

kw <- object$kw wmc <- object$wmc