greport (version 0.5-2)

exReport: Exclusion Report

Description

Generates graphics for sequential exclusion criteria

Usage

exReport(formula, data = NULL, subset = NULL, na.action = na.retain,
  ignoreExcl = NULL, ignoreRand = NULL, autoother = FALSE, sort = TRUE,
  whenapp = NULL, erdata = NULL, panel = "excl", subpanel = NULL,
  head = NULL, tail = NULL, apptail = NULL, h = 5.5, w = 6.5,
  hc = 4.5, wc = 5, adjustwidth = "-0.75in", append = FALSE,
  popts = NULL, app = TRUE)

Arguments

formula

a formula with only a right-hand side, possibly containing a term of the form pending(x) to inform the function of which subjects have incomplete randomization ("randomization pending"). The pending variable is ignored if a subj

data

input data frame

subset

subsetting criteria

na.action

function for handling NAs when creating analysis frame

ignoreExcl

a formula with only a right-hand side, specifying the names of exclusion variable names that are to be ignored when counting exclusions (screen failures)

ignoreRand

a formula with only a right-hand side, specifying the names of exclusion variable names that are to be ignored when counting randomized subjects marked as exclusions

autoother

set to TRUE to add another exclusion Unspecified that is set to TRUE for non-pending subjects that have no other exclusions

sort

set to FALSE to not sort variables by descending exclusion frequency

whenapp

a named character vector (with names equal to names of variables in formula). For each variable that is only assessed (i.e., is not NA) under certain conditions, add an element to this vector naming the condition

erdata

a data frame that is subsetted on the combination of id variables when randomized is present, to print auxiliary information about randomized subjects who have exclusion criteria

panel

panel string

subpanel

If calling exReport more than once (e.g., for different values of sort), specify subpanel to distinguish the multiple calls. In that case, -subpanel will be appended to panel when creating

head

character string. Specifies initial text in the figure caption, otherwise a default is used.

tail

a character string to add to end of automatic caption

apptail

a character string to add to end of automatic caption for appendix table with listing of subject IDs

h

height of 2-panel graph

w

width of 2-panel graph

hc

height of cumulative exclusion 1-panel graph

wc

width of this 1-panel graph

adjustwidth

used to allow wide detailed exclusion table to go into left margin in order to be centered on the physical page. The default is '-0.75in', which works well when using article document class with default page width. To use the geometry packa

append

set to TRUE if adding to an existing sub-report

popts

a list of options to pass to graphing functions

app

set to FALSE to prevent writing appendix information

Details

With input being a series of essentially binary variables with positive indicating that a subject is excluded for a specific reason, orders the reasons so that the first excludes the highest number of subjects, the second excludes the highest number of remaining subjects, and so on. First draws a single vertical axis graph showing cumulative exclusions, then creates a 2-panel dot chart with the first panel showing that information, along with the marginal frequencies of exclusions and the second showing the number of subjects remaining in the study after the sequential exclusions. A pop-up table is created showing those quantities plus fractions. There is an option to not sort by descending exclusion frequencies but instead to use the original variable order. Assumes that any factor variable exclusions that have only one level and that level indicates a positive finding, that variable has a denominator equal to the overall number of subjects.

Examples

# See test.Rnw in tests directory