aeReport2: Report Summarizing All Adverse Events
In harrelfe/rreport: Research Reporting Package

Description Usage Arguments Details Side Effects See Also Examples

This report uses a data format in which records exist only for events, and these events are classified as major and minor events. Typically major refers to organ system and minor to preferred term. As only events are signaled in the data, the denominator (number of subjects at risk and having some likelihood of having had adverse events collected had they occured) for each treatment must be specified. Produces an open meeting table not stratified by treatment (for open report) and one stratified by treatment (for closed report) in the gentex directory.

  aeReport2(major, minor = rep("", length(major)), treat,
    id, denom, panel = "ae",
    caption = "Summary of adverse events by system organ class and preferred term",
    ncaption = "",
    descending = c("both", "major", "minor", "none"),
    sortby = c("incidence", "% difference"),
    headerStr = "AE", minpct = c(0, 0), mindif = c(0, 0),
    size = NULL, longtable = FALSE, lines.page = 50,
    landscape = FALSE, maxcol = NULL, append = FALSE,
    ref.label = NULL, minfreq = 7, major.filter = TRUE,
    minor.filter = FALSE, appendix = TRUE)

`major`	factor or character vector specifying the major classification of events, usually organ system
`minor`	factor or character vector specifying the minor classification, usually an individual event given by the preferred term. If `minor` is omitted, breakdowns are only by `major`.
`treat`	discrete treatment variable
`id`	subject ID, used to determine when multiple events arise from the same subject
`denom`	a vector giving the number of subjects on each treatment (in order of treatment levels), i.e., number of subjects at risk
`panel`	base name for `.tex` files. Default is `"ae"`. Table for the open report has an `"O"` put at the front, and files are written to directory `gentex`.
`caption`	text string containing the table caption. Other information is automatically appended to this, especially related to `minpct` and `mindif`. `caption` should not end with a period.
`ncaption`	NEEDDOC
`descending`	By default, `major` categories are sorted in order of descending frequency (ignoring `minor`), and `minor` categories are sorted in order of descending frequency within each major category. Specify `descending='none'` to have categories in order of factor levels or alphabetic for character variables, or to `'major'` or `'minor'`.
`sortby`	Specify `sortby='% difference'` to have `descending` apply to difference in percent incidence between two treatments, instead of to the pooled incidence over treatments. For the open report, sorting is always alphabetic by category or by descending pooled (over treatments) incidence.
`headerStr`	NEEDDOC
`minpct`	a 2-vector specifying the minimum percents for which to output results for `major` and `minor` categories, respectively. The default is `c(0,0)` so that all results are output. Specify `minpct=c(10,0)` for example to only print `major` categories for which at least a ten percent incidence of events in those categories are present, ignoring `treat`, and for any qualifying `major` category, output all `minor` ones. The percents pertain to the per-subject incidences, not counting multiple events per subject.
`mindif`	a 2-vector specifying the minimum difference in percent per-subject incidence between treatments, corresponding to `major` and `minor`. The sign of differences is ignored. This only applies to the case of two treatments. Output not meeting the minimum difference in percents is suppressed.
`size`	see `latex.default`
`longtable`	see `latex.default`
`lines.page`	see `latex.default`
`landscape`	passed to `latex.default`
`maxcol`	the maximum number of columns to allow for a `major` or `minor` label (note that two extra spaces are added to `minor` labels as they are indented). Longer event labels are wrapped to multiple lines. By default, LaTeX will attempt to display the full labels no matter how long.
`append`	set to `TRUE` to have LaTeX code appended to existing files
`ref.label`	NEEDDOC
`minfreq`	NEEDDOC
`major.filter`	NEEDDOC
`minor.filter`	NEEDDOC
`appendix`	NEEDDOC

Values of minor are not assumed to be unique across values of major.

creates or appends to files "gentex/Ox.tex" and "gentex/x.tex" under the current working directory, where x is the value of panel.

aeReport

## Not run: 
major <- c('A', 'A', 'A', 'B', 'B', 'C')
minor <- c('a1','a1','a2','b1','b2','c1')
id <- c(1, 1, 1, 1, 2, 3)
treat <- c('drug','placebo','drug','placebo','drug','placebo')
aeReport2(major, minor, treat, id, denom=c(placebo=10,drug=10))
aeReport2(major, minor, treat, id, denom=c(placebo=10,drug=10),
          sortby='% difference')

## End(Not run)