README.md

In RhoInc/aeplot: Adverse Event Plot

Overview

aeplot() is an R package that generates summary Plots of Adverse Event Prevelance using lattice.

Typical usage

A typical call to aeplot() creates output like this:

Using code like this:

install_github("rhoinc/aeplot")
library(aeplot)

myData<-read.csv("myData.csv")
plot1<- aeplot(
    myData,                        
    groups=c("intervention","placebo"),
    ngroups=c(280,272),                     
    grouplabel=c("Treatment","Control"),                                
    cut=3,
    cut_organ_class=F,
    title="AE Prevelance (3% or greater)"
)    

pdf(file="myplot.pdf", height=11, width=8.5)
    print(plot1)
dev.off()

Configuration

aeplot() takes several arguements:

data

RData required

An Rdata file with one record per AE, and (at a minimum) the following 4 columns: 1. ID (text or numeric) 2. SystemOrganClass (text) 3. PreferredName(text) 4. Group (text)

groups

array required

Array specifying the groups to be included in the plot. wording must match the raw data, like c("placebo","treatment")

ngroups

array required

Array of integers indicating the number of participants in each group. The number and order of the elements should match those given groups like c(149,147)

cut

numeric

A cutpoint for filtering low prevelence events. Rows with no group prevelance above this value are supressed.

default: 0

cut_organ_class

boolean

Flag to indicate whether cut should be applied to organ class as well as preferred name.

default: false

numerator

character

Indicates the numerator for rates given in the adverse event plot. Valid options are:

• "pt" = participants w. 1+ ae
• "ae" = total # of AEs

default: "pt"

colors

array

Sets group colors in the adverse event plot. Group colors default to "set1" in RColorBrewer, but can be specified using c("#200","#020",etc...)

default: c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#FFFF33", "#A65628", "#F781BF","#999999")

grouplabels

array

Group names to be printed in the column header.

RhoInc/aeplot documentation built on May 9, 2019, 10:03 a.m.