swCRTdesign (version 2.1)

swPlot: Plot of Mean Response/Outcome for Stepped Wedge Cluster Randomized Trial (SW CRT)

Description

swPlot returns plot of the mean response versus time based on waves and/or clusters from a SW CRT.

Usage

swPlot(response.var, tx.var, time.var, cluster.var, data, choose.mfrow=NULL, 
by.wave=TRUE, combined.plot=TRUE, choose.xlab="Time", choose.main=NULL, 
choose.pch=NULL, choose.cex=1, choose.tx.col=NULL, choose.ncol=2, 
choose.tx.pos="topright", choose.legend.pos=locator(1))

Arguments

response.var

numeric(vector): Response (Outcome) variable.

tx.var

numeric(vector): Treatment (Predictor of Interest) variable. Typically, 0=control, 1=intervention, values between 0 and 1 correspond to fractional treatment/intervention effects, and values greater than 1 correspond to other treatment options.

time.var

integer(vector): Time (points) variable, corresponding to the time points when data were collected during the SW CRT.

cluster.var

integer(vector): Cluster (identification) variable, corresponding to the cluster where an observation is from.

data

An optional data frame containing (at least) the response, treatment (tx), time, and cluster variables.

choose.mfrow

numeric (vector): Choose mfrow for plot. If NULL, mfrow is automatically assigned based on the plot created. The default is NULL.

by.wave

logical: If TRUE, plot mean response according to each wave. If FALSE, plot mean response according to each cluster. The default is TRUE.

combined.plot

logical: If TRUE, plot mean response on same plot (what is plotted depends on by.wave). If FALSE, plot mean response on separate plots for each wave (what is plotted depends on by.wave). The default is TRUE.

choose.xlab

Choose xlab for plot. The default is "Time".

choose.main

Choose main for plot. If NULL, main is chosen for the user; which is highly recommended. The default is NULL.

choose.pch

Choose pch for plot. If NULL, pch are chosen for the user; which is highly recommended. The default is NULL.

choose.cex

Choose cex for choose.pch. Standard cex option in points() applies. The default is 1.

choose.tx.col

Choose colors for different treatment options (at least two: 0=placebo, 1=intervention). If NULL, colors are chosen for the unique treatment options in the data supplied. The default is NULL.

choose.ncol

Choose number of columns for non-treatment legend. Standard ncol option in legend() applies. The default is 2.

choose.tx.pos

Choose where to place treatment colors "legend". Standard legend() positions apply. The default is "topright".

choose.legend.pos

Choose where to place the non-treatment legend. Standard legend() positions apply. The default is locator(1), user specifies location with mouse/trackpad. Specify NULL to remove legend.

Details

Returns a plot of the mean response versus time with a combination of by wave (TRUE / FALSE) and combined plot (TRUE / FALSE) from a SW CRT.

References

Hussey MA, Hughes JP. Design and analysis of stepped wedge cluster randomized trials. Contemporary Clinical Trials 2007;28:182-191.

Examples

library(swCRTdesign)
# Example 1 (Generating SW CRT data)
# (binary response with 1 missing value, 5 clusters, 4 time points)

n.Ex1 <- 120
p0.Ex1 <- 0.05
clusters.Ex1 <- c(2,2,1)
dsn.Ex1 <- swDsn( clusters=clusters.Ex1 )
time.Ex1 <- c(1:dsn.Ex1$total.time)*4 - 4
response.Ex1 <- rbinom(n.Ex1 * dsn.Ex1$n.clusters * dsn.Ex1$total.time, 1, p0.Ex1)
response.Ex1[1] <- NA
tx.Ex1 <- as.vector( apply( dsn.Ex1$swDsn, 1, function(z){rep(z, n.Ex1)}) )
time.Ex1 <- rep( time.Ex1, n.Ex1 * dsn.Ex1$n.clusters )
cluster.Ex1 <- rep( 1:dsn.Ex1$n.clusters, each=n.Ex1 * dsn.Ex1$total.time )
data.Ex1 <- data.frame(response.Ex1, tx.Ex1, time.Ex1, cluster.Ex1)

# Example 1 (Mean Response vs Time, by.wave=TRUE, combined.plot=TRUE)
swPlot(response.Ex1, tx.Ex1, time.Ex1, cluster.Ex1, data.Ex1, by.wave=TRUE, 
combined.plot=TRUE, choose.tx.pos="bottomright", choose.legend.pos="bottom")

# Example 2 (Mean Response vs Time, by.wave=TRUE, combined.plot=FALSE)
swPlot(response.Ex1, tx.Ex1, time.Ex1, cluster.Ex1, data.Ex1, by.wave=TRUE, 
combined.plot=FALSE, choose.tx.pos="bottomright", choose.legend.pos="bottom")

# Example 3 (Mean Response vs Time, by.wave=FALSE, combined.plot=TRUE)
swPlot(response.Ex1, tx.Ex1, time.Ex1, cluster.Ex1, data.Ex1, by.wave=FALSE, 
combined.plot=TRUE, choose.tx.pos="bottomright", choose.legend.pos="bottom")

# Example 4 (Mean Response vs Time, by.wave=FALSE, combined.plot=FALSE)
swPlot(response.Ex1, tx.Ex1, time.Ex1, cluster.Ex1, data.Ex1, by.wave=FALSE, 
combined.plot=FALSE, choose.tx.pos="bottomright", choose.legend.pos="bottom")