ascorbic: ascorbic data from Crowder and Hand
In wgalvord/owprm: Occasions Within Phases Repeated Measures

Description Usage Format Details Source References Examples

A dataset containing ascorbic acid measures on 12 patients The data come from Table 3.3 in Crowder and Hand.

ascorbic

A data frame with 84 observations on the following 7 variables.

patient: a factor with levels Pat.01 Pat.02Pat.03Pat.04Pat.05 Pat.06Pat.07Pat.08Pat.09 Pat.10Pat.11Pat.12
week: a numeric vector
occ: a factor with levels 1 2 3 4 5 6 7
phase.num: a numeric vector
Phase: a factor with levels post pre Rx
ascorbic.acid: a numeric vector
Occasion: a numeric vector

The data were taken from Table 3.3 in Crowder and Hand (1991). The variable patient is a factor variable, which should be used in fitting the correct model. The variable phase.num is a numeric variable. The variable Phase is a factor variable, which should be used instead of phase.num for fitting the correct model. The variable Occasion is a numeric variable. The variable occ is a factor variable, which should be used instead of Occasion in fitting the correct model.

Crowder MJ and Hand DJ (1990) Analysis of Repeated Measures, Chapman and Hall.

{
##
## ***** Get Simple BoxPlots with Points
##
data(ascorbic)
with(ascorbic, plot(ascorbic.acid ~ occ,
xlab = 'Occasions [occ]',
ylab = 'Ascorbic Acid [ascorbic.acid]',
main = 'Ascorbic Acid responses for 12
patients\nacross 7 Occasions'))
with(ascorbic,
points(ascorbic.acid ~ occ, pch = 16,
col = c('black', 'brown', 'blue', 'purple',
'red', 'green', 'orange', 'yellow', 'pink',
'turquoise', 'gray', 'violet')))
##
## ***** End Simple BoxPlots with Points
##
}
##
## ***** Plot groupedData data frame with nlme
##
## Create and plot ascorbic.gD.df,
## a groupedData data frame
##
library(nlme)
ascorbic.gD.df <-groupedData(ascorbic.acid ~ week | patient,
    data = ascorbic)

## plot ascorbic.gD.df
plot(ascorbic.gD.df, outer = ~ 1, key = FALSE,
ylab = 'Ascorbic Acid', xlab = 'week',
aspect = 0.6, main = 'Reaction of Patients to Rx')
##
## ***** End plot of groupedData data frame
##
##
## ***** Get ggplot
##
## Create ggplot2 plot object
library(ggplot2)
##
occ.p0 <- ggplot(ascorbic, aes(occ, ascorbic.acid))
## set.seed(11) ## for jittered points to stay fixed
occ.p1 <- occ.p0 +
geom_boxplot(stat = 'boxplot', outlier.shape = 3) +
labs(y = 'Ascorbic Acid', x = 'Occasion',
title = 'Ascorbic Acid Responses for 12 Patients
Across Occasions in 3 Phases')
occ.p1 ## basic boxplot
##
set.seed(11) ## for jittered points to stay fixed
occ.p2 <- occ.p1 +
geom_point(position = position_jitter(width = 0.2),
aes(colour = patient))
occ.p2 # add points color-coded by patient
##
set.seed(11) ## for jittered points to stay fixed
occ.p3 <- occ.p2 +
geom_vline(xintercept = c(2.5, 5.5), col = 'blue', lwd = 1.2,
linetype = 'longdash')
occ.p3 # add vertical lines to separate Phases
##
set.seed(11) ## for jittered points to stay fixed
occ.p4 <- occ.p3 +
annotate('text', x = 1.5, y = 1.6, label = 'pre Rx') +
annotate('text', x = 4, y = 0.3, label = 'Rx') +
annotate('text', x = 4, y = 0.2, label = '(treatment)') +
annotate('text', x = 6.5, y = 1.6, label = 'post Rx')
occ.p4 # label Phases
##
set.seed(11) ## for jittered points to stay fixed
occ.p5 <- occ.p4 +
annotate('text', x = 1.5, y = 1.7, label = 'Phase 1') +
annotate('text', x = 4, y = 0.4, label = 'Phase 2') +
annotate('text', x = 6.5, y = 1.7, label = 'Phase 3')
occ.p5 # further label Phases
##
## ***** End ggplot
##
##
## ***** Produce Traditional DotPlot
##
with(ascorbic,
plot(jitter(Occasion), ascorbic.acid,
ylab = 'Ascorbic Acid', ylim = c(0,5),
xlab = 'Occasions (occ)',
main = 'Ascorbic Acid - Occasions and Phases',
col = c('black', 'brown', 'blue', 'purple',
'red', 'green', 'orange', 'yellow', 'pink',
'turquoise', 'gray', 'violet'), pch = 16,
xaxt = 'n'))
##
## Note: jitter() takes a numeric value, not a factor.
## In data the 'ascorbic' data frame
## 'Occasion' is a numeric variable
## and 'occ' is a factor variable.
##
axis(side = 1, at = c(1:7),
labels = c(1:7), tick = TRUE, las = 2, cex.axis = .7)
abline(v = c(2.5, 5.5), lty = 1, col = 'blue', lwd = 1)
##
## Add text above data - ascorbic.acid
##
text(1.0, 4.4, "Phase 1: 'pre'",
  pos = 4, offset = 0, cex = 1.0)
text(3.4, 4.4, "Phase 2: 'Rx'",
  pos = 4, offset = 0, cex = 1.0)
text(5.8, 4.4, "Phase 3: 'post'",
  pos = 4, offset = 0, cex = 1.0)
## Add legend to the dot plot
##
legend.vec <- c('01', '02', '03', '04', '05', '06',
                '07', '08', '09', '10', '11', '12')
## Phase 1
legend(1.2, 3.8, legend = legend.vec[1:4],
col = c('black', 'brown', 'blue', 'purple'),
pch = 16, cex = .8, pt.cex = .8 )
## Phase 2
legend(3.8, 3.8, legend = legend.vec[5:8],
col = c('red', 'green', 'orange', 'yellow'),
pch = 16, cex = .8, pt.cex = .8 )
## Phase 3
legend(6.2, 3.8, legend = legend.vec[9:12],
col = c('pink', 'turquoise', 'gray', 'violet'),
pch = 16, cex = .8, pt.cex = .8)
##
## ***** End Traditional DotPlot
##