1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
|
\name{barNest}
\alias{barNest}
\title{Display a nested breakdown of numeric values}
\description{Breaks down the elements of a data frame by one or more
categorical elements and displays the breakdown as a bar plot.}
\usage{
barNest(formula=NULL,data=NULL,FUN=c("mean","sd"),ylim=NULL,
main="",xlab="",ylab="",shrink=0.1,errbars=FALSE,col=NA,
labelcex=1,lineht=NA,showall=TRUE,barlabels=NULL,showlabels=TRUE,mar=NULL,
arrow.cap=NA,trueval=NA)
}
\arguments{
\item{formula}{A formula with a numeric element of a data frame on the left and
one or more categorical elements on the right.}
\item{data}{A data frame containing the elements in \samp{formula}.}
\item{FUN}{The functions to apply to x.}
\item{ylim}{Optional y limits for the plot, usually necessary for counts.}
\item{main}{Title for the plot.}
\item{xlab,ylab}{Axis labels for the plot. The x axis label is typically blank}
\item{shrink}{The proportion to shrink the width of the bars at each level.}
\item{errbars}{Whether to display error bars on the lowest level of breakdown.}
\item{col}{The colors to use to fill the bars. See Details.}
\item{labelcex}{Character size for the group labels.}
\item{lineht}{The height of a line of text in the lower margin of the plot in user
units. This will be calculated by the function if a value is not passed.}
\item{showall}{Whether to display bars for the entire breakdown.}
\item{barlabels}{Optional group labels that may be useful if the factors used to
break down the numeric variable are fairly long strings.}
\item{showlabels}{Whether to display the labels below the bars.}
\item{mar}{If not NULL, a four element vector to set the plot margins. If new
margins are set, the user must reset the margins after the function exits.}
\item{arrow.cap}{The width of the "cap" on error bars in user units,
calculated on the basis of the number of bars in the final breakdown if NA.}
\item{trueval}{If this is not NA, the call to \samp{brkdnNest} will return the
proportions of the response variable that are equal to \samp{trueval}.
See Details.}
}
\value{The summary list produced by brkdnNest.}
\details{
\samp{barNest} displays a bar plot illustrating the hierarchic breakdown of
the elements of a data frame. The breakdown is performed by \samp{brkdnNest}
and the actual display is performed by \samp{drawNestedBars}. The heights of
the bars will be proportional to the values returned by the first function in
\samp{FUN}. If \samp{showall} is TRUE, the entire nested breakdown will be
displayed. This can be useful in visualizing the relationship between groups
and subgroups in a compact format.
If \samp{trueval} is not NA and brkdnNest is called to calculate the values for
the heights of the bars, the proportions of the dichotomous response variable
that are equal to \samp{trueval} will be returned.
A number of functions can be passed in the \samp{FUN} argument. Two functions,
\samp{propbrk} and \samp{valid.n} that are provided can be used as bar heights,
giving proportions and counts in each group and subgroup respectively.
Binomial confidence limits can be added to the proportions returned by
\samp{propbrk} with \samp{binciWl} and \samp{binciWu} as in the second last
example.
The colors of the bars are determined by \samp{col}. If \samp{showall} is FALSE,
the user only need pass a vector of colors, usually the same length as the number
of categories in the final (last on the right side) element in the formula. If
\samp{showall} is TRUE and the user wants to color all of the bars, a list with
as many elements as there are levels in the breakdown should be passed. Each
element should be a vector of colors, again usually the same length as the number
of categories. As the categorical variables are likely to be factors, it is
important to remember that the colors must be in the correct order for the levels
of the factors. When the levels are not in the default alphanumeric order, it is
quite easy to get this wrong. As a \samp{barNest} plot with more than a few
factors and levels in each factor is quite dense, easily distinguished colors
for each level of the breakdown may be preferable.
}
\author{Jim Lemon and Ofir Levy}
\references{
Lemon, J. & Levy, O. (2011) barNest: Illustrating nested summary measures.
Statistical Computing and Graphics Newsletter of the American Statistical
Association, 21(2): 5-10.
}
\seealso{\link{brkdnNest}, \link{drawNestedBars}, superbarplot(UsingR)}
\examples{
# recreate the Titanic data frame and show the three way breakdown
titanic<-data.frame(
class=c(rep("1st",325),rep("2nd",285),rep("3rd",706),rep("Crew",885)),
age=c(rep("Adult",319),rep("Child",6),rep("Adult",261),rep("Child",24),
rep("Adult",627),rep("Child",79),rep("Adult",885)),
sex=c(rep("M",175),rep("F",144),rep("M",5),rep("F",1),
rep("M",168),rep("F",93),rep("M",11),rep("F",13),
rep("M",462),rep("F",165),rep("M",48),rep("F",31),
rep("M",862),rep("F",23)),
survived=c(rep("Yes",57),rep("No",118),rep("Yes",140),rep("No",4),rep("Yes",6),
rep("Yes",14),rep("No",154),rep("Yes",80),rep("No",13),rep("Yes",24),
rep("Yes",75),rep("No",387),rep("Yes",76),rep("No",89),
rep("Yes",13),rep("No",35),rep("Yes",14),rep("No",17),
rep("Yes",192),rep("No",670),rep("Yes",20),rep("No",3)))
require(plotrix)
titanic.colors<-list("gray90",c("#0000ff","#7700ee","#aa00cc","#dd00aa"),
c("#ddcc00","#ee9900"),c("pink","lightblue"))
barNest(survived~class+age+sex,titanic,col=titanic.colors,showall=TRUE,
main="Titanic survival by class, age and sex",ylab="Proportion surviving",
FUN="propbrk",shrink=0.15,trueval="Yes")
# now show the actual numbers of passengers
barNest(survived~class+age+sex,titanic,col=titanic.colors,showall=TRUE,
main="Titanic passengers and crew by class, age and sex",ylab="Number",
FUN="valid.n",shrink=0.15)
# to see this properly displayed, start a wide plot window
# x11(width=10)
test.df<-data.frame(Age=rnorm(100,25,10),
Sex=sample(c("Male","Female"),100,TRUE),
Marital=sample(c("Div","Mar","Sing","Wid"),100,TRUE),
Employ=sample(c("FT","PT","Un"),100,TRUE))
test.col<-list(Overall="gray",Sex=c("pink","lightblue"),
Marital=c("mediumpurple","orange","tan","lightgreen"),
Employ=c("#1affd8","#caeecc","#ff90d0"))
barNest(formula=Age~Sex+Marital+Employ,data=test.df,ylab="Mean age (years)",
main="Mean age by subgroups",errbars=TRUE,col=test.col)
# set up functions for 20th and 80th percentiles
q20<-function(x,na.rm=TRUE) return(quantile(x,probs=0.2,na.rm=TRUE))
q80<-function(x,na.rm=TRUE) return(quantile(x,probs=0.8,na.rm=TRUE))
# show the asymmetric dispersion measures
barNest(formula=Age~Sex+Marital+Employ,data=test.df,ylab="Mean age (years)",
main="Use median and quantiles for dispersion",FUN=c("median","q80","q20"),
errbars=TRUE,col=test.col)
barNest(formula=Employ~Sex+Marital,data=test.df,ylab="Proportion unemployed",
main="Show the proportion unemployed",FUN=c("propbrk","binciWu","binciWl"),
errbars=TRUE,col=test.col,trueval="Un")
barNest(formula=Age~Sex+Marital+Employ,data=test.df,ylab="Counts",
main="Show the counts in subgroups (final level only)",FUN="valid.n",
col=test.col,showall=FALSE,ylim=c(0,10))
}
\keyword{misc}
|
