knitr::opts_chunk$set( collapse = TRUE, warning = FALSE, fig.height = 6, fig.width = 7, fig.path = "fig/tut01", dev = "png", comment = "##" ) # save some typing knitr::set_alias(w = "fig.width", h = "fig.height", cap = "fig.cap") # Old Sweave options # \SweaveOpts{engine=R,eps=TRUE,height=6,width=7,results=hide,fig=FALSE,echo=TRUE} # \SweaveOpts{engine=R,height=6,width=7,results=hide,fig=FALSE,echo=TRUE} # \SweaveOpts{prefix.string=fig/vcdtut,eps=FALSE} # \SweaveOpts{keep.source=TRUE} # preload datasets ??? set.seed(1071) library(vcd) library(vcdExtra) library(ggplot2) data(HairEyeColor) data(PreSex) data(Arthritis, package="vcd") art < xtabs(~Treatment + Improved, data = Arthritis) if(!file.exists("fig")) dir.create("fig")
R provides many methods for creating frequency and contingency tables. Several are
described below. In the examples below, we use some real examples and some anonymous
ones, where the variables A
, B
, and C
represent
categorical variables, and X
represents an arbitrary R data object.
The first thing you need to know is that categorical data can be represented in
three different forms in R, and it is sometimes necessary to convert
from one form to another, for carrying out statistical tests, fitting models
or visualizing the results. Once a data object exists in R,
you can examine its complete structure with
the str()
function, or view the names of its components with the
names()
function.
Categorical data in case form are simply data frames containing individual observations, with one or
more factors, used as the classifying variables. In case form, there may also
be numeric covariates.
The total number of observations is nrow(X)
, and the number of variables is ncol(X)
.
Example:
The Arthritis
data is available in case form in the vcd
package.
There are two explanatory factors: Treatment
and Sex
. Age
is a numeric covariate, and Improved
is the response an ordered factor,
with levels
r paste(levels(Arthritis$Improved),collapse=' < ')
.
Excluding Age
, this represents
a $2 \times 2 \times 3$ contingency table for Treatment
, Sex
and Improved
, but in case form.
names(Arthritis) # show the variables str(Arthritis) # show the structure head(Arthritis,5) # first 5 observations, same as Arthritis[1:5,]
Data in frequency form is also a data frame containing one or more factors, and a frequency
variable, often called Freq
or count
. The total number of observations
is: sum(X$Freq)
, sum(X[,"Freq"])
or some equivalent form.
The number of cells in the table is given by nrow(X)
.
Example:
For small frequency tables, it is often convenient to enter them in frequency form
using expand.grid()
for the factors and c()
to list the counts in a vector.
The example below, from [@vcd:Agresti:2002] gives results for the 1991 General Social Survey,
with respondents classified by sex and party identification.
# Agresti (2002), table 3.11, p. 106 GSS < data.frame( expand.grid(sex = c("female", "male"), party = c("dem", "indep", "rep")), count = c(279,165,73,47,225,191)) GSS names(GSS) str(GSS) sum(GSS$count)
Table form data is represented by a matrix
, array
or table
object, whose elements are the frequencies
in an $n$way table. The variable names (factors) and their levels are given by
dimnames(X)
. The total number of observations
is sum(X)
. The number of dimensions of the table is length(dimnames(X))
,
and the table sizes are given by sapply(dimnames(X), length)
.
Example:
The HairEyeColor
is stored in table form in vcd
.
str(HairEyeColor) # show the structure sum(HairEyeColor) # number of cases sapply(dimnames(HairEyeColor), length) # table dimension sizes
Example:
Enter frequencies in a matrix, and assign dimnames
,
giving the variable names and category labels. Note that, by default,
matrix()
uses the elements supplied by columns in the
result, unless you specify byrow=TRUE
.
# A 4 x 4 table Agresti (2002, Table 2.8, p. 57) Job Satisfaction JobSat < matrix(c( 1, 2, 1, 0, 3, 3, 6, 1, 10,10,14, 9, 6, 7,12,11), 4, 4) dimnames(JobSat) = list( income = c("< 15k", "1525k", "2540k", "> 40k"), satisfaction = c("VeryD", "LittleD", "ModerateS", "VeryS") ) JobSat
JobSat
is a matrix, not an object of class("table")
, and some functions
are happier with tables than matrices.
You can coerce it to a table with as.table()
,
JobSat < as.table(JobSat) str(JobSat)
In table form, the values of the table factors are ordered by their position in the table.
Thus in the JobSat
data, both income
and satisfaction
represent ordered
factors, and the positions of the values in the rows and columns reflects their
ordered nature.
Yet, for analysis, there are time when you need numeric values for the levels
of ordered factors in a table, e.g., to treat a factor as a quantitative variable.
In such cases, you can simply reassign the dimnames
attribute of the table
variables. For example, here, we assign numeric values to income
as the middle of their
ranges, and treat satisfaction
as equally spaced with integer scores.
dimnames(JobSat)$income < c(7.5,20,32.5,60) dimnames(JobSat)$satisfaction < 1:4
For the HairEyeColor
data, hair color and eye color are ordered arbitrarily.
For visualizing the data using mosaic plots and other methods described below, it
turns out to be more useful to assure that both hair color and eye color are
ordered from dark to light.
Hair colors are actually ordered this way already, and it is easiest to reorder
eye colors by indexing. Again str()
is your friend.
HairEyeColor < HairEyeColor[, c(1,3,4,2), ] str(HairEyeColor)
This is also the order for both hair color and eye color shown in the result of a correspondence analysis (\figref{fig:cahaireye}) below.
With data in case form or frequency form, when you have ordered factors represented with character values, you must ensure that they are treated as ordered in R.
Imagine that the Arthritis
data was read from a text file.
By default the Improved
will be ordered alphabetically:
Marked
,
None
,
Some
 not what we want. In this case, the function
ordered()
(and others) can be useful.
Arthritis < read.csv("arthritis.txt",header=TRUE) Arthritis$Improved < ordered(Arthritis$Improved, levels=c("None", "Some", "Marked") )
The dataset Arthritis
in the vcd
package is a data.frame in this form
With this order of Improved
, the response in this data,
a mosaic display of Treatment
and Improved
(\figref{fig:arthritis}) shows a clearly
interpretable pattern.
The original version of mosaic
in the vcd
package required the input to be
a contingency table in array form, so we convert using xtabs()
.
# Arthritis, # fig.height = 6, # fig.width = 6, # fig.cap = "Mosaic plot for the `Arthritis` data, showing the marginal model of independence for Treatment and Improved. Age, a covariate, and Sex are ignored here." data(Arthritis, package="vcd") art < xtabs(~Treatment + Improved, data = Arthritis) mosaic(art, gp = shading_max, split_vertical = TRUE, main="Arthritis: [Treatment] [Improved]")
Finally, there are situations where, particularly for display purposes, you
want to reorder the dimensions of an $n$way table, or change the
labels for the variables or levels.
This is easy when the data are in table form: aperm()
permutes
the dimensions, and assigning to names
and dimnames
changes variable names and level labels respectively.
We will use the following version of UCBAdmissions
in
\@(sec:mantel) below.
^[Changing Admit
to Admit?
might be useful for display purposes, but is
dangerous because it is then difficult to use that variable name in a model formula.
See \@(sec:tips) for options labeling_args
and set_labels
to change variable and level names for displays in the strucplot
framework.]
UCB < aperm(UCBAdmissions, c(2, 1, 3)) dimnames(UCB)[[2]] < c("Yes", "No") names(dimnames(UCB)) < c("Sex", "Admit?", "Department") # display as a flattened table stats::ftable(UCB)
structable()
{#sec:structable}For 3way and larger tables
the structable()
function in vcd
provides a convenient and flexible tabular display.
The variables assigned to the rows and columns of a twoway display can be specified
by a model formula.
structable(HairEyeColor) # show the table: default structable(Hair+Sex ~ Eye, HairEyeColor) # specify col ~ row variables
It also returns an object of class "structable"
which may be plotted with
mosaic()
(not shown here).
HSE <  structable(Hair+Sex ~ Eye, HairEyeColor) # save structable object mosaic(HSE) # plot it
table()
and friends {#sec:table}You can generate frequency tables from factor variables using the table()
function, tables of
proportions using the prop.table()
function, and marginal frequencies using
margin.table()
.
For these examples, create some categorical vectors:
n=500 A < factor(sample(c("a1","a2"), n, rep=TRUE)) B < factor(sample(c("b1","b2"), n, rep=TRUE)) C < factor(sample(c("c1","c2"), n, rep=TRUE)) mydata < data.frame(A,B,C)
These lines illustrate table
related functions:
# 2Way Frequency Table attach(mydata) mytable < table(A,B) # A will be rows, B will be columns mytable # print table margin.table(mytable, 1) # A frequencies (summed over B) margin.table(mytable, 2) # B frequencies (summed over A) prop.table(mytable) # cell percentages prop.table(mytable, 1) # row percentages prop.table(mytable, 2) # column percentages
table()
can also generate multidimensional tables based on 3 or more
categorical variables. In this case, you can use the ftable()
or structable()
function to print the results more attractively.
# 3Way Frequency Table mytable < table(A, B, C) ftable(mytable)
table()
ignores missing values by default.
To include NA
as a category in counts, include the
table option exclude=NULL
if the variable is a vector. If the variable is a
factor you have to create a new factor using \code{newfactor < factor(oldfactor,
exclude=NULL)}.
xtabs()
{#sec:xtabs}The xtabs()
function allows you to create crosstabulations of data using formula style input.
This typically works with caseform data supplied in a data frame or a matrix.
The result is a contingency table in array format, whose dimensions are determined by
the terms on the right side of the formula.
# 3Way Frequency Table mytable < xtabs(~A+B+C, data=mydata) ftable(mytable) # print table summary(mytable) # chisquare test of indepedence
If a variable is included on the left side of the formula, it is assumed to be a vector of frequencies (useful if the data have already been tabulated in frequency form).
(GSStab < xtabs(count ~ sex + party, data=GSS)) summary(GSStab)
aggregate()
, margin.table()
and apply()
}It sometimes happens that we have a data set with more variables or factors than we want to analyse, or else, having done some initial analyses, we decide that certain factors are not important, and so should be excluded from graphic displays by collapsing (summing) over them. For example, mosaic plots and fourfold displays are often simpler to construct from versions of the data collapsed over the factors which are not shown in the plots.
The appropriate tools to use again depend on
the form in which the data are represented a caseform data frame, a
frequencyform data frame (aggregate()
), or a tableform array or
table object (margin.table()
or apply()
).
When the data are in frequency form, and we want to produce another
frequency data frame, aggregate()
is a handy tool, using
the argument FUN=sum
to sum the frequency variable over the
factors not mentioned in the formula.
Example:
The data frame DaytonSurvey
in the vcdExtra
package represents a
$2^5$ table giving the frequencies of reported use (``ever used?'') of
alcohol, cigarettes and marijuana in a sample of high school seniors,
also classified by sex and race.
str(DaytonSurvey) head(DaytonSurvey)
To focus on the associations among the
substances, we want to collapse over sex and race. The righthand side of the formula
used in the call to aggregate()
gives the factors to be retained in the
new frequency data frame, Dayton.ACM.df
.
# data in frequency form # collapse over sex and race Dayton.ACM.df < aggregate(Freq ~ cigarette+alcohol+marijuana, data=DaytonSurvey, FUN=sum) Dayton.ACM.df
When the data are in table form, and we want to produce another
table, apply()
with FUN=sum
can be used in a similar way
to sum the table over dimensions not mentioned in the MARGIN
argument. margin.table()
is just a wrapper for apply()
using the sum()
function.
Example:
To illustrate, we first convert the DaytonSurvey
to a 5way
table using xtabs()
, giving Dayton.tab
.
# in table form Dayton.tab < xtabs(Freq ~ cigarette+alcohol+marijuana+sex+race, data=DaytonSurvey) structable(cigarette+alcohol+marijuana ~ sex+race, data=Dayton.tab)
Then, use apply()
on Dayton.tab
to give the
3way table Dayton.ACM.tab
summed over sex and race.
The elements in this new table are the column sums for
Dayton.tab
shown by structable()
just above.
# collapse over sex and race Dayton.ACM.tab < apply(Dayton.tab, MARGIN=1:3, FUN=sum) Dayton.ACM.tab < margin.table(Dayton.tab, 1:3) # same result structable(cigarette+alcohol ~ marijuana, data=Dayton.ACM.tab)
Many of these operations can be performed using the **ply()
functions
in the plyr
package.
For example, with the data in a frequency form data frame, use ddply()
to collapse over unmentioned factors, and plyr::summarise()
as the function to be applied to each piece.
library(plyr) Dayton.ACM.df < plyr::ddply(DaytonSurvey, .(cigarette, alcohol, marijuana), plyr::summarise, Freq=sum(Freq)) Dayton.ACM.df
collapse.table()
A related problem arises when we have a table or array and for some purpose
we want to reduce the number of levels of some factors by summing subsets
of the frequencies. For example, we may have initially coded Age in 10year
intervals, and decide that, either for analysis or display purposes, we
want to reduce Age to 20year intervals. The collapse.table()
function
in vcdExtra
was designed for this purpose.
Example: Create a 3way table, and collapse Age from 10year to 20year intervals. First, we generate a $2 \times 6 \times 3$ table of random counts from a Poisson distribution with mean of 100.
# create some sample data in frequency form sex < c("Male", "Female") age < c("1019", "2029", "3039", "4049", "5059", "6069") education < c("low", 'med', 'high') data < expand.grid(sex=sex, age=age, education=education) counts < rpois(36, 100) # random Possion cell frequencies data < cbind(data, counts) # make it into a 3way table t1 < xtabs(counts ~ sex + age + education, data=data) structable(t1)
Now collapse age
to 20year intervals, and education
to 2 levels. In the arguments, levels of age
and education
given the same label are summed in the resulting smaller table.
# collapse age to 3 levels, education to 2 levels t2 < collapse.table(t1, age=c("1029", "1029", "3049", "3049", "5069", "5069"), education=c("<high", "<high", "high")) structable(t2)
As we've seen, a given contingency table can be represented equivalently in different forms, but some R functions were designed for one particular representation.
The table below shows some handy tools for converting from one form to another.
 From this   To this  
:::
  Case form  Frequency form  Table form 
 Case form  noop  xtabs(~A+B)
 table(A,B)

 Frequency form  expand.dft(X)
 noop  xtabs(count~A+B)

 Table form  expand.dft(X)
 as.data.frame(X)
 noop 
For example, a contingency table in table form (an object of class(table)
) can be converted
to a data.frame with as.data.frame()
.
^[Because R is objectoriented, this is actually a shorthand for the function as.data.frame.table()
.]
The resulting
data.frame
contains columns
representing the classifying factors and the table entries (as a column named by
the responseName
argument, defaulting to Freq
. This is the inverse of xtabs()
.
Example:
Convert the GSStab
in table form to a data.frame in frequency form.
as.data.frame(GSStab)
Example: Convert the Arthritis
data in case form to a 3way table of
Treatment
$\times$ Sex
$\times$ Improved
.
Note the use of with()
to avoid having to use Arthritis\$Treatment
etc. within the call to table()
.%
^[table()
does not allow a data
argument to provide an environment in which the table variables are to be found. In the examples in \@(sec:table) I used attach(mydata)
for this purpose,
but attach()
leaves the variables in the global environment, while with()
just evaluates the table()
expression in a temporary environment of the data.]
Art.tab < with(Arthritis, table(Treatment, Sex, Improved)) str(Art.tab) ftable(Art.tab)
There may also be times that you will need an equivalent case form data.frame
with factors representing the table variables
rather than the frequency table.
For example, the mca()
function in package MASS
only operates on data in this format.
Marc Schwartz initially provided code for expand.dft()
on the Rhelp
mailing list for converting a table back into a case form data.frame
.
This function is included in vcdExtra
.
Example: Convert the Arthritis
data in table form (Art.tab
) back to a data.frame
in case form, with factors
Treatment
, Sex
and Improved
.
Art.df < expand.dft(Art.tab) str(Art.df)
If you've followed so far, you're ready for a more complicated example.
The data file, tv.dat
represents a 4way table of size
$5 \times 11 \times 5 \times 3$ where the table variables (unnamed in the file)
are read as V1
 V4
, and the cell frequency is read
as V5
. The file, stored in the doc/extdata
directory
of vcdExtra
, can be read as follows:
tv.data<read.table(system.file("extdata","tv.dat", package="vcdExtra")) head(tv.data,5)
For a local file, just use read.table()
in this form:
tv.data<read.table("C:/R/data/tv.dat")
The data tv.dat
came from the initial implementation of
mosaic displays in R by Jay Emerson.
In turn, they came from the initial development of mosaic displays
[@vcd:Hartigan+Kleiner:1984]
that illustrated the method with data on a large sample of TV viewers
whose behavior had been recorded for the Neilson ratings.
This data set contains sample television audience data from Neilsen
Media Research for the week starting November 6, 1995.
The table variables are:
V1
 values 1:5 correspond to the days MondayFriday;V2
 values 1:11 correspond to the quarter hour times 8:00PM through 10:30PM;V3
 values 1:5 correspond to ABC, CBS, NBC, Fox, and nonnetwork choices;V4
 values 1:3 correspond to transition states: turn the television Off, Switch channels, or Persist in viewing the current channel.We are interested just the cell frequencies, and rely on the facts that the
(a) the table is complete there are no missing cells, so nrow(tv.data)
= r nrow(tv.data)
;
(b) the observations are ordered so that V1
varies most rapidly and V4
most slowly. From this, we can just extract the frequency column and reshape it into an array. [That would be dangerous if any observations were out of order.]
TV < array(tv.data[,5], dim=c(5,11,5,3)) dimnames(TV) < list(c("Monday","Tuesday","Wednesday","Thursday","Friday"), c("8:00","8:15","8:30","8:45","9:00","9:15","9:30", "9:45","10:00","10:15","10:30"), c("ABC","CBS","NBC","Fox","Other"), c("Off","Switch","Persist")) names(dimnames(TV))<c("Day", "Time", "Network", "State")
More generally (even if there are missing cells), we can
use xtabs()
(or plyr::daply()
)
to do the crosstabulation, using V5
as the
frequency variable. Here's how to do this same operation with xtabs()
:
TV < xtabs(V5 ~ ., data=tv.data) dimnames(TV) < list(Day = c("Monday","Tuesday","Wednesday","Thursday","Friday"), Time = c("8:00","8:15","8:30","8:45","9:00","9:15","9:30", "9:45","10:00","10:15","10:30"), Network = c("ABC","CBS","NBC","Fox","Other"), State = c("Off","Switch","Persist")) # table dimensions dim(TV)
But this 4way table is too large and awkward to work with. Among the networks,
Fox and Other occur infrequently.
We can also cut it down to a 3way table by considering only viewers who persist
with the current station.
^[This relies on the fact that that indexing an array drops dimensions of length 1 by default, using the argument drop=TRUE
; the result is coerced to the lowest possible dimension.]
TV2 < TV[,,1:3,] # keep only ABC, CBS, NBC TV2 < TV2[,,,3] # keep only Persist  now a 3 way table structable(TV2)
Finally, for some purposes, we might want to collapse the 11 times into a smaller number.
Halfhour time slots make more sense.
Here, we use as.data.frame.table()
to convert the table back to a data frame,
levels()
to reassign the values of Time
,
and finally, xtabs()
to give a new, collapsed frequency table.
TV.df < as.data.frame.table(TV2) levels(TV.df$Time) < c(rep("8:00", 2), rep("8:30", 2), rep("9:00", 2), rep("9:30", 2), rep("10:00",2), "10:30" ) TV3 < xtabs(Freq ~ Day + Time + Network, TV.df) structable(Day ~ Time+Network, TV3)
We've come this far, so we might as well show a mosaic display. This is analogous to that used by @vcd:Hartigan+Kleiner:1984.
mosaic(TV3, shade = TRUE, labeling = labeling_border(rot_labels = c(0, 0, 0, 90)))
This mosaic displays can be read at several levels, corresponding to the successive splits of the tiles and the residual shading. Several trends are clear for viewers who persist:
From the residual shading of the tiles:
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