| summarize {Hmisc} | R Documentation |
summarize is a fast version of summary(formula,
method="cross",overall=FALSE) for producing stratified summary statistics
and storing them in a data frame for plotting (especially with trellis
xyplot and dotplot and Hmisc xYplot). Unlike
aggregate, summarize accepts a matrix as its first
argument and a multi-valued FUN
argument and summarize also labels the variables in the new data
frame using their original names. Unlike methods based on
tapply, summarize stores the values of the stratification
variables using their original types, e.g., a numeric by variable
will remain a numeric variable in the collapsed data frame.
summarize also retains "label" attributes for variables.
summarize works especially well with the Hmisc xYplot
function for displaying multiple summaries of a single variable on each
panel, such as means and upper and lower confidence limits.
subsAttr saves attributes that are commonly preserved across row
subsetting (i.e., it does not save dim, dimnames, or
names attributes).
asNumericMatrix converts a data frame into a numeric matrix.
matrix2dataFrame converts a numeric matrix back into a data
frame if attributes and storage modes of the original variables are
saved by calling subsAttr.
summarize(X, by, FUN, ...,
stat.name=deparse(substitute(X)),
type=c('variables','matrix'), subset=TRUE)
asNumericMatrix(x)
subsAttr(x)
matrix2dataFrame(x, at, restoreAll=TRUE)
X |
a vector or matrix capable of being operated on by the
function specified as the FUN argument
|
by |
one or more stratification variables. If a single
variable, by may be a vector, otherwise it should be a list.
Using the Hmisc llist function instead of list will result
in individual variable names being accessible to summarize. For
example, you can specify llist(age.group,sex) or
llist(Age=age.group,sex). The latter gives age.group a
new temporary name, Age.
|
FUN |
a function of a single vector argument, used to create the statistical
summaries for summarize. FUN may compute any number of
statistics.
|
... |
extra arguments are passed to FUN |
stat.name |
the name to use when creating the main summary variable. By default,
the name of the X argument is used. Set stat.name to
NULL to suppress this name replacement.
|
type |
Specify type="matrix" to store the summary variables (if there are
more than one) in a matrix.
|
subset |
a logical vector or integer vector of subscripts used to specify the subset of data to use in the analysis. The default is to use all observations in the data frame. |
x |
a data frame (for asNumericMatrix) or a numeric matrix (for
matrix2dataFrame). For subsAttr, x may be a data
frame, list, or a vector.
|
at |
result of subsAttr
|
restoreAll |
set to FALSE to only restore attributes label,
units, and levels instead of all attributes
|
For summarize, a data frame containing the by variables and the
statistical summaries (the first of which is named the same as the X
variable unless stat.name is given). If type="matrix", the
summaries are stored in a single variable in the data frame, and this
variable is a matrix.
asNumericMatrix returns a numeric matrix.
matrix2dataFrame returns a data frame.
subsAttr returns a list of attribute lists if its argument is a
list or data frame, and a list containing attributes of a single
variable.
Frank Harrell
Department of Biostatistics
Vanderbilt University
f.harrell@vanderbilt.edu
## Not run:
s <- summarize(ap>1, llist(size=cut2(sz, g=4), bone), mean,
stat.name='Proportion')
dotplot(Proportion ~ size | bone, data=s7)
## End(Not run)
set.seed(1)
temperature <- rnorm(300, 70, 10)
month <- sample(1:12, 300, TRUE)
year <- sample(2000:2001, 300, TRUE)
g <- function(x)c(Mean=mean(x,na.rm=TRUE),Median=median(x,na.rm=TRUE))
summarize(temperature, month, g)
mApply(temperature, month, g)
mApply(temperature, month, mean, na.rm=TRUE)
w <- summarize(temperature, month, mean, na.rm=TRUE)
if(.R.) library(lattice)
xyplot(temperature ~ month, data=w) # plot mean temperature by month
w <- summarize(temperature, llist(year,month),
quantile, probs=c(.5,.25,.75), na.rm=TRUE, type='matrix')
xYplot(Cbind(temperature[,1],temperature[,-1]) ~ month | year, data=w)
mApply(temperature, llist(year,month),
quantile, probs=c(.5,.25,.75), na.rm=TRUE)
# Compute the median and outer quartiles. The outer quartiles are
# displayed using "error bars"
set.seed(111)
dfr <- expand.grid(month=1:12, year=c(1997,1998), reps=1:100)
attach(dfr)
y <- abs(month-6.5) + 2*runif(length(month)) + year-1997
s <- summarize(y, llist(month,year), smedian.hilow, conf.int=.5)
s
mApply(y, llist(month,year), smedian.hilow, conf.int=.5)
xYplot(Cbind(y,Lower,Upper) ~ month, groups=year, data=s,
keys='lines', method='alt')
# Can also do:
s <- summarize(y, llist(month,year), quantile, probs=c(.5,.25,.75),
stat.name=c('y','Q1','Q3'))
xYplot(Cbind(y, Q1, Q3) ~ month, groups=year, data=s, keys='lines')
# To display means and bootstrapped nonparametric confidence intervals
# use for example:
s <- summarize(y, llist(month,year), smean.cl.boot)
xYplot(Cbind(y, Lower, Upper) ~ month | year, data=s)
# For each subject use the trapezoidal rule to compute the area under
# the (time,response) curve using the Hmisc trap.rule function
x <- cbind(time=c(1,2,4,7, 1,3,5,10),response=c(1,3,2,4, 1,3,2,4))
subject <- c(rep(1,4),rep(2,4))
trap.rule(x[1:4,1],x[1:4,2])
summarize(x, subject, function(y) trap.rule(y[,1],y[,2]))
## Not run:
# Another approach would be to properly re-shape the mm array below
# This assumes no missing cells. There are many other approaches.
# mApply will do this well while allowing for missing cells.
m <- tapply(y, list(year,month), quantile, probs=c(.25,.5,.75))
mm <- array(unlist(m), dim=c(3,2,12),
dimnames=list(c('lower','median','upper'),c('1997','1998'),
as.character(1:12)))
# aggregate will help but it only allows you to compute one quantile
# at a time; see also the Hmisc mApply function
dframe <- aggregate(y, list(Year=year,Month=month), quantile, probs=.5)
# Compute expected life length by race assuming an exponential
# distribution - can also use summarize
g <- function(y) { # computations for one race group
futime <- y[,1]; event <- y[,2]
sum(futime)/sum(event) # assume event=1 for death, 0=alive
}
mApply(cbind(followup.time, death), race, g)
# To run mApply on a data frame:
m <- mApply(asNumericMatrix(x), race, h)
# Here assume h is a function that returns a matrix similar to x
at <- subsAttr(x) # get original attributes and storage modes
matrix2dataFrame(m, at)
# Get stratified weighted means
g <- function(y) wtd.mean(y[,1],y[,2])
summarize(cbind(y, wts), llist(sex,race), g, stat.name='y')
mApply(cbind(y,wts), llist(sex,race), g)
# Compare speed of mApply vs. by for computing
d <- data.frame(sex=sample(c('female','male'),100000,TRUE),
country=sample(letters,100000,TRUE),
y1=runif(100000), y2=runif(100000))
g <- function(x) {
y <- c(median(x[,'y1']-x[,'y2']),
med.sum =median(x[,'y1']+x[,'y2']))
names(y) <- c('med.diff','med.sum')
y
}
system.time(by(d, llist(sex=d$sex,country=d$country), g))
system.time({
x <- asNumericMatrix(d)
a <- subsAttr(d)
m <- mApply(x, llist(sex=d$sex,country=d$country), g)
})
system.time({
x <- asNumericMatrix(d)
summarize(x, llist(sex=d$sex, country=d$country), g)
})
# An example where each subject has one record per diagnosis but sex of
# subject is duplicated for all the rows a subject has. Get the cross-
# classified frequencies of diagnosis (dx) by sex and plot the results
# with a dot plot
count <- rep(1,length(dx))
d <- summarize(count, llist(dx,sex), sum)
Dotplot(dx ~ count | sex, data=d)
## End(Not run)
detach('dfr')
# Run summarize on a matrix to get column means
x <- c(1:19,NA)
y <- 101:120
z <- cbind(x, y)
g <- c(rep(1, 10), rep(2, 10))
summarize(z, g, colMeans, na.rm=TRUE, stat.name='x')
# Also works on an all numeric data frame
summarize(as.data.frame(z), g, colMeans, na.rm=TRUE, stat.name='x')