Hmisc: bystats – R documentation

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bystats

Statistics by Categories

Description

For any number of cross-classification variables, bystats returns a matrix with the sample size, number missing y, and fun(non-missing y), with the cross-classifications designated by rows. Uses Harrell's modification of the interaction function to produce cross-classifications. The default fun is mean, and if y is binary, the mean is labeled as Fraction. There is a print method as well as a latex method for objects created by bystats. bystats2 handles the special case in which there are 2 classifcation variables, and places the first one in rows and the second in columns. The print method for bystats2 uses the print.char.matrix function to organize statistics for cells into boxes.

Usage

bystats(y, ..., fun, nmiss, subset)
## S3 method for class 'bystats'
print(x, ...)
## S3 method for class 'bystats'
latex(object, title, caption, rowlabel, ...)
bystats2(y, v, h, fun, nmiss, subset)
## S3 method for class 'bystats2'
print(x, abbreviate.dimnames=FALSE,
   prefix.width=max(nchar(dimnames(x)[[1]])), ...)
## S3 method for class 'bystats2'
latex(object, title, caption, rowlabel, ...)

Arguments

`y`	a binary, logical, or continuous variable or a matrix or data frame of such variables. If `y` is a data frame it is converted to a matrix. If `y` is a data frame or matrix, computations are done on subsets of the rows of `y`, and you should specify `fun` so as to be able to operate on the matrix. For matrix `y`, any column with a missing value causes the entire row to be considered missing, and the row is not passed to `fun`.
`...`	For `bystats`, one or more classifcation variables separated by commas. For `print.bystats`, options passed to `print.default` such as `digits`. For `latex.bystats`, and `latex.bystats2`, options passed to `latex.default` such as `digits`. If you pass `cdec` to `latex.default`, keep in mind that the first one or two positions (depending on `nmiss`) should have zeros since these correspond with frequency counts.
`v`	vertical variable for `bystats2`. Will be converted to `factor`.
`h`	horizontal variable for `bystats2`. Will be converted to `factor`.
`fun`	a function to compute on the non-missing `y` for a given subset. You must specify `fun=` in front of the function name or definition. `fun` may return a single number or a vector or matrix of any length. Matrix results are rolled out into a vector, with names preserved. When `y` is a matrix, a common `fun` is `function(y) apply(y, 2, ff)` where `ff` is the name of a function which operates on one column of `y`.
`nmiss`	A column containing a count of missing values is included if `nmiss=TRUE` or if there is at least one missing value.
`subset`	a vector of subscripts or logical values indicating the subset of data to analyze
`abbreviate.dimnames`	set to `TRUE` to abbreviate `dimnames` in output
`prefix.width`	see `print.char.matrix`
`title`	`title` to pass to `latex.default`. Default is the first word of the character string version of the first calling argument.
`caption`	caption to pass to `latex.default`. Default is the `heading` attribute from the object produced by `bystats`.
`rowlabel`	`rowlabel` to pass to `latex.default`. Default is the `byvarnames` attribute from the object produced by `bystats`. For `bystats2` the default is `""`.
`x`	an object created by `bystats` or `bystats2`
`object`	an object created by `bystats` or `bystats2`

Value

for bystats, a matrix with row names equal to the classification labels and column names N, Missing, funlab, where funlab is determined from fun. A row is added to the end with the summary statistics computed on all observations combined. The class of this matrix is bystats. For bystats, returns a 3-dimensional array with the last dimension corresponding to statistics being computed. The class of the array is bystats2.

Side Effects

latex produces a .tex file.

Author(s)

Frank Harrell
Department of Biostatistics
Vanderbilt University
fh@fharrell.com

Examples

## Not run: 
bystats(sex==2, county, city)
bystats(death, race)
bystats(death, cut2(age,g=5), race)
bystats(cholesterol, cut2(age,g=4), sex, fun=median)
bystats(cholesterol, sex, fun=quantile)
bystats(cholesterol, sex, fun=function(x)c(Mean=mean(x),Median=median(x)))
latex(bystats(death,race,nmiss=FALSE,subset=sex=="female"), digits=2)
f <- function(y) c(Hazard=sum(y[,2])/sum(y[,1]))
# f() gets the hazard estimate for right-censored data from exponential dist.
bystats(cbind(d.time, death), race, sex, fun=f)
bystats(cbind(pressure, cholesterol), age.decile, 
        fun=function(y) c(Median.pressure   =median(y[,1]),
                          Median.cholesterol=median(y[,2])))
y <- cbind(pressure, cholesterol)
bystats(y, age.decile, 
        fun=function(y) apply(y, 2, median))   # same result as last one
bystats(y, age.decile, fun=function(y) apply(y, 2, quantile, c(.25,.75)))
# The last one computes separately the 0.25 and 0.75 quantiles of 2 vars.
latex(bystats2(death, race, sex, fun=table))

## End(Not run)

Hmisc

Harrell Miscellaneous

v4.5-0

GPL (>= 2)

Authors

Frank E Harrell Jr <fh@fharrell.com>, with contributions from Charles Dupont and many others.

Initial release

2021-02-27