Package ‘arsenal’

October 12, 2022

Title An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Version 3.6.3
Date 2021-06-04
Description An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of one or more categorical
variables; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on one or more endpoints
for many variables (univariate or adjusted for covariates);
freqlist(), a powerful frequency table across many categorical variables;
comparedf(), a function for comparing data.frames; and
write2(), a function to output tables to a document.
Suggests broom (>= 0.7.1), magrittr, rmarkdown, testthat, xtable,
pander, survival (>= 2.43-1), coin, pROC, MASS, splines, rpart,
yaml, geepack
Depends R (>= 3.4.0), stats (>= 3.4.0)
Imports knitr (>= 1.29), utils (>= 3.4.0)

URL https://github.com/mayoverse/arsenal,
https://cran.r-project.org/package=arsenal,
https://mayoverse.github.io/arsenal/

BugReports https://github.com/mayoverse/arsenal/issues
VignetteBuilder knitr
License GPL (>= 2)
RoxygenNote 7.1.1
LazyData true
Encoding UTF-8
NeedsCompilation no

1
2 R topics documented:

Author Ethan Heinzen [aut, cre],

Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb],
Maddie McCullough [art]
Maintainer Ethan Heinzen <[email protected]>
Repository CRAN
Date/Publication 2021-06-04 21:50:02 UTC

R topics documented:
arsenal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
arsenal-defunct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
arsenal-deprecated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
arsenal_table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
as.data.frame.freqlist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
as.data.frame.modelsum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
as.data.frame.tableby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
comparedf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
comparedf.control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
comparedf.tolerances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
diffs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
formulize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
freq.control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
freqlist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
freqlist.internal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
internal.functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
keep.labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
mdy.Date . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
mockstudy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
modelsum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
modelsum.control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
modelsum.family . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
modelsum.internal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
NA.operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
padjust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
paired . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
paired.control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
paired.internal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
arsenal 3

selectall . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
summary.comparedf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
summary.freqlist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
summary.modelsum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
summary.tableby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
tableby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
tableby.control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
tableby.internal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
tableby.stats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
tableby.stats.internal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
write2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
write2.internal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
write2specific . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
yaml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
%nin% . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Index 60

arsenal An Arsenal of ’R’ Functions for Large-Scale Statistical Summaries

Description
An Arsenal of ’R’ functions for large-scale statistical summaries, which are streamlined to work
within the latest reporting tools in ’R’ and ’RStudio’ and which use formulas and versatile summary
statistics for summary tables and models.

Details
The package download, NEWS, and README are available on CRAN: https://cran.r-project.
org/package=arsenal

Functions
Below are listed some of the most widely used functions available in arsenal:
tableby: Summary statistics of a set of independent variables by a categorical variable.
paired: Summary statistics of a set of independent variables paired across two timepoints.
modelsum: Fit models over each of a set of independent variables with a response variable.
freqlist: Approximate the output from SAS’s PROC FREQ procedure when using the /list option
of the TABLE statement.
comparedf: Compare two data.frames and report any differences between them, much like SAS’s
PROC COMPARE procedure.
write2word, write2html, write2pdf: Functions to output tables to a single Word, HTML, or PDF
document.
write2: Functions to output tables to a single document. (Also the S3 backbone behind the write2*
functions.)
4 arsenal-defunct

keep.labels: Keep the 'label' attribute on an R object when subsetting.

formulize: A shortcut to generate one-, two-, or many-sided formulas.
mdy.Date and Date.mdy: Convert numeric dates for month, day, and year to Date object, and vice
versa.
is.Date: Test if an object is a date.
%nin%: Test for "not in".
allNA and includeNA: some useful functions for dealing with NAs.

Data
mockstudy: Mock study data for examples.

Examples
library(arsenal)

arsenal-defunct Defunct functions in arsenal

Description
Details about defunct functions in arsenal

Arguments
x, y See comparedf.
... Other arguments.

Details
comparison.control was renamed to comparedf.control in version 3.0.0.
compare.data.frame was renamed to comparedf in version 3.0.0.
length.tableby was removed in version 2.0.0.
includeNA.character and includeNA.numeric were removed in version 2.0.0 and replaced with
a default method.
rangeTime was removed in version 1.5.0.

See Also
arsenal-deprecated, comparedf
arsenal-deprecated 5

arsenal-deprecated Deprecated functions in arsenal

Description
Details about deprecated functions in arsenal

See Also
arsenal-defunct

arsenal_table arsenal tables with common structure

Description
arsenal tables with common structure

Usage
has_strata(x)

## S3 method for class 'arsenal_table'

x[i, j, ...]

## S3 method for class 'arsenal_table'

labels(object, ...)

## S3 replacement method for class 'arsenal_table'

labels(x) <- value

## S3 method for class 'arsenal_table'

print(x, ...)

## S3 method for class 'arsenal_table'

merge(x, y, all = FALSE, all.x = all, all.y = all, ...)

## S3 method for class 'freqlist'

merge(x, y, all = TRUE, ...)

## S3 method for class 'summary.arsenal_table'

print(
x,
...,
format = if (!is.null(x$text) && x$text %in% c("html", "latex")) x$text else
6 as.data.frame.freqlist

"markdown",
escape = x$text %nin% c("html", "latex"),
width = NULL,
min.split = NULL
)

Arguments

x, y, object An object of class "arsenal_table"

i, j A vector to index x with: either names of variables, a numeric vector, or a
logical vector of appropriate length. i indexes the x-variables, and j indexes the
by-variables.
... Other arguments (only used in print.summary.arsenal_table)
value A list of new labels.
all, all.x, all.y
Logicals, denoting which terms to keep if not all are in common.
format Passed to kable: the format for the table. The default here is "markdown".
To use the default in kable, pass NULL. If x$text specifies LaTeX or HTML
formatting, that format is used in the table.
escape Passed to kable: should special characters be escaped when printed?
width, min.split
Passed to smart.split for formatting of the "term" column.

See Also

merge, labels

as.data.frame.freqlist
as.data.frame.freqlist

Description

Convert freqlist object to a data.frame.

Usage

## S3 method for class 'freqlist'

as.data.frame(x, ..., labelTranslations = NULL, list.ok = FALSE)
as.data.frame.modelsum 7

Arguments
x An object of class "freqlist".
... Arguments to pass to freq.control
labelTranslations
A named list (or vector) where the name is the label in the output to be replaced
in the pretty rendering by the character string value for the named element of
the list, e.g., list(age = "Age(Years)", meansd = "Mean(SD)").
list.ok If the object has multiple by-variables, is it okay to return a list of data.frames
instead of a single data.frame? If FALSE but there are multiple by-variables, a
warning is issued.

Value
A data.frame corresponding to the freqlist object.

as.data.frame.modelsum
as.data.frame.modelsum

Description
Coerce a modelsum object to a data.frame.

Usage
## S3 method for class 'modelsum'
as.data.frame(x, ..., labelTranslations = NULL, list.ok = FALSE)

Arguments
x A modelsum object.
... Arguments to pass to modelsum.control.
labelTranslations
A named list (or vector) where the name is the label in the output to be replaced
in the pretty rendering by the character string value for the named element of
the list, e.g., list(age = "Age(Years)", meansd = "Mean(SD)").
list.ok If the object has multiple by-variables, is it okay to return a list of data.frames
instead of a single data.frame? If FALSE but there are multiple by-variables, a
warning is issued.

Value
A data.frame.
8 as.data.frame.tableby

Author(s)
Ethan Heinzen, based on code originally by Greg Dougherty

See Also
modelsum, summary.modelsum

as.data.frame.tableby as.data.frame.tableby

Description
Coerce a tableby object to a data.frame.

Usage
## S3 method for class 'tableby'
as.data.frame(x, ..., labelTranslations = NULL, list.ok = FALSE)

Arguments
x A tableby object.
... Arguments to pass to tableby.control.
labelTranslations
A named list (or vector) where the name is the label in the output to be replaced
in the pretty rendering by the character string value for the named element of
the list, e.g., list(age = "Age(Years)", meansd = "Mean(SD)").
list.ok If the object has multiple by-variables, is it okay to return a list of data.frames
instead of a single data.frame? If FALSE but there are multiple by-variables, a
warning is issued.

Value
A data.frame.

Author(s)
Ethan Heinzen, based on code originally by Greg Dougherty

See Also
tableby, tableby
comparedf 9

comparedf Compare two data.frames and report differences

Description
Compare two data.frames and report any differences between them, much like SAS’s PROC COMPARE
procedure.

Usage
comparedf(x, y, by = NULL, by.x = by, by.y = by, control = NULL, ...)

## S3 method for class 'comparedf'

print(x, ...)

Arguments
x, y A data.frame to compare
by, by.x, by.y Which variables are IDs to merge the two data.frames? If set to "row.names",
merging will occur over the row.names. If set to NULL (default), merging will
occur row-by-row.
control A list of control parameters from comparedf.control.
... Other arguments, passed to comparedf.control when appropriate.

Author(s)
Ethan Heinzen, adapted from code from Andrew Hanson

See Also
summary.comparedf, comparedf.control, diffs, n.diffs, n.diff.obs

Examples

df1 <- data.frame(id = paste0("person", 1:3), a = c("a", "b", "c"),

b = c(1, 3, 4), c = c("f", "e", "d"),
row.names = paste0("rn", 1:3), stringsAsFactors = FALSE)
df2 <- data.frame(id = paste0("person", 3:1), a = c("c", "b", "a"),
b = c(1, 3, 4), d = paste0("rn", 1:3),
row.names = paste0("rn", c(1,3,2)), stringsAsFactors = FALSE)
summary(comparedf(df1, df2))
summary(comparedf(df1, df2, by = "id"))
summary(comparedf(df1, df2, by = "row.names"))
10 comparedf.control

comparedf.control Control settings for comparedf function

Description
Control tolerance definitions for the comparedf function.

Usage
comparedf.control(
tol.logical = "none",
tol.num = c("absolute", "percent", "pct"),
tol.num.val = sqrt(.Machine$double.eps),
int.as.num = FALSE,
tol.char = c("none", "trim", "case", "both"),
tol.factor = c("none", "levels", "labels"),
factor.as.char = FALSE,
tol.date = "absolute",
tol.date.val = 0,
tol.other = "none",
tol.vars = "none",
max.print.vars = NA,
max.print.obs = NA,
max.print.diffs.per.var = 10,
max.print.diffs = 50,
max.print.attrs = NA,
...,
max.print.diff = 10
)

Arguments
tol.logical, tol.num, tol.char, tol.factor, tol.date, tol.other
A function or one of the shortcut character strings or a list thereof, denoting the
tolerance function to use for a given data type. See "details", below.
tol.num.val Numeric; maximum value of differences allowed in numerics (fed to the func-
tion given in tol.num).
int.as.num Logical; should integers be coerced to numeric before comparison? Default
FALSE.
factor.as.char Logical; should factors be coerced to character before comparison? Default
FALSE.
tol.date.val Numeric; maximum value of differences allowed in dates (fed to the function
given in tol.date).
tol.vars Either "none" (the default), denoting that variable names are to be matched as-
is, a named vector manually specifying variable names to compare (where the
comparedf.control 11

names correspond to columns of x and the values correspond to columns of y),

or a character vector denoting equivalence classes for characters in the variable
names. See "details", below.
max.print.vars Integer denoting maximum number of variables to report in the "variables not
shared" and "variables not compared" output. NA will print all differences.
max.print.obs Integer denoting maximum number of not-shared observations to report. NA will
print all differences.
max.print.diffs.per.var, max.print.diffs
Integers denoting the maximum number of differences to report for each variable
or overall. NA will print all differences for each variable or overall.
max.print.attrs
Integers denoting the maximum number of non-identical attributes to report.NA
will print all differences.
... Other arguments (not in use at this time).
max.print.diff Deprecated.

Details
The following character strings are accepted:
• tol.logical = "none": compare logicals exactly as they are.
• tol.num = "absolute": compare absolute differences in numerics.
• tol.num = "percent", tol.num = "pct" compare percent differences in numerics.
• tol.char = "none": compare character strings exactly as they are.
• tol.char = "trim": left-justify and trim all trailing white space.
• tol.char = "case": allow differences in upper/lower case.
• tol.char = "both": combine "trim" and "case".
• tol.factor = "none": match both character labels and numeric levels.
• tol.factor = "levels": match only the numeric levels.
• tol.factor = "labels": match only the labels.
• tol.date = "absolute": compare absolute differences in dates.
• tol.other = "none": expect objects of other classes to be exactly identical.
A list with names mapped to x can be used to specify tolerances by variable. One unnamed element
is supported as the default.
tol.vars: If not set to "none" (the default) or a named vector, the tol.vars argument is a character
vector denoting equivalence classes for the characters in the variable names. A single character in
this vector means to replace that character with "". All other strings in this vector are split by
character and replaced by the first character in the string.
E.g., a character vector c("._", "aA", " ") would denote that the dot and underscore are equivalent
(to be translated to a dot), that "a" and "A" are equivalent (to be translated to "a"), and that spaces
should be removed.
The special character string "case" in this vector is the same as specifying paste0(letters,
LETTERS).
12 comparedf.tolerances

Value
A list containing the necessary parameters for the comparedf function.

Author(s)
Ethan Heinzen

See Also
comparedf, comparedf.tolerances, summary.comparedf

Examples
cntl <- comparedf.control(
tol.num = "pct", # calculate percent differences
tol.vars = c("case", # ignore case
"._", # set all underscores to dots.
"e") # remove all letter e's
)

cntl <- comparedf.control(tol.char = list(

"none", # the default
x1 = "case", # be case-insensitive for the variable "x1"
x2 = function(x, y) tol.NA(x, y, x != y | y == "NA") # a custom-defined tolerance
))

comparedf.tolerances comparedf tolerances

Description
Internal functions defining tolerances for the comparedf.control function. To create your own
tolerance definitions, see the vignette.

Usage
tol.NA(x, y, idx)

tol.num.absolute(x, y, tol)

tol.num.percent(x, y, tol)

tol.num.pct(x, y, tol)

tol.factor.none(x, y)

tol.factor.levels(x, y)
comparedf.tolerances 13

tol.factor.labels(x, y)

tol.char.both(x, y)

tol.char.case(x, y)

tol.char.trim(x, y)

tol.char.none(x, y)

tol.date.absolute(x, y, tol)

tol.logical.none(x, y)

tol.other.none(x, y)

Arguments

x, y vectors of the appropriate lengths and types.

idx A logical vector of appropriate length.
tol A numeric tolerance

Details

tol.NA takes as differences between two vectors any elements which are NA in one but not the
other, or which are non-NA in both and TRUE in idx. It is useful for handling NAs in custom
tolerance functions.

Value

A logical vector of length equal to that of x and y, where TRUE denotes a difference between x and
y, and FALSE denotes no difference between x and y.

Author(s)

Ethan Heinzen

See Also

comparedf.control, comparedf
14 diffs

diffs Extract differences

Description

Extract differences (diffs()), number of differences (n.diffs()), or number of not-shared obser-

vations (n.diff.obs()) from a comparedf object.

Usage

n.diff.obs(object, ...)

## S3 method for class 'comparedf'

n.diff.obs(object, ...)

## S3 method for class 'summary.comparedf'

n.diff.obs(object, ...)

n.diffs(object, ...)

## S3 method for class 'comparedf'

n.diffs(object, ...)

## S3 method for class 'summary.comparedf'

n.diffs(object, ...)

diffs(object, ...)

## S3 method for class 'comparedf'

diffs(
object,
what = c("differences", "observations"),
vars = NULL,
...,
by.var = FALSE
)

## S3 method for class 'summary.comparedf'

diffs(
object,
what = c("differences", "observations"),
vars = NULL,
...,
by.var = FALSE
)
formulize 15

Arguments
object An object of class comparedf or summary.comparedf.
... Other arguments (not in use at this time).
what Should differences or the not-shared observations be returned?
vars A character vector of variable names to subset the results to.
by.var Logical: should the number of differences by variable be reported, or should all
differences be reported (the default).

Author(s)
Ethan Heinzen

See Also
comparedf summary.comparedf

formulize formulize

Description
A shortcut to generate one-, two-, or many-sided formulas from vectors of variable names.

Usage
formulize(
y = "",
x = "",
...,
data = NULL,
collapse = "+",
collapse.y = collapse,
escape = FALSE
)

Arguments
y, x, ... Character vectors, names, or calls to be collapsed (by "+") and put left-to-right
in the formula. If data is supplied, these can also be numeric, denoting which
column name to use. See examples.
data An R object with non-null column names.
collapse How should terms be collapsed? Default is addition.
collapse.y How should the y-terms be collapsed? Default is addition. Also accepts the spe-
cial string "list", which combines them into a multiple-left-hand-side formula,
for use in other functions.
escape A logical indicating whether character vectors should be coerced to names (that
is, whether names with spaces should be surrounded with backticks or not)
16 formulize

Author(s)

Ethan Heinzen

See Also

reformulate

Examples
## two-sided formula
f1 <- formulize("y", c("x1", "x2", "x3"))

## one-sided formula
f2 <- formulize(x = c("x1", "x2", "x3"))

## multi-sided formula
f3 <- formulize("y", c("x1", "x2", "x3"), c("z1", "z2"), "w1")

## can use numerics for column names

data(mockstudy)
f4 <- formulize(y = 1, x = 2:4, data = mockstudy)

## mix and match

f5 <- formulize(1, c("x1", "x2", "x3"), data = mockstudy)

## get an interaction
f6 <- formulize("y", c("x1*x2", "x3"))

## get only interactions

f7 <- formulize("y", c("x1", "x2", "x3"), collapse = "*")

## no intercept
f8 <- formulize("y", "x1 - 1")
f9 <- formulize("y", c("x1", "x2", "-1"))

## LHS as a list to use in arsenal functions

f10 <- formulize(c("y1", "y2", "y3"), c("x", "z"), collapse.y = "list")

## use in an lm
f11 <- formulize(2, 3:4, data = mockstudy)
summary(lm(f11, data = mockstudy))

## using non-syntactic names or calls (like reformulate example)

f12 <- formulize(as.name("+-"), c("`P/E`", "`% Growth`"))
f12 <- formulize("+-", c("P/E", "% Growth"), escape = TRUE)

f <- Surv(ft, case) ~ a + b

f13 <- formulize(f[[2]], f[[3]])
freq.control 17

freq.control Control settings for freqlist function

Description
Control test and summary settings for the freqlist function.

Usage
freq.control(
sparse = FALSE,
single = FALSE,
dupLabels = FALSE,
digits.count = 0L,
digits.pct = 2L,
...,
digits = NULL
)

Arguments
sparse a logical value indicating whether to keep rows with counts of zero. The default
is FALSE (drop zero-count rows).
single logical, indicating whether to collapse results created using a strata variable into
a single table for printing
dupLabels logical: should labels which are the same as the row above be printed? The
default (FALSE) more closely approximates PROC FREQ output from SAS, where
a label carried down from the row above is left blank.
digits.count Number of decimal places for count values.
digits.pct Number of decimal places for percents.
... additional arguments.
digits A deprecated argument

Value
A list with settings to be used within the freqlist function.

Author(s)
Ethan Heinzen

See Also
freqlist, summary.freqlist, freqlist.internal
18 freqlist

freqlist freqlist

Description
Approximate the output from SAS’s PROC FREQ procedure when using the /list option of the
TABLE statement.

Usage
freqlist(object, ...)

## S3 method for class 'table'

freqlist(
object,
na.options = c("include", "showexclude", "remove"),
strata = NULL,
labelTranslations = NULL,
control = NULL,
...
)

## S3 method for class 'formula'

freqlist(
formula,
data,
subset,
na.action,
na.options = c("include", "showexclude", "remove"),
strata = NULL,
labelTranslations = NULL,
control = NULL,
addNA,
exclude,
drop.unused.levels,
...
)

Arguments
object An R object, usually of class "table" or class "xtabs"
... additional arguments. In the formula method, these are passed to the table
method. These are also passed to freq.control
na.options a character string indicating how to handling missing values: "include" (in-
clude values with NAs in counts and percentages), "showexclude" (show NAs
but exclude from cumulative counts and all percentages), "remove" (remove
values with NAs); default is "include".
freqlist.internal 19

strata (formerly groupBy) an optional character string specifying a variable(s) to use

for grouping when calculating cumulative counts and percentages. summary.freqlist
will also separate by grouping variable for printing. Note that this is different
from modelsum and tableby, which take bare column names (and only one, at
that!)
labelTranslations
an optional character string (or list) of labels to use for variable levels when
summarizing. Names will be matched appropriately.
control control parameters to handle optional settings within freqlist. See freq.control
formula, data, subset, na.action, addNA, exclude, drop.unused.levels
Arguments passed to xtabs.

Value

An object of class c("freqlist", "arsenal_table")

Author(s)

Tina Gunderson, with revisions by Ethan Heinzen

See Also

arsenal_table, summary.freqlist, freq.control, freqlist.internal, table, xtabs

Examples
# load mockstudy data
data(mockstudy)
tab.ex <- table(mockstudy[c("arm", "sex", "mdquality.s")], useNA = "ifany")
noby <- freqlist(tab.ex, na.options = "include")
summary(noby)

# show the top 6 rows' frequencies and percents

head(summary(sort(noby, decreasing = TRUE)[c(1:4, 6)]))

withby <- freqlist(tab.ex, strata = c("arm","sex"), na.options = "showexclude")

summary(withby)

freqlist.internal Helper functions for freqlist

Description

A set of helper functions for freqlist.

20 internal.functions

Usage
is.freqlist(x)

is.summary.freqlist(x)

## S3 method for class 'summary.freqlist'

head(x, n = 6L, ...)

## S3 method for class 'summary.freqlist'

tail(x, n = 6L, ...)

## S3 method for class 'freqlist'

sort(x, decreasing = FALSE, ...)

Arguments
x A freqlist object.
n A single integer. See head or tail for more details
... Other arguments.
decreasing Should the sort be increasing or decreasing?

Details
Note that sort() has to recalculate cumulative statistics. Note also that the reordering of rows will
also affect which labels are duplicates; you may also want to consider using dupLabels=TRUE in
freq.control().

See Also
merge.freqlist, arsenal_table, sort, freqlist, summary.freqlist, freq.control,

internal.functions Internal Functions

Description
Internal Functions

Usage
smart.split(string, width = Inf, min.split = -Inf)

replace2(x, list, values)

keep.labels 21

Arguments
string A character vector
width Either Inf or NULL to specify no splitting, or a positive integer giving the largest
allowed string length.
min.split Either -Inf or NULL to specify no lower bound on the string length, or a positive
integer giving the minimum string length.
x vector
list an index vector
values replacement values

Value
For smart.split, a list of the same length as string, with each element being the "intelligently"
split string.
For replace2, a vector with the proper values replaced.

See Also
replace

keep.labels Keep Labels

Description
Keep the 'label' attribute on an R object when subsetting. loosen.labels allows the 'label'
attribute to be lost again.

Usage
keep.labels(x, ...)

## S3 method for class 'data.frame'

keep.labels(x, ...)

## Default S3 method:
keep.labels(x, ...)

## S3 method for class 'keep_labels'

x[...]

## S3 replacement method for class 'keep_labels'

x[i] <- value

loosen.labels(x, ...)
22 labels

## S3 method for class 'data.frame'

loosen.labels(x, ...)

## Default S3 method:
loosen.labels(x, ...)

Arguments
x An R object
... Other arguments (not in use at this time).
i, value See [<-.

Value
A copy of x with a "keep_labels" class appended on or removed. Note that for the data.frame
method, only classes on the columns are changed; the data.frame won’t have an extra class ap-
pended. This is different from previous versions of arsenal.

Author(s)
Ethan Heinzen

See Also
labels

labels Labels

Description
Assign and extract the 'label' attribute on an R object. set_labels is the same as labels(x) <-
value but returns x for use in a pipe chain. set_attr is the same as attr(x, which) <- value but
returns x for use in a pipe chain.

Usage
## S3 method for class 'data.frame'
labels(object, ...)

## S3 method for class 'keep_labels'

labels(object, ...)

labels(x) <- value

## S3 replacement method for class 'keep_labels'

mdy.Date 23

labels(x) <- value

## Default S3 replacement method:

labels(x) <- value

## S3 replacement method for class 'data.frame'

labels(x) <- value

set_labels(x, value)

set_attr(x, which, value)

Arguments

... Other arguments (not in use at this time).

x, object An R object.
value A vector or list containing labels to assign. Labels are assigned based on names,
if available; otherwise, they’re assigned in order. Can pass NULL to remove all
labels.
which See attr<-

Details

The data.frame methods put labels on and extract labels from the columns of object.

Value

The labels of object, or object with new labels.

Author(s)

Ethan Heinzen

See Also

keep.labels

mdy.Date Convert numeric dates to Date object, and vice versa

Description

Convert numeric dates for month, day, and year to Date object, and vice versa.
24 mdy.Date

Usage

mdy.Date(month, day, year, yearcut = 120)

Date.mdy(date)

is.Date(x)

Arguments

month integer, month (1-12).

day integer, day of the month (1-31, depending on the month).
year integer, either 2- or 4-digit year. If two-digit number, will add 1900 onto it,
depending on range.
yearcut cutoff for method to know if to convert to 4-digit year.
date A date value.
x An object.

Details

Test if an object is a date.

More work may need to be done with yearcut and 2-digit years. Best to give a full 4-digit year.

Value

mdy.Date returns a Date object, and Date.mdy returns a list with integer values for month, day, and
year. is.Date returns a single logical value.

See Also

Date, DateTimeClasses

Examples

mdy.Date(9, 2, 2013)

tmp <- mdy.Date(9, 2, 2013)

Date.mdy(tmp)

is.Date(tmp)
mockstudy 25

mockstudy Mock study data for examples

Description
Mock clinical study data for examples to test data manipulation and statistical functions. The func-
tion muck_up_mockstudy() is used in examples for comparedf.

Usage
mockstudy

muck_up_mockstudy()

Format
A data frame with 1499 observations on the following 15 variables:

case a numeric identifier-patient ID

age age in years
arm treatment arm divided into 3 groups, character string
sex a factor with levels Male Female
race self-reported race/ethnicity, character string
fu.time survival or censoring time in years
fu.stat censoring status; 1=censor, 2=death
ps integer, ECOG performance score
hgb numeric, hemoglobin count
bmi numeric, body mass index, kg/m^2
alk.phos numeric, alkaline phosphatase
ast numeric, aspartate transaminase
mdquality.s integer, LASA QOL 0=Clinically Deficient, 1=Not Clinically Deficient
age.ord an ordered factor split of age, with levels 10-19 < 20-29 < 30-39 < 40-49 < 50-59 <
60-69 < 70-79 < 80-89

An object of class data.frame with 1499 rows and 14 columns.

Examples
data(mockstudy)
str(mockstudy)
26 modelsum

modelsum Fit models over each of a set of independent variables with a response
variable

Description
Fit and summarize models for each independent (x) variable with a response variable (y), with
options to adjust by variables for each model.

Usage
modelsum(
formula,
family = "gaussian",
data,
adjust = NULL,
na.action = NULL,
subset = NULL,
weights = NULL,
id,
strata,
control = NULL,
...
)

Arguments
formula an object of class formula; a symbolic description of the variables to be mod-
eled. See "Details" for more information.
family similar mechanism to glm, where the model to be fit is driven by the family. Op-
tions include: binomial, gaussian, survival, poisson, negbin, clog, and ordinal.
These can be passed as a string, as a function, or as a list resulting from a call
to one of the functions. See modelsum.family for details on survival, ordinal,
negbin, and clog families.
data an optional data.frame, list or environment (or object coercible by as.data.frame
to a data frame) containing the variables in the model. If not found in data,
the variables are taken from environment(formula), typically the environment
from which modelsum is called.
adjust an object of class formula or a list of formulas, listing variables to adjust by in
all models. Specify as a one-sided formula, like: ~Age+ Sex. If a list, the names
are used for the summary function. Unadjusted models can be specified as ~ 1
or as a list: list(Unadjusted = NULL).
na.action a function which indicates what should happen when the data contain NAs. The
default (NULL) is to use the defaults of lm, glm, or coxph, depending on the
family specifications.
modelsum 27

subset an optional vector specifying a subset of observations (rows of data) to be used

in the results. If strata is missing, this works as vector of logicals or an index;
otherwise, it should be a logical vector.
weights an optional vector specifying the weights to apply to each data observation (rows
of data)
id A vector to identify clusters. Only used for relrisk at this time.
strata a vector of strata to separate model summaries by an additional group. Note
that for families like "clog", the "usual" strata term to indicate subject groupings
should be given in the adjust argument.
control control parameters to handle optional settings within modelsum. Arguments for
modelsum.control can be passed to modelsum via the ... argument, but if a
control object and ... arguments are both supplied, the latter are used. See
modelsum.control for other details.
... additional arguments to be passed to internal modelsum functions.

Value

An object with class c("modelsum", "arsenal_table")

Author(s)

Jason Sinnwell, Patrick Votruba, Beth Atkinson, Gregory Dougherty, and Ethan Heinzen, adapted
from SAS Macro of the same name

See Also

arsenal_table, modelsum.control, summary.modelsum, modelsum.internal, formulize

Examples

data(mockstudy)

tab1 <- modelsum(bmi ~ sex + age, data = mockstudy)

summary(tab1, text = TRUE)

tab2 <- modelsum(alk.phos ~ arm + ps + hgb, adjust = ~ age + sex,

family = "gaussian", data = mockstudy)
summary(tab2, text = TRUE)

summary(tab2, show.intercept = FALSE, text = TRUE)

tab2.df <- as.data.frame(tab2)

tab2.df[1:5,]
28 modelsum.control

modelsum.control Control settings for modelsum function

Description
Control test and summary settings for modelsum function.

Usage
modelsum.control(
digits = 3L,
digits.ratio = 3L,
digits.p = 3L,
format.p = TRUE,
show.adjust = TRUE,
show.intercept = TRUE,
conf.level = 0.95,
ordinal.stats = c("OR", "CI.lower.OR", "CI.upper.OR", "p.value", "Nmiss"),
binomial.stats = c("OR", "CI.lower.OR", "CI.upper.OR", "p.value", "concordance",
"Nmiss"),
gaussian.stats = c("estimate", "std.error", "p.value", "adj.r.squared", "Nmiss"),
poisson.stats = c("RR", "CI.lower.RR", "CI.upper.RR", "p.value", "Nmiss"),
negbin.stats = c("RR", "CI.lower.RR", "CI.upper.RR", "p.value", "Nmiss"),
relrisk.stats = c("RR", "CI.lower.RR", "CI.upper.RR", "p.value", "Nmiss"),
clog.stats = c("OR", "CI.lower.OR", "CI.upper.OR", "p.value", "concordance", "Nmiss"),
survival.stats = c("HR", "CI.lower.HR", "CI.upper.HR", "p.value", "concordance",
"Nmiss"),
stat.labels = list(),
...
)

Arguments
digits Numeric, denoting the number of digits after the decimal point for beta coeffi-
cients and standard errors.
digits.ratio Numeric, denoting the number of digits after the decimal point for ratios, e.g.
OR, RR, HR.
digits.p Numeric, denoting the number of digits for p-values. See "Details", below.
format.p Logical, denoting whether to format p-values. See "Details", below.
show.adjust Logical, denoting whether to show adjustment terms.
show.intercept Logical, denoting whether to show intercept terms.
conf.level Numeric, giving the confidence level.
ordinal.stats, binomial.stats, survival.stats, gaussian.stats, poisson.stats, negbin.stats, clog.stats,
Character vectors denoting which stats to show for the various model types.
stat.labels A named list of labels for all the stats used above.
... Other arguments (not in use at this time).
modelsum.family 29

Details
If format.p is FALSE, digits.p denotes the number of significant digits shown. The p-values will
be in exponential notation if necessary. If format.p is TRUE, digits.p will determine the number
of digits after the decimal point to show. If the p-value is less than the resulting number of places,
it will be formatted to show so.

Value
A list with settings to be used within the modelsum function.

See Also
modelsum, summary.modelsum, modelsum.internal

modelsum.family Family functions for modelsum

Description
A set of family functions for modelsum.

Usage
survival()

ordinal(method = c("logistic", "probit", "loglog", "cloglog", "cauchit"))

negbin(link = c("log", "identity", "sqrt"))

clog()

relrisk(link = "log")

Arguments
method See MASS::polr.
link See MASS::glm.nb.

Value
A list, in particular with element family.

See Also
family, coxph, polr
30 NA.operations

modelsum.internal Helper functions for modelsum

Description
A set of helper functions for modelsum.

Usage
is.modelsum(x)

is.summary.modelsum(x)

na.modelsum(object, ...)

Arguments
x A modelsum object.
object A data.frame resulting from evaluating a modelsum formula.
... Other arguments, or a vector of indices for extracting.

Value
na.modelsum returns a subsetted version of object (with attributes).

See Also
arsenal_table

NA.operations Some functions to handle NAs

Description
allNA tests if all elements are NA, and includeNA sets the NAs in a character vector or factor to an
explicit label.

Usage
allNA(x)

includeNA(x, label, ...)

## S3 method for class 'factor'

includeNA(x, label = "(Missing)", first = FALSE, ...)

## Default S3 method:
includeNA(x, label = "(Missing)", ...)
padjust 31

Arguments
x An object
label A character string denoting the label to set NAs to.
... Other arguments (not in use at this time).
first Logical; should the new label be the first level?

Author(s)
Ethan Heinzen

See Also
is.na, anyNA

padjust Adjust P-values for Multiple Comparisons

Description
Adjust P-values for Multiple Comparisons

Usage
padjust(p, method, n, ...)

## Default S3 method:
padjust(p, method, n, ...)

## S3 method for class 'tableby'

padjust(p, method, n, suffix = " (adjusted for multiple comparisons)", ...)

## S3 method for class 'summary.tableby'

padjust(p, method, n, suffix = " (adjusted for multiple comparisons)", ...)

Arguments
p An object.
method correction method. Can be abbreviated.
n number of comparisons, must be at least length(p); only set this (to non-
default) when you know what you are doing!
... Other arguments.
suffix A suffix to add to the footnotes indicating that the tests were adjusted.

See Also
p.adjust, modpval.tableby, tests.tableby
32 paired

paired Summary Statistics of a Set of Independent Variables Paired Across

Two Timepoints

Description
Summarize one or more variables (x) by a paired time variable (y). Variables on the right side of
the formula, i.e. independent variables, are summarized by the two time points on the left of the
formula. Optionally, an appropriate test is performed to test the distribution of the independent
variables across the time points.

Usage
paired(
formula,
data,
id,
na.action,
subset = NULL,
strata,
control = NULL,
...
)

Arguments
formula an object of class formula of the form time ~ var1 + .... See "Details" for
more information.
data an optional data frame, list or environment (or object coercible by as.data.frame
to a data frame) containing the variables in the model. If not found in data,
the variables are taken from environment(formula), typically the environment
from which the function is called.
id The vector giving IDs to match up data for the same subject across two time-
points.
na.action a function which indicates what should happen when the data contain NAs. The
default is na.paired("in.both"). See na.paired for more details
subset an optional vector specifying a subset of observations (rows of data) to be used
in the results. Works as vector of logicals or an index.
strata a vector of strata to separate summaries by an additional group.
control control parameters to handle optional settings within paired. Two aspects of
paired are controlled with these: test options of RHS variables and x variable
summaries. Arguments for paired.control can be passed to paired via the
... argument, but if a control object and ... arguments are both supplied, the
latter are used. See paired.control for more details.
... additional arguments to be passed to internal paired functions or paired.control.
paired.control 33

Details
Do note that this function piggybacks off of tableby quite heavily, so there is no summary.paired
function (for instance).
These tests are accepted:

• paired.t: a paired t-test.

• mcnemar: McNemar’s test.
• signed.rank: a signed rank test.
• sign.test: a sign test.
• notest: no test is performed.

Value
An object with class c("paired", "tableby", "arsenal_table")

Author(s)
Jason Sinnwell, Beth Atkinson, Ryan Lennon, and Ethan Heinzen

See Also
arsenal_table, paired.control, tableby, formulize, selectall

paired.control Control settings for paired function

Description
Control test and summary settings for the paired function.

Usage
paired.control(
diff = TRUE,
numeric.test = "paired.t",
cat.test = "mcnemar",
ordered.test = "signed.rank",
date.test = "paired.t",
mcnemar.correct = TRUE,
signed.rank.exact = NULL,
signed.rank.correct = TRUE,
...
)
34 paired.internal

Arguments
diff logical, telling paired whether to calculate a column of differences between
time points.
numeric.test name of test for numeric RHS variables in paired: paired.t, signed.rank, sign.test.
cat.test name of test for categorical variables: mcnemar
ordered.test name of test for ordered variables: signed.rank, sign.test
date.test name of test to perform for date variables: paired.t, signed.rank, sign.test
mcnemar.correct, signed.rank.exact, signed.rank.correct
Options for statistical tests. See wilcox.test and mcnemar.test for details.
... Arguments passed to tableby.control

Details
Note that (with the exception of total) all arguments to tableby.control are accepted in this
function (in fact, this function passes everything through to tableby.control). However, there are
different defaults for the statistical tests (shown here). For details on the other arguments, please
see the help page for tableby.control.

Value
A list with settings to be used within the paired function.

Author(s)
Ethan Heinzen

See Also
paired, tableby, tableby.control, summary.tableby

paired.internal Helper functions for paired

Description
A set of helper functions for paired.

Usage
na.paired(missings = c("in.both", "fill", "asis"))

Arguments
missings A character string denoting which action to take. See "Details", below.
selectall 35

Details
All methods subset out any NA time points or IDs. "in.both" (the default) subsets the data.frame
to individuals who appear at both time points. "fill" adds explicit missings for the people missing
second time points. "asis" does nothing to add or remove missings.

Value
na.paired returns a function used to subset data.frames in paired.

See Also
tableby.internal

selectall Make a column for "select all" input

Description
Make a column for "select all" input

Usage
selectall(...)

as.selectall(x)

## S3 method for class 'selectall'

as.matrix(x, ...)

## S3 method for class 'selectall'

x[i, j, drop = FALSE]

## S3 method for class 'selectall'

is.na(x)

is.selectall(x)

Arguments
... Named arguments of the same length. These should be logical, numeric (0/1) or
a factor with two levels.
x An object of class "selectall"
i, j, drop Arguments to ‘[.matrix‘

See Also
tableby, paired
36 summary.comparedf

Examples
d <- data.frame(grp = rep(c("A", "B"), each = 5))
d$s <- selectall(
`Option 1` = c(rep(1, 4), rep(0, 6)),
`Option 2` = c(0, 1, 0, 0, 0, 1, 1, 1, 0, 0),
`Option 3` = 1,
`Option 4` = 0
)
summary(tableby(grp ~ s, data = d), text = TRUE)

summary.comparedf The summary method for a comparedf object

Description
Print a more detailed output of the comparedf object.

Usage
## S3 method for class 'comparedf'
summary(object, ..., show.attrs = FALSE)

## S3 method for class 'summary.comparedf'

print(x, ..., format = "pandoc")

Arguments
object An object of class "comparedf", as made by the comparedf S3 method.
... Other arguments passed to comparedf.control. In print, these are passed to
kable.
show.attrs Logical, denoting whether to show the actual attributes which are different. For
(e.g.) factors with lots of levels, this can make the tables quite wide, so this
feature is FALSE by default.
x An object returned by the summary.comparedf function.
format Passed to kable: the format for the table. The default here is "pandoc". To use
the default in kable, pass NULL.

Value
An object of class "summary.comparedf" is returned.

See Also
comparedf, comparedf.control
summary.freqlist 37

summary.freqlist summary.freqlist

Description
Summarize the freqlist object.

Usage
## S3 method for class 'freqlist'
summary(object, ..., labelTranslations = NULL, title = NULL)

## S3 method for class 'summary.freqlist'

as.data.frame(x, ..., list.ok = FALSE)

Arguments
object an object of class freqlist
... For summary.freqlist, these are passed to as.data.frame.freqlist (and
hence to freq.control). For the print method, these are additional arguments
passed to the kable function.
labelTranslations
A named list (or vector) where the name is the label in the output to be replaced
in the pretty rendering by the character string value for the named element of
the list, e.g., list(age = "Age(Years)", meansd = "Mean(SD)").
title Title/caption for the table, defaulting to NULL (no title). Passed to kable. Can
be length > 1 if the more than one table is being printed.
x An object of class summary.freqlist.
list.ok If the object has multiple by-variables, is it okay to return a list of data.frames
instead of a single data.frame? If FALSE but there are multiple by-variables, a
warning is issued.

Value
An object of class "summary.freqlist" (invisibly for the print method).

Author(s)
Tina Gunderson, with major revisions by Ethan Heinzen

See Also
freqlist, table, xtabs, kable, freq.control, freqlist.internal
38 summary.modelsum

Examples
# load mockstudy data
data(mockstudy)
tab.ex <- table(mockstudy[c("arm", "sex", "mdquality.s")], useNA = "ifany")
noby <- freqlist(tab.ex, na.options = "include")
summary(noby)
withby <- freqlist(tab.ex, strata = c("arm","sex"), na.options = "showexclude")
summary(withby)
summary(withby, dupLabels = TRUE)

summary.modelsum Summarize a modelsum object.

Description
Format the information in object as a table using Pandoc coding or plain text, and cat it to stdout.

Usage
## S3 method for class 'modelsum'
summary(
object,
...,
labelTranslations = NULL,
text = FALSE,
title = NULL,
term.name = "",
adjustment.names = FALSE
)

## S3 method for class 'summary.modelsum'

as.data.frame(
x,
...,
text = x$text,
term.name = x$term.name,
adjustment.names = x$adjustment.names,
width = NULL,
min.split = NULL,
list.ok = FALSE
)

Arguments
object A modelsum object.
summary.modelsum 39

... For summary.modelsum, other arguments passed to as.data.frame.modelsum.

For as.data.frame.summary.modelsum, "width" and "min.split" are passed
to smart.split. For printing the summary object, these are passed to both
as.data.frame.summary.modelsum and kable.
labelTranslations
A named list (or vector) where the name is the label in the output to be replaced
in the pretty rendering by the character string value for the named element of
the list, e.g., list(age = "Age(Years)", meansd = "Mean(SD)").
text An argument denoting how to print the summary to the screen. Default is FALSE
(show markdown output). TRUE and NULL output a text-only version, with the
latter avoiding all formatting. "html" uses the HTML tag <strong> instead of
the markdown formatting, and "latex" uses the LaTeX command \textbf.
title Title/caption for the table, defaulting to NULL (no title). Passed to kable. Can
be length > 1 if the more than one table is being printed.
term.name A character vector denoting the column name for the "terms" column. It should
be the same length as the number of tables or less (it will get recycled if needed).
The special value TRUE will use the y-variable’s label for each table.
adjustment.names
Logical, denoting whether the names of the adjustment models should be printed.
x An object of class "summary.modelsum".
width Passed to smart.split for formatting of the "term" column.
min.split Passed to smart.split for formatting of the "term" column.
list.ok If the object has multiple by-variables, is it okay to return a list of data.frames
instead of a single data.frame? If FALSE but there are multiple by-variables, a
warning is issued.

Value

An object of class "summary.modelsum"

Author(s)

Ethan Heinzen, based on code originally by Greg Dougherty

See Also

modelsum, as.data.frame.modelsum
40 summary.tableby

summary.tableby The summary method for a tableby object

Description
The summary method for a tableby object, which is a pretty rendering of a tableby object into a
publication-quality results table in R Markdown, and can render well in text-only.

Usage
## S3 method for class 'tableby'
summary(
object,
...,
labelTranslations = NULL,
text = FALSE,
title = NULL,
pfootnote = FALSE,
term.name = ""
)

## S3 method for class 'summary.tableby'

as.data.frame(
x,
...,
text = x$text,
pfootnote = x$pfootnote,
term.name = x$term.name,
width = NULL,
min.split = NULL,
list.ok = FALSE
)

Arguments
object An object of class "tableby", made by the tableby function.
... For summary.tableby, other arguments passed to as.data.frame.tableby.
For printing the summary object, these are passed to both as.data.frame.summary.tableby
and kable.
labelTranslations
A named list (or vector) where the name is the label in the output to be replaced
in the pretty rendering by the character string value for the named element of
the list, e.g., list(age = "Age(Years)", meansd = "Mean(SD)").
text An argument denoting how to print the summary to the screen. Default is FALSE
(show markdown output). TRUE and NULL output a text-only version, with the
latter avoiding all formatting. "html" uses the HTML tag <strong> instead of
the markdown formatting, and "latex" uses the LaTeX command \textbf.
summary.tableby 41

title Title/caption for the table, defaulting to NULL (no title). Passed to kable. Can
be length > 1 if the more than one table is being printed.
pfootnote Logical, denoting whether to put footnotes describing the tests used to gener-
ate the p-values. Alternatively, "html" to surround the outputted footnotes with
<li>.
term.name A character vector denoting the column name for the "terms" column. It should
be the same length as the number of tables or less (it will get recycled if needed).
The special value TRUE will use the y-variable’s label for each table.
x An object of class "summary.tableby".
width Passed to smart.split for formatting of the "term" column.
min.split Passed to smart.split for formatting of the "term" column.
list.ok If the object has multiple by-variables, is it okay to return a list of data.frames
instead of a single data.frame? If FALSE but there are multiple by-variables, a
warning is issued.

Value
An object of class summary.tableby

Author(s)
Ethan Heinzen, based on code by Gregory Dougherty, Jason Sinnwell, Beth Atkinson, adapted from
SAS Macros written by Paul Novotny and Ryan Lennon

See Also
tableby.control, tableby

Examples

set.seed(100)
## make 3+ categories for response
nsubj <- 90
mdat <- data.frame(Response=sample(c(1,2,3),nsubj, replace=TRUE),
Sex=sample(c("Male", "Female"), nsubj,replace=TRUE),
Age=round(rnorm(nsubj,mean=40, sd=5)),
HtIn=round(rnorm(nsubj,mean=65,sd=5)))

## allow default summaries on RHS variables

out <- tableby(Response ~ Sex + Age + HtIn, data=mdat)
summary(out, text=TRUE)
labels(out)
labels(out) <- c(Age="Age (years)", HtIn="Height (inches)")
summary(out, stats.labels=c(meansd="Mean-SD", q1q3 = "Q1-Q3"), text=TRUE)
42 tableby

tableby Summary Statistics of a Set of Independent Variables by a Categorical

Variable

Description
Summarize one or more variables (x) by a categorical variable (y). Variables on the right side of
the formula, i.e. independent variables, are summarized by the levels of a categorical variable on
the left of the formula. Optionally, an appropriate test is performed to test the distribution of the
independent variables across the levels of the categorical variable.

Usage
tableby(
formula,
data,
na.action,
subset = NULL,
weights = NULL,
strata,
control = NULL,
...
)

Arguments
formula an object of class formula; a symbolic description of the variables to be sum-
marized by the group, or categorical variable, of interest. See "Details" for more
information. To only view overall summary statistics, a one-sided formula can
be used.
data an optional data frame, list or environment (or object coercible by as.data.frame
to a data frame) containing the variables in the model. If not found in data,
the variables are taken from environment(formula), typically the environment
from which the function is called.
na.action a function which indicates what should happen when the data contain NAs. The
default is na.tableby(TRUE) if there is a by-variable, and na.tableby(FALSE)
if there is not. This schema thus includes observations with NAs in x variables,
but removes those with NA in the categorical group variable and strata (if used).
subset an optional vector specifying a subset of observations (rows of data) to be used
in the results. Works as vector of logicals or an index.
weights a vector of weights. Using weights will disable statistical tests.
strata a vector of strata to separate summaries by an additional group.
control control parameters to handle optional settings within tableby. Two aspects of
tableby are controlled with these: test options of RHS variables across levels of
the categorical grouping variable, and x variable summaries within the grouping
tableby 43

variable. Arguments for tableby.control can be passed to tableby via the

... argument, but if a control object and ... arguments are both supplied, the
latter are used. See tableby.control for more details.
... additional arguments to be passed to internal tableby functions or tableby.control.

Details
The group variable (if any) is categorical, which could be an integer, character, factor, or ordered
factor. tableby makes a simple summary of the counts within the k-levels of the independent
variables on the right side of the formula. Note that unused levels are dropped.
The data argument allows data.frames with label attributes for the columns, and those labels will
be used in the summary methods for the tableby class.
The independent variables are a mixture of types: categorical (discrete), numeric (continuous), and
time to event (survival). These variables are split by the levels of the group variable (if any), then
summarized within those levels, specific to the variable type. A statistical test is performed to
compare the distribution of the independent variables across the levels of the grouping variable.
The tests differ by the independent variable type, but can be specified explicitly in the formula
statement or in the control function. These tests are accepted:

• anova: analysis of variance test; the default test for continuous variables. When LHS variable
has two levels, equivalent to two-sample t-test.
• kwt: Kruskal-Wallis Rank Test, optional test for continuous variables. When LHS variable
has two levels, equivalent to Wilcoxon test.
• wt: An explicit Wilcoxon test.
• medtest: A median test.
• chisq: chi-square goodness of fit test for equal counts of a categorical variable across cate-
gories; the default for categorical or factor variables
• fe: Fisher’s exact test for categorical variables
• trend: trend test for equal distribution of an ordered variable across a categorical variable;
the default for ordered factor variables
• logrank: log-rank, the default for time-to-event variables
• notest: no test is performed.

To perform a mixture of asymptotic and rank-based tests on two different continuous variables, an
example formula is: formula = group ~ anova(age) + kwt(height). The test settings in tableby.control
apply to all independent variables of a given type.
The summary statistics reported for each independent variable within the group variable can be set
in tableby.control.
Finally, multiple by-variables can be set using list(). See the examples for more details.

Value
An object with class c("tableby", "arsenal_table")
44 tableby.control

Author(s)
Jason Sinnwell, Beth Atkinson, Gregory Dougherty, and Ethan Heinzen, adapted from SAS Macros
written by Paul Novotny and Ryan Lennon

See Also
arsenal_table, anova, chisq.test, tableby.control, summary.tableby, tableby.internal,
formulize, selectall

Examples
data(mockstudy)
tab1 <- tableby(arm ~ sex + age, data=mockstudy)
summary(tab1, text=TRUE)

mylabels <- list(sex = "SEX", age ="Age, yrs")

summary(tab1, labelTranslations = mylabels, text=TRUE)

tab3 <- tableby(arm ~ sex + age, data=mockstudy, test=FALSE, total=FALSE,

numeric.stats=c("median","q1q3"), numeric.test="kwt")
summary(tab3, text=TRUE)

# multiple LHS
summary(tableby(list(arm, sex) ~ age, data = mockstudy, strata = ps), text = TRUE)

tab.test <- tableby(arm ~ kwt(age) + anova(bmi) + kwt(ast), data=mockstudy)

tests(tab.test)

tableby.control Control settings for tableby function

Description
Control test and summary settings for the tableby function.

Usage
tableby.control(
test = TRUE,
total = TRUE,
total.pos = c("after", "before"),
test.pname = NULL,
numeric.simplify = FALSE,
cat.simplify = FALSE,
cat.droplevels = FALSE,
ordered.simplify = FALSE,
date.simplify = FALSE,
tableby.control 45

numeric.test = "anova",
cat.test = "chisq",
ordered.test = "trend",
surv.test = "logrank",
date.test = "kwt",
selectall.test = "notest",
test.always = FALSE,
numeric.stats = c("Nmiss", "meansd", "range"),
cat.stats = c("Nmiss", "countpct"),
ordered.stats = c("Nmiss", "countpct"),
surv.stats = c("Nmiss", "Nevents", "medSurv"),
date.stats = c("Nmiss", "median", "range"),
selectall.stats = c("Nmiss", "countpct"),
stats.labels = list(),
digits = 3L,
digits.count = 0L,
digits.pct = 1L,
digits.p = 3L,
format.p = TRUE,
digits.n = 0L,
conf.level = 0.95,
wilcox.correct = FALSE,
wilcox.exact = NULL,
chisq.correct = FALSE,
simulate.p.value = FALSE,
B = 2000,
times = 1:5,
...
)

Arguments
test logical, telling tableby whether to perform tests of x variables across levels of
the group variable.
total logical, telling tableby whether to calculate a column of totals across group
variable.
total.pos One of "before" or "after", denoting where to put the total column relative to
the by-variable columns.
test.pname character string denoting the p-value column name in summary.tableby. Mod-
ifiable also with modpval.tableby.
numeric.simplify, date.simplify
logical, tell tableby whether to condense numeric/date output to a single line.
NOTE: this only simplifies to one line if there is only one statistic reported, such
as meansd. In particular, if Nmiss is specified and there are missings, then the
output is not simplified.
cat.simplify, ordered.simplify
logical, tell tableby whether to remove the first level of the categorical/ordinal
variable if binary. If TRUE, only the summary stats of the second level are re-
46 tableby.control

ported (unless there’s only one level, in which case it’s reported). If "label",
the second level’s label is additionally appended to the label. NOTE: this only
simplifies to one line if there is only one statistic reported, such as countpct.
In particular, if Nmiss is specified and there are missings, then the output is not
simplified.
cat.droplevels Should levels be dropped for categorical variables? If set to true, p-values will
not be displayed unless test.always = TRUE as well.
numeric.test name of test for numeric RHS variables in tableby: anova, kwt (Kruskal-
Wallis), medtest (median test). If no LHS variable exists, then a mean is required
for a univariate test.
cat.test name of test for categorical variables: chisq, fe (Fisher’s Exact)
ordered.test name of test for ordered variables: trend
surv.test name of test for survival variables: logrank
date.test name of test for date variables: kwt
selectall.test name of test for date variables: notest
test.always Should the test be performed even if one or more by-group has 0 observations?
Relevant for kwt and anova.
numeric.stats, cat.stats, ordered.stats, surv.stats, date.stats, selectall.stats
summary statistics to include for the respective class of RHS variables within
the levels of the group LHS variable.
stats.labels A named list of labels for all the statistics function names, where the function
name is the named element in the list and the value that goes with it is a string
containing the formal name that will be printed in all printed renderings of the
output, e.g., list(countpct="Count (Pct)"). Any unnamed elements will be
ignored. Passing NULL will disable labels.
digits Number of decimal places for numeric values.
digits.count Number of decimal places for count values.
digits.pct Number of decimal places for percents.
digits.p Number of decimal places for p-values.
format.p Logical, denoting whether to format p-values. See "Details", below.
digits.n Number of decimal places for N’s in the header. Set it to NA to suppress the
N’s.
conf.level Numeric, denoting what confidence level to use for confidence intervals. (See,
e.g., binomCI)
wilcox.correct, wilcox.exact
See wilcox.test
chisq.correct logical, correction factor for chisq.test
simulate.p.value
logical, simulate p-value for categorical tests (fe and chisq)
B number of simulations to perform for simulation-based p-value
times A vector of times to use for survival summaries.
... additional arguments.
tableby.internal 47

Details
All tests can be turned off by setting test to FALSE. Otherwise, test are set to default settings in
this list, or set explicitly in the formula of tableby.
If format.p is FALSE, digits.p denotes the number of significant digits shown. The p-values will
be in exponential notation if necessary. If format.p is TRUE, digits.p will determine the number
of digits after the decimal point to show. If the p-value is less than the resulting number of places,
it will be formatted to show so.
Options for statistics are described more thoroughly in the vignette and are listed in tableby.stats

Value
A list with settings to be used within the tableby function.

Author(s)
Jason Sinnwell, Beth Atkinson, Ethan Heinzen, Terry Therneau, adapted from SAS Macros written
by Paul Novotny and Ryan Lennon

See Also
anova, chisq.test, tableby, summary.tableby, tableby.stats.

Examples
set.seed(100)
## make 3+ categories for Response
mdat <- data.frame(Response=c(0,0,0,0,0,1,1,1,1,1),
Sex=sample(c("Male", "Female"), 10,replace=TRUE),
Age=round(rnorm(10,mean=40, sd=5)),
HtIn=round(rnorm(10,mean=65,sd=5)))

## allow default summaries in RHS variables, and pass control args to

## main function, to be picked up with ... when calling tableby.control
outResp <- tableby(Response ~ Sex + Age + HtIn, data=mdat, total=FALSE, test=TRUE)
outCtl <- tableby(Response ~ Sex + Age + HtIn, data=mdat,
control=tableby.control(total=TRUE, cat.simplify=TRUE,
cat.stats=c("Nmiss","countpct"),digits=1))
summary(outResp, text=TRUE)
summary(outCtl, text=TRUE)

tableby.internal Helper functions for tableby

Description
A set of helper functions for tableby.
48 tableby.internal

Usage
is.tableby(x)

is.summary.tableby(x)

modpval.tableby(x, pdata, use.pname = FALSE)

tests(x)

## S3 method for class 'tableby'

tests(x)

na.tableby(lhs = TRUE)

## S3 method for class 'tableby'

xtfrm(x)

## S3 method for class 'tableby'

sort(x, ...)

## S3 method for class 'tableby'

Ops(e1, e2)

## S3 method for class 'tableby'

head(x, n = 6L, ...)

## S3 method for class 'tableby'

tail(x, n = 6L, ...)

Arguments
x A tableby object.
pdata A named data.frame where the first column is the by-variable names, the (op-
tional) second is the strata value, the next is the x variable names, the next is
p-values (or some test stat), and the (optional) next column is the method name.
use.pname Logical, denoting whether the column name in pdata corresponding to the p-
values should be used in the output of the object.
lhs Logical, denoting whether to remove NAs from the first column of the data.frame
(the "left-hand side")
... Other arguments.
e1, e2 tableby objects, or numbers to compare them to.
n A single integer. See head or tail for more details

Details
Logical comparisons are implemented for Ops.tableby.
tableby.stats 49

Value
na.tableby returns a subsetted version of object (with attributes). Ops.tableby returns a logical
vector. xtfrm.tableby returns the p-values (which are ordered by order to sort).

See Also
arsenal_table, sort, head, tail, tableby, summary.tableby, tableby.control

tableby.stats tableby Summary Statistics Functions

Description
A collection of functions that will report summary statistics. To create a custom function, consider
using a function with all three arguments and .... See the tableby vignette for an example.

Usage
arsenal_sum(x, na.rm = TRUE, ...)

arsenal_min(x, na.rm = TRUE, ...)

arsenal_max(x, na.rm = TRUE, ...)

arsenal_mean(x, na.rm = TRUE, weights = NULL, ...)

arsenal_sd(x, na.rm = TRUE, weights = NULL, ...)

arsenal_var(x, na.rm = TRUE, weights = NULL, ...)

meansd(x, na.rm = TRUE, weights = NULL, ...)

meanse(x, na.rm = TRUE, weights = NULL, ...)

meanCI(x, na.rm = TRUE, weights = NULL, conf.level = 0.95, ...)

medianrange(x, na.rm = TRUE, weights = NULL, ...)

medianmad(x, na.rm = TRUE, weights = NULL, ...)

arsenal_median(x, na.rm = TRUE, weights = NULL, ...)

arsenal_range(x, na.rm = TRUE, ...)

gmean(x, na.rm = TRUE, weights = NULL, ...)

gsd(x, na.rm = TRUE, weights = NULL, ...)

50 tableby.stats

gmeansd(x, na.rm = TRUE, weights = NULL, ...)

gmeanCI(x, na.rm = TRUE, weights = NULL, conf.level = 0.95, ...)

Nsigntest(x, na.rm = TRUE, weights = NULL, ...)

Nevents(x, na.rm = TRUE, weights = NULL, ...)

medSurv(x, na.rm = TRUE, weights = NULL, ...)

NeventsSurv(x, na.rm = TRUE, weights = NULL, times = 1:5, ...)

NriskSurv(x, na.rm = TRUE, weights = NULL, times = 1:5, ...)

Nrisk(x, na.rm = TRUE, weights = NULL, times = 1:5, ...)

medTime(x, na.rm = TRUE, weights = NULL, ...)

q1q3(x, na.rm = TRUE, weights = NULL, ...)

medianq1q3(x, na.rm = TRUE, weights = NULL, ...)

iqr(x, na.rm = TRUE, weights = NULL, ...)

Nmiss(x, weights = NULL, ...)

Nmiss2(x, weights = NULL, ...)

N(x, na.rm = TRUE, weights = NULL, ...)

Npct(
x,
levels = NULL,
by,
by.levels = sort(unique(by)),
na.rm = TRUE,
weights = NULL,
...,
totallab = "Total"
)

count(x, levels = NULL, na.rm = TRUE, weights = NULL, ...)

countpct(x, levels = NULL, na.rm = TRUE, weights = NULL, ...)

countN(x, levels = NULL, na.rm = TRUE, weights = NULL, ...)

tableby.stats 51

countrowpct(
x,
levels = NULL,
by,
by.levels = sort(unique(by)),
na.rm = TRUE,
weights = NULL,
...,
totallab = "Total"
)

countcellpct(
x,
levels = NULL,
by,
by.levels = sort(unique(by)),
na.rm = TRUE,
weights = NULL,
...,
totallab = "Total"
)

binomCI(x, levels = NULL, na.rm = TRUE, weights = NULL, conf.level = 0.95, ...)

rowbinomCI(
x,
levels = NULL,
by,
by.levels = sort(unique(by)),
na.rm = TRUE,
weights = NULL,
conf.level = 0.95,
...,
totallab = "Total"
)

Arguments
x Usually a vector.
na.rm Should NAs be removed?
... Other arguments.
weights A vector of weights.
conf.level Numeric, denoting what confidence level to use for confidence intervals.
times A vector of times to use for survival summaries.
levels A vector of levels that character xs should have.
by a vector of the by-values.
52 tableby.stats.internal

by.levels a vector of the levels of by.

totallab What to call the total "column"

Details
Not all these functions are exported, in order to avoid conflicting NAMESPACES. Note also that
the functions prefixed with "arsenal_" can be referred to by their short names (e.g., "min" for
"arsenal_min").

Value
Usually a vector of the appropriate numbers.

See Also
includeNA, tableby.control

tableby.stats.internal
Internal tableby functions

Description
A collection of functions that may help users create custom functions that are formatted correctly.

Usage
as.tbstat(
x,
oldClass = NULL,
sep = NULL,
parens = NULL,
sep2 = NULL,
pct = NULL,
...
)

as.countpct(
x,
...,
which.count = setdiff(seq_along(x), which.pct),
which.pct = 0L
)

as.tbstat_multirow(x)
write2 53

Arguments
x Usually a vector.
oldClass class(es) to add to the resulting object.
sep The separator between x[1] and the rest of the vector.
parens A length-2 vector denoting parentheses to use around x[2] and x[3].
sep2 The separator between x[2] and x[3].
pct For statistics of length 2, the symbol to use after the second one. (It’s called
"pct" because usually the first statistic is never a percent, but the second often
is.)
... arguments to pass to as.tbstat.
which.count Which statistics are counts? The default is everything except the things that are
percents.
which.pct Which statistics are percents? The default is 0, indicating that none are.

Details
The vignette has an example on how to use these.
as.tbstat defines a tableby statistic with its appropriate formatting.
as.countpct adds another class to as.tbstat to use different "digits" arguments (i.e., digits.count
or digits.pct). See tableby.control.
as.tbstat_multirow marks an object (usually a list) for multiple-row printing.

write2 write2

Description
Functions to output tables to a single document. (Also the S3 backbone behind the write2* func-
tions.)

Usage
write2(object, file, ..., output_format)

## S3 method for class 'arsenal_table'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'summary.arsenal_table'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'comparedf'

write2(object, file, ..., output_format = NULL)
54 write2

## S3 method for class 'summary.comparedf'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'verbatim'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'yaml'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'code.chunk'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'knitr_kable'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'xtable'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'character'

write2(object, file, ..., output_format = NULL)

## S3 method for class 'list'

write2(
object,
file,
...,
append. = FALSE,
render. = TRUE,
keep.rmd = !render.,
output_format = NULL
)

## Default S3 method:
write2(
object,
file,
FUN = NULL,
...,
append. = FALSE,
render. = TRUE,
keep.rmd = !render.,
output_format = NULL
)

Arguments

object An object.
file A single character string denoting the filename for the output document.
write2 55

... Additional arguments to be passed to FUN, rmarkdown::render, etc. One pop-

ular option is to use quiet = TRUE to suppress the command line output.
output_format One of the following:
1. An output format object, e.g. rmarkdown::html_document(...).
2. A character string denoting such a format function, e.g. "html_document".
In this case, the "..." are NOT passed.
3. The format function itself, e.g. rmarkdown::html_document. In this case,
the "..." arguments are passed.
4. One of "html", "pdf", and "word", shortcuts implemented here. In this
case, the "..." arguments are passed.
5. NULL, in which the output is HTML by default.
See rmarkdown::render for details.
append. Logical, denoting whether (if a temporary .Rmd file of the same name already
exists) to append on. Used mostly for write2.list.
render. Logical, denoting whether to render the temporary .Rmd file. Used mostly for
write2.list.
keep.rmd Logical, denoting whether to keep the intermediate .Rmd file. Used mostly for
write2.list.
FUN The summary-like or print-like function to use to generate the markdown con-
tent. Can be passed as a function or a character string. It’s expected that
FUN(object, ...) looks "good" when put directly in a .Rmd file.

Details
write2 is an S3 method. The default prints the object (using print) inside a section surrounded by
three back ticks. See verbatim for details.
There are methods implemented for tableby, modelsum, and freqlist, all of which use the
summary function. There are also methods compatible with kable, xtable, and pander_return.
Another option is to coerce an object using verbatim() to print out the results monospaced (as if
they were in the terminal). To output multiple tables into a document, simply make a list of them and
call the same function as before. Finally, to output code chunks to be evaluated, use code.chunk.
For more information, see vignette("write2").

Value
object is returned invisibly, and file is written.

Author(s)
Ethan Heinzen, adapted from code from Krista Goergen

See Also
write2word, write2pdf, write2html, render, word_document, html_document, pdf_document,
rtf_document, md_document, odt_document
56 write2.internal

Examples
## Not run:
data(mockstudy)
# tableby example
tab1 <- tableby(arm ~ sex + age, data=mockstudy)
write2(tab1, tempfile(fileext = ".rtf"),
toc = TRUE, # passed to rmarkdown::rtf_document, though in this case it's not practical
quiet = TRUE, # passed to rmarkdown::render
title = "My cool new title", # passed to summary.tableby
output_format = rmarkdown::rtf_document)

write2html(list(
"# Header 1", # a header
code.chunk(a <- 1, b <- 2, a + b), # a code chunk
verbatim("hi there") # verbatim output
),
tempfile(fileext = ".html"),
quite = TRUE)

## End(Not run)

write2.internal Helper functions for write2

Description
Helper functions for write2.

Usage
verbatim(...)

code.chunk(..., chunk.opts = "r")

Arguments
... For verbatim, objects to print out monospaced (as if in the terminal). For
code.chunk, either expressions or single character strings to paste into the code
chunk.
chunk.opts A single character string giving the code chunk options. Make sure to specify
the engine!

Details
The "verbatim" class is to tell write2 to print the object inside a section surrounded by three back
ticks. The results will look like it would in the terminal (monospaced).
code.chunk() is to write explicit code chunks in the .Rmd file; it captures the call and writes it to
the file, to execute upon knitting.
write2specific 57

write2specific write2word, write2html, write2pdf

Description
Functions to output tables to a single Word, HTML, or PDF document.

Usage
write2word(object, file, ...)

write2pdf(object, file, ...)

write2html(object, file, ...)

Arguments
object An object.
file A single character string denoting the filename for the output document.
... Additional arguments to be passed to FUN, rmarkdown::render, etc. One pop-
ular option is to use quiet = TRUE to suppress the command line output.

Details
To generate the appropriate file type, the write2* functions use one of rmarkdown::word_document,
rmarkdown::html_document, and rmarkdown::pdf_document to get the job done. "..." argu-
ments are passed to these functions, too.

Value
object is returned invisibly, and file is written.

Author(s)
Ethan Heinzen, adapted from code from Krista Goergen

See Also
write2

Examples
## Not run:
data(mockstudy)
# tableby example
tab1 <- tableby(arm ~ sex + age, data=mockstudy)
write2html(tab1, "~/trash.html")
58 yaml

# freqlist example
tab.ex <- table(mockstudy[, c("arm", "sex", "mdquality.s")], useNA = "ifany")
noby <- freqlist(tab.ex, na.options = "include")
write2pdf(noby, "~/trash2.pdf")

# A more complicated example

write2word(tab1, "~/trash.doc",
keep.md = TRUE,
reference_docx = mystyles.docx, # passed to rmarkdown::word_document
quiet = TRUE, # passed to rmarkdown::render
title = "My cool new title") # passed to summary.tableby

## End(Not run)

yaml Include a YAML header in write2

Description
Include a YAML header in write2

Usage
yaml(...)

## S3 method for class 'yaml'

print(x, ...)

## S3 method for class 'yaml'

c(..., recursive = FALSE)

is.yaml(x)

Arguments
... For yaml(), arguments to be bundled into a list and passed to as.yaml. For
print.yaml(), extra arguments. For c.yaml(), "yaml" objects to be concate-
nated.
x An object of class "yaml".
recursive Not in use at this time.

Value
A text string of class "yaml".

Author(s)
Ethan Heinzen, adapted from an idea by Brendan Broderick
%nin% 59

See Also
as.yaml, write2

Examples
x <- yaml(title = "My cool title", author = "Ethan P Heinzen")
x
y <- yaml("header-includes" = list("\\usepackage[labelformat=empty]{caption}"))
y
c(x, y)

%nin% Not in

Description
The not-in operator for R.

Usage
x %nin% table

Arguments
x vector or NULL: the values to be matched.
table vector or NULL: the values to be matched against.

Value
The negation of %in%.

Author(s)
Raymond Moore

See Also
%in%

Examples
1 %nin% 2:10
c("a", "b") %nin% c("a", "c", "d")
Index

∗ datasets as.tbstat_multirow
mockstudy, 25 (tableby.stats.internal), 52
[.arsenal_table (arsenal_table), 5 as.yaml, 58, 59
[.keep_labels (keep.labels), 21
[.selectall (selectall), 35 binomCI, 46
[<-.keep_labels (keep.labels), 21 binomCI (tableby.stats), 49
%in%, 59
c.yaml (yaml), 58
%nin%, 4, 59 chisq.test, 44, 47
clog (modelsum.family), 29
allNA, 4 code.chunk, 55
allNA (NA.operations), 30 code.chunk (write2.internal), 56
anova, 44, 47 comparedf, 3, 4, 9, 10, 12, 13, 15, 25, 36
anyNA, 31 comparedf.control, 4, 9, 10, 12, 13, 36
arsenal, 3 comparedf.tolerances, 12, 12
arsenal-defunct, 4 count (tableby.stats), 49
arsenal-deprecated, 5 countcellpct (tableby.stats), 49
arsenal_max (tableby.stats), 49 countN (tableby.stats), 49
arsenal_mean (tableby.stats), 49 countpct (tableby.stats), 49
arsenal_median (tableby.stats), 49 countrowpct (tableby.stats), 49
arsenal_min (tableby.stats), 49 coxph, 26, 29
arsenal_range (tableby.stats), 49
arsenal_sd (tableby.stats), 49 data.frame, 23
arsenal_sum (tableby.stats), 49 Date, 24
arsenal_table, 5, 19, 20, 27, 30, 33, 44, 49 Date.mdy, 4
arsenal_var (tableby.stats), 49 Date.mdy (mdy.Date), 23
as.countpct (tableby.stats.internal), 52 DateTimeClasses, 24
as.data.frame, 26, 32, 42 diffs, 9, 14
as.data.frame.freqlist, 6, 37 family, 29
as.data.frame.modelsum, 7, 39 formula, 26, 32, 42
as.data.frame.summary.freqlist formulize, 4, 15, 27, 33, 44
(summary.freqlist), 37 freq.control, 7, 17, 18–20, 37
as.data.frame.summary.modelsum freqlist, 3, 6, 17, 18, 19, 20, 37, 55
(summary.modelsum), 38 freqlist.internal, 17, 19, 19, 37
as.data.frame.summary.tableby
(summary.tableby), 40 glm, 26
as.data.frame.tableby, 8, 40 glm.nb, 29
as.matrix.selectall (selectall), 35 gmean (tableby.stats), 49
as.selectall (selectall), 35 gmeanCI (tableby.stats), 49
as.tbstat (tableby.stats.internal), 52 gmeansd (tableby.stats), 49

60
INDEX 61

gsd (tableby.stats), 49 medianrange (tableby.stats), 49

medSurv (tableby.stats), 49
has_strata (arsenal_table), 5 medTime (tableby.stats), 49
head, 20, 48, 49 merge, 6
head.summary.freqlist merge.arsenal_table (arsenal_table), 5
(freqlist.internal), 19 merge.freqlist, 20
head.tableby (tableby.internal), 47 merge.freqlist (arsenal_table), 5
html_document, 55 mockstudy, 4, 25
modelsum, 3, 7, 8, 26, 28–30, 38, 39, 55
includeNA, 4, 52 modelsum.control, 7, 27, 28
includeNA (NA.operations), 30 modelsum.family, 26, 29
internal.functions, 20 modelsum.internal, 27, 29, 30
iqr (tableby.stats), 49 modpval.tableby, 31, 45
is.Date, 4 modpval.tableby (tableby.internal), 47
is.Date (mdy.Date), 23 muck_up_mockstudy (mockstudy), 25
is.freqlist (freqlist.internal), 19
is.modelsum (modelsum.internal), 30 N (tableby.stats), 49
is.na, 31 n.diff.obs, 9
is.na.selectall (selectall), 35 n.diff.obs (diffs), 14
is.selectall (selectall), 35 n.diffs, 9
is.summary.freqlist n.diffs (diffs), 14
(freqlist.internal), 19 na.modelsum (modelsum.internal), 30
is.summary.modelsum NA.operations, 30
(modelsum.internal), 30 na.paired, 32
is.summary.tableby (tableby.internal), na.paired (paired.internal), 34
47 na.tableby (tableby.internal), 47
is.tableby (tableby.internal), 47 negbin (modelsum.family), 29
is.yaml (yaml), 58 Nevents (tableby.stats), 49
NeventsSurv (tableby.stats), 49
kable, 6, 36, 37, 39–41, 55 nin (%nin%), 59
keep.labels, 4, 21, 23 Nmiss (tableby.stats), 49
Nmiss2 (tableby.stats), 49
labels, 6, 22, 22 Npct (tableby.stats), 49
labels.arsenal_table (arsenal_table), 5 Nrisk (tableby.stats), 49
labels<- (labels), 22 NriskSurv (tableby.stats), 49
labels<-.arsenal_table (arsenal_table), Nsigntest (tableby.stats), 49
5
lm, 26 odt_document, 55
loosen.labels (keep.labels), 21 Ops.tableby (tableby.internal), 47
order, 49
McNemar’s test, 33 ordinal (modelsum.family), 29
mcnemar.test, 34
md_document, 55 p.adjust, 31
mdy.Date, 4, 23 padjust, 31
meanCI (tableby.stats), 49 paired, 3, 32, 33–35
meansd (tableby.stats), 49 paired.control, 32, 33, 33
meanse (tableby.stats), 49 paired.internal, 34
medianmad (tableby.stats), 49 pander_return, 55
medianq1q3 (tableby.stats), 49 pdf_document, 55
62 INDEX

polr, 29 tol.char.both (comparedf.tolerances), 12

print, 55 tol.char.case (comparedf.tolerances), 12
print.arsenal_table (arsenal_table), 5 tol.char.none (comparedf.tolerances), 12
print.comparedf (comparedf), 9 tol.char.trim (comparedf.tolerances), 12
print.summary.arsenal_table tol.date.absolute
(arsenal_table), 5 (comparedf.tolerances), 12
print.summary.comparedf tol.factor.labels
(summary.comparedf), 36 (comparedf.tolerances), 12
print.yaml (yaml), 58 tol.factor.levels
(comparedf.tolerances), 12
q1q3 (tableby.stats), 49 tol.factor.none (comparedf.tolerances),
12
reformulate, 16 tol.logical.none
relrisk, 27 (comparedf.tolerances), 12
relrisk (modelsum.family), 29 tol.NA (comparedf.tolerances), 12
render, 55 tol.num.absolute
replace, 21 (comparedf.tolerances), 12
replace2 (internal.functions), 20 tol.num.pct (comparedf.tolerances), 12
rowbinomCI (tableby.stats), 49 tol.num.percent (comparedf.tolerances),
rtf_document, 55 12
tol.other.none (comparedf.tolerances),
selectall, 33, 35, 44 12
set_attr (labels), 22
set_labels (labels), 22 verbatim, 55
signed rank test, 33 verbatim (write2.internal), 56
smart.split, 6, 39, 41
smart.split (internal.functions), 20 wilcox.test, 34, 46
sort, 20, 49 word_document, 55
sort.freqlist (freqlist.internal), 19 write2, 3, 53, 56, 57, 59
sort.tableby (tableby.internal), 47 write2.internal, 56
summary.comparedf, 9, 12, 15, 36 write2html, 3, 55
summary.freqlist, 17, 19, 20, 37 write2html (write2specific), 57
summary.modelsum, 8, 27, 29, 38 write2pdf, 3, 55
summary.tableby, 34, 40, 44, 45, 47, 49 write2pdf (write2specific), 57
survival (modelsum.family), 29 write2specific, 57
write2word, 3, 55
table, 19, 37 write2word (write2specific), 57
tableby, 3, 8, 33–35, 40, 41, 42, 44, 47–49, 55
tableby.control, 8, 34, 41, 43, 44, 44, 49, xtable, 55
52, 53 xtabs, 19, 37
tableby.internal, 35, 44, 47 xtfrm.tableby (tableby.internal), 47
tableby.stats, 47, 49
yaml, 58
tableby.stats.internal, 52
tail, 20, 48, 49
tail.summary.freqlist
(freqlist.internal), 19
tail.tableby (tableby.internal), 47
tests (tableby.internal), 47
tests.tableby, 31