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The arsenal Package

Overview

The goal of library(arsenal) is to make statistical reporting easy. It includes many functions which the useR will find useful to have in his/her "arsenal" of functions. There are, at this time, 6 main functions, documented below. Each of these functions is motivated by a local SAS macro or procedure of similar functionality.

Note that arsenal v3.0.0 is not backwards compatible with previous versions (mainly because compare() got renamed to comparedf()). See the NEWS file for more details.

arsenal now has a pkgdown site: https://mayoverse.github.io/arsenal/

The tableby() Function

tableby() is a function to easily summarize a set of independent variables by one or more categorical variables. Optionally, an appropriate test is performed to test the distribution of the independent variables across the levels of the categorical variable. Options for this function are easily controlled using tableby.control().

The tableby() output is easily knitted in an Rmarkdown document or displayed in the command line using the summary() function. Other S3 methods are implemented for objects from tableby(), including print(), [, as.data.frame(), sort(), merge(), padjust(), head(), and tail().

The paired() Function

paired() is a function to easily summarize a set of independent variables across two time points. Optionally, an appropriate test is performed to test the distribution of the independent variables across the time points. Options for this function are easily controlled using paired.control().

The paired() output is easily knitted in an Rmarkdown document or displayed in the command line using the summary() function. It has the same S3 methods as tableby(), since it's a special case of the tableby() object.

The modelsum() Function

modelsum() is a function to fit and summarize models for each independent variable with one or more response variables, with options to adjust for covariates for each model. Options for this function are easily controlled using modelsum.control().

The modelsum output is easily knitted in an Rmarkdown document or displayed in the command line using the summary() function. Other S3 methods are implemented for objects from modelsum(), including print(), [, as.data.frame(), and merge().

The freqlist() Function

freqlist() is a function to approximate the output from SAS's PROC FREQ procedure when using the /list option of the TABLE statement. Options for this function are easily controlled using freq.control().

The freqlist() output is easily knitted in an Rmarkdown document or displayed in the command line using the summary() function. Other S3 methods are implemented for objects from freqlist(), including print(), [, as.data.frame(), sort(), and merge(). Additionally, the summary() output can be used with head() or tail().

The comparedf() Function

comparedf() compares two data.frames and reporting any differences between them, much like SAS's PROC COMPARE procedure.

The comparedf() output is easily knitted in an Rmarkdown document or displayed in the command line using the summary() function. Other S3 methods are implemented for objects of class "comparedf", including print(), n.diffs(), n.diff.obs(), and diffs().

The write2*() Family of Functions

write2word(), write2pdf(), and write2html() are functions to output a table into a document, much like SAS's ODS procedure. The S3 method behind them is write2(). There are methods implemented for tableby(), modelsum(), freqlist(), and comparedf(), and also methods for knitr::kable(), xtable::xtable(), and pander::pander_return(). Another option is to coerce an object using verbatim() to print out the results monospaced (as if they were in the terminal)--the default method does this automatically. To output multiple tables into a document, simply make a list of them and call the same function as before. A YAML header can be added using yaml(). Code chunks can be written using code.chunk().

For more information, see vignette("write2").

Other Notable Functions

  • keep.labels() keeps the 'label' attribute on an R object when subsetting. loosen.labels() allows the labels to drop again.

  • formulize() is a shortcut to collapse variable names into a formula.

  • mdy.Date() and Date.mdy() convert numeric dates for month, day, and year to Date object, and vice versa.

  • is.Date: tests if an object is a date.

  • %nin% tests for "not in", the negation of %in%.

  • allNA() tests for all elements being NA, and includeNA() makes NAs explicit values.

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Version

Install

install.packages('arsenal')

Monthly Downloads

8,569

Version

3.6.3

License

GPL (>= 2)

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Maintainer

Last Published

June 4th, 2021

Functions in arsenal (3.6.3)

formulize

formulize
%nin%

Not in
padjust

Adjust P-values for Multiple Comparisons
internal.functions

Internal Functions
paired

Summary Statistics of a Set of Independent Variables Paired Across Two Timepoints
arsenal

An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
diffs

Extract differences
paired.internal

Helper functions for paired
comparedf.tolerances

comparedf tolerances
paired.control

Control settings for paired function
keep.labels

Keep Labels
summary.tableby

The summary method for a tableby object
labels

Labels
mdy.Date

Convert numeric dates to Date object, and vice versa
freqlist.internal

Helper functions for freqlist
modelsum

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

freqlist
modelsum.control

Control settings for modelsum function
tableby.stats

tableby Summary Statistics Functions
tableby.stats.internal

Internal tableby functions
mockstudy

Mock study data for examples
tableby.internal

Helper functions for tableby
tableby.control

Control settings for tableby function
freq.control

Control settings for freqlist function
selectall

Make a column for "select all" input
write2

write2
write2.internal

Helper functions for write2
summary.comparedf

The summary method for a comparedf object
modelsum.internal

Helper functions for modelsum
summary.modelsum

Summarize a modelsum object.
summary.freqlist

summary.freqlist
modelsum.family

Family functions for modelsum
tableby

Summary Statistics of a Set of Independent Variables by a Categorical Variable
yaml

Include a YAML header in write2
write2specific

write2word, write2html, write2pdf
arsenal-defunct

Defunct functions in arsenal
as.data.frame.tableby

as.data.frame.tableby
comparedf.control

Control settings for comparedf function
as.data.frame.freqlist

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

as.data.frame.modelsum
NA.operations

Some functions to handle NAs
comparedf

Compare two data.frames and report differences
arsenal-deprecated

Deprecated functions in arsenal
arsenal_table

arsenal tables with common structure