The vtable
package serves the purpose of outputting automatic variable documentation that can be easily viewed while continuing to work with data.
vtable
contains four main functions: vtable()
(or vt()
), sumtable()
(or st()
), labeltable()
, and dftoHTML()
/dftoLaTeX()
. This vignette focuses on vtable()
.
vtable()
takes a dataset and outputs a formatted variable documentation file. This serves several purposes.
First, it allows for an easy generation of a variable documentation file, without requiring that one has already been created and made accessible through help(data)
, or dealing with creating and finding R help documentation files.
Second, it produces a list of variables (and, if provided, their labels) that can be easily viewed while working with the data, preventing repeated calls to head()
, and making it much easier to work with confusingly-named variables.
Third, the variable documentation file can be opened in a browser (with option out='browser'
, saving to file and opening directly, or by opening in the RStudio Viewer pane and clicking 'Show in New Window') where it can be easily searched with standard Find-in-Page functions like Ctrl/Cmd-F, allowsing you to search for the variable or variable label you want.
vtable()
functionvtable()
(or vt()
for short) syntax follows the following outline:
vtable(data, out=NA, file=NA, labels=NA, class=TRUE, values=TRUE, missing=FALSE, index=FALSE, factor.limit=5, char.values=FALSE, data.title=NA, desc=NA, note=NA, anchor=NA, col.width=NA, col.align=NA, align=NA, note.align='l', fit.page=NA, summ=NA, lush=FALSE, opts=list())
The goal of vtable()
is to take a data set data
and output a usually-HTML (but data.frame
, kable
, csv
, and latex
options are there too) file with documentation concerning each of the variables in data
. There are several options as to what will be included in the documentation file, and each of these options are explained below. Throughout, the output will be built as kable
s since this is an RMarkdown document. However, generally you can leave out
at its default and it will publish an HTML table to Viewer (in RStudio) or the browser (otherwise). This will also include some additional information about your data that can't be demonstrated in this vignette:
data
The data
argument can take any data.frame
, data.table
, tibble
, or matrix
, as long as it has a valid set of variable names stored in the colnames()
attribute. The goal of vtable()
is to produce documentation of each of the variables in this data set and display that documentation, one variable per row on the output vtable
.
If data
has embedded variable or value labels, as the data set efc
does below, vtable()
will extract and use them automatically.
library(vtable) #Example 1, using base data LifeCycleSavings data(LifeCycleSavings) vtable(LifeCycleSavings, out='kable')
#Example 2, using efc data with embedded variable labels library(sjlabelled) data(efc) #Don't forget the handy shortcut vt()! vt(efc)
out
The out
option determines what will be done with the resulting variable documentation file. There are several options for out
:
| Option | Result |
|------------| -----------------------------------------|
| browser | Loads variable documentation in web browser. |
| viewer | Loads variable documentation in Viewer pane (RStudio only). |
| htmlreturn | Returns HTML code for variable documentation file. |
| return | Returns variable documentation table in data frame format. |
| csv | Returns variable documentatoin in data.frame format and, with a file
option, saves that to CSV. |
| kable | Returns a knitr::kable()
|
| latex | Returns a LaTeX table. |
| latexpage | Returns an independently-buildable LaTeX document. |
By default, vtable
will select 'viewer' if running in RStudio, and 'browser' otherwise. If it's being built in an RMarkdown document with knitr
, it will default to 'kable'. Note that an RMarkdown default to 'kable' will also include some nice formatting, where out = 'kable'
directly will give you a more basic kable
you can format yourself.
data(LifeCycleSavings) vtable(LifeCycleSavings) vtable(LifeCycleSavings,out='browser') vtable(LifeCycleSavings,out='viewer') htmlcode <- vtable(LifeCycleSavings,out='htmlreturn') vartable <- vtable(LifeCycleSavings,out='return') #I can easily \input this into my LaTeX doc: vt(LifeCycleSavings,out='latex',file='mytable1.tex')
file
The file
argument will write the variable documentation file to an HTML or LaTeX file and save it. Will automatically append 'html' or 'tex' filetype if the filename does not include a period.
data(LifeCycleSavings) vt(LifeCycleSavings,file='lifecycle_variabledocumentation')
labels
The labels
argument will attach variable labels to the variables in data
. If variable labels are embedded in data
and those labels are what you want, the labels
argument is unnecessary. Set labels='omit'
if there are embedded labels but you do not want them in the table.
labels
can be used in any one of three formats.
labels
as a vectorlabels
can be set to be a vector of equal length to the number of variables in data
, and in the same order. NA
values can be used for padding if some variables do not have labels.
#Note that LifeCycleSavings has five variables data(LifeCycleSavings) #These variable labels are taken from help(LifeCycleSavings) labs <- c('numeric aggregate personal savings', 'numeric % of population under 15', 'numeric % of population over 75', 'numeric real per-capita disposable income', 'numeric % growth rate of dpi') vtable(LifeCycleSavings,labels=labs)
labs <- c('numeric aggregate personal savings',NA,NA,NA,NA) vtable(LifeCycleSavings,labels=labs)
labels
as a two-column data setlabels
can be set to a two-column data set (any type will do) where the first column has the variable names, and the second column has the labels. The column names don't matter.
This approach does not require that every variable name in data
has a matching label.
#Note that LifeCycleSavings has five variables #with names 'sr', 'pop15', 'pop75', 'dpi', and 'ddpi' data(LifeCycleSavings) #These variable labels are taken from help(LifeCycleSavings) labs <- data.frame(nonsensename1 = c('sr', 'pop15', 'pop75'), nonsensename2 = c('numeric aggregate personal savings', 'numeric % of population under 15', 'numeric % of population over 75')) vt(LifeCycleSavings,labels=labs)
labels
as a one-row data setlabels
can be set to a one-row data set in which the column names are the variable names in data
and the first row is the variable names. The labels
argument can take any data type including data frame, data table, tibble, or matrix, as long as it has a valid set of variable names stored in the colnames()
attribute.
This approach does not require that every variable name in data
has a matching label.
#Note that LifeCycleSavings has five variables #with names 'sr', 'pop15', 'pop75', 'dpi', and 'ddpi' data(LifeCycleSavings) #These variable labels are taken from help(LifeCycleSavings) labs <- data.frame(sr = 'numeric aggregate personal savings', pop15 = 'numeric % of population under 15', pop75 = 'numeric % of population over 75') vtable(LifeCycleSavings,labels=labs)
class
The class
flag will either report or not report the class of each variable in the resulting variable table. By default this is set to TRUE
.
values
The values
flag will either report or not report the values that each variable takes. Numeric variables will report a range, logicals will report 'TRUE FALSE', and factor variables will report the first factor.limit
(default 5) factors listed.
If the variable is numeric but has value labels applied by the sjlabelled
package, vtable()
will find them and report the numeric-label crosswalk.
data(LifeCycleSavings) vtable(LifeCycleSavings,values=FALSE) vtable(LifeCycleSavings) #CO2 contains factor variables data(CO2) vtable(CO2)
#efc contains labeled values #Note that the original value labels do not easily tell you what numerical #value each label maps to, but vtable() does. library(sjlabelled) data(efc) vtable(efc)
missing
The missing
flag, set to TRUE, will report the number of missing values in each variable. Defaults to FALSE.
index
The index
flag will either report or not report the index number of each variable. Defaults to FALSE.
factor.limit
If values
is set to TRUE
, then factor.limit
limits the number of factors displayed on the variable table. factor.limit
is by default 5, to cut down on clutter. The table will include the phrase "and more" to indicate that some factors have been cut off.
Setting factor.limit=0
will include all factors. If values=FALSE
, factor.limit
does nothing.
char.values
If values
is set to TRUE
, then char.values = TRUE
instructs vtable
to list the values that character variables take, as though they were factors. If you only want some of the character variables to have their values listed, use a character vector to indicate which variables.
data(USJudgeRatings) USJudgeRatings$Judge <- row.names(USJudgeRatings) USJudgeRatings$SecondCharacter <- 'Less Interesting' USJudgeRatings$ThirdCharacter <- 'Less Interesting Still!' #Show values for all character variables vtable(USJudgeRatings,char.values=TRUE) #Or just for a subset vtable(USJudgeRatings,char.values=c('Judge','SecondCharacter'))
data.title
, desc
, note
, and anchor
data.title
will include a data title in the variable documentation file. If not set manually, this will default to the variable name for data
.
desc
will include a description of the data set in the variable documentation file. This will by default include information on the number of observations and the number of columns. To remove this, set desc='omit'
, or include any description and then include 'omit' as the last four characters.
note
will add a table note in the last row. note.align
determines its left/right/center alignment, but is only used with LaTeX (see below).
anchor
will add an anchor ID (<a name =
in HTML or \label{}
in LaTeX) to allow other parts of your document to link to it, if you are including your vtable
in a larger document.
data.title
and desc
will only show up in full-page vtable
s. That is, you won't get them with out = 'return'
, out = 'csv'
, or out = 'latex'
(although out = 'latexpage'
works). note
and anchor
will only show up in formats that support multi-column cells and anchoring, so they won't work with out = 'return'
or out = 'csv'
.
out = 'kable'
is a half-exception in that it will use data.title
as the caption for the kable
, and will use the note
as a footnote, but won't use desc
or anchor
.
library(vtable) data(LifeCycleSavings) vtable(LifeCycleSavings) vtable(LifeCycleSavings,data.title='Intercountry Life-Cycle Savings Data', desc='omit') vtable(LifeCycleSavings,data.title='Intercountry Life-Cycle Savings Data', desc='Data on the savings ratio 1960–1970. omit') vtable(LifeCycleSavings,data.title='Intercountry Life-Cycle Savings Data', desc='Data on the savings ratio 1960–1970', note='Data from Belsley, Kuh, and Welsch (1980)')
col.width
vtable()
will select default column widths for the variable table depending on which measures (name, class, label, values, summ)
are included. col.width
, as a vector of percentage column widths on the 0-100 scale, will override these defaults.
library(sjlabelled) data(efc) #The variable names in this data set are pretty short, and the value labels are #a little cramped, so let's move that over. vtable(efc,col.width=c(10,10,40,40))
col.align
col.align
can be used to adjust text alignment in HTML output. Set to 'left', 'right', or 'center' to align all columns, or give a vector of column alignments to do each column separately.
If you want to get tricky, you can add a semicolon afterwards and keep putting in whatever CSS attributes you want. They will be applied to the whole column.
This option is only for HTML output and will only work with out
values of 'browser', 'viewer', or 'htmlreturn'.
library(sjlabelled) data(efc) vtable(efc,col.align = 'right')
align
, note.align
, and fit.page
These options are used only with LaTeX output (out
is 'latex' or 'latexpage').
align
and note.align
are single strings used for alignment. align
will be used as column alignment in standard LaTeX syntax, for example 'lccc' for the left column left-aligned and the other three centered. note.align
is an alignment note specifically for any table notes set with note
(or significance stars), which enters as part of a \multicolumn
argument. These both accept 'p{}' and other LaTeX column types.
Defaults to left-aligned 'Variable' columns and right-aligned everything else. If col.widths
is specified, align
defaults to 'p{}' columns, with widths set by col.width
.
fit.page
can be used to ensure that the table is a certain width, and will be used as an entry to a \resizebox{}
. Set to \\textwidth
to set the table to text width, or .9\\textwidth
for 90% of the page, and so on, or any recognized width value in LaTeX.
For all of these, be sure to escape special characters, in particular backslashes.
library(sjlabelled) data(efc) vtable(efc,align = 'p{.3\\textwidth}cc', fit.page = '\\textwidth', out = 'latex')
summ
summ
will calculate summary statistics for all variables that report valid output on the given summary statistics functions. summ
is very flexible. It takes a character vector in which each element is of the form function(x)
, where function(x)
is any function that takes a vector and returns a single numeric value. For example, summ=c('mean(x)','median(x)','mean(log(x))')
would calculate the mean, median, and mean of the log for each variable.
summ
treats as special two vtable
functions: propNA(x)
and countNA(x)
, which give the proportion and count of NA values, and the count of non-NA values in the variable, respectively. These two functions are always reported first, and are the only functions that include NA values in their calculations.
library(sjlabelled) data(efc) vtable(efc,summ=c('mean(x)','countNA(x)'))
lush
The default vtable
settings may not be to your liking, and in particular you may prefer more information. Setting lush = TRUE
is an easy way to get more information. It will force char.values
and missing
to TRUE
, and will also set a default summ
value of c('mean(x)', 'sd(x)', 'nuniq(x)')
.
opts
You can create a named list where the names are the above options and the values are the settings for those options, and input it into vtable
using opts=
. This is an easy way to set the same options for many vtable
s.
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