Overview
To enable the printing methods defined in this package, just
library(printr) or loadNamespace('printr') in
a code chunk (in the beginning) of your knitr document.
Then some objects will be printed differently with what you would have
seen in a normal R console. For example:
- matrices, data frames, and contingency tables are printed as tables
(LaTeX, HTML, or Markdown, depending on your output format)
- the help page (from
?foo or help(foo)) can
be rendered as HTML, LaTeX, or plain text, and you can also specify
which section(s) of the help page to include in the output
- the results from
browseVignettes(),
help.search(), data(), and
vignette() are rendered as tables
- the package information from
library(help = 'foo') is
rendered as plain text
To disable the printing methods in this package, you can call
detach('package:printr', unload = TRUE) if you
attached the package via library(printr) before,
or unloadNamespace('printr') if you loaded it via
loadNamespace('printr').
This package aims to be portable in the sense that it should work in
most document formats, including *.Rnw (R + LaTeX),
*.Rmd (R Markdown), and *.Rhtml (R + HTML)
files, etc.
You can find the package source as well as installation instructions
on Github, and you are
welcome to contribute code via pull requests, or file feature requests
and bug reports via Github issues.
Examples
First we take a look at a quick example of printing some R objects in
the R console:
> # R uses plain text representation for data frames/matrices/...
> head(mtcars)
mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
Then we attach the printr package in this R session,
and see how things change later:
## Registered S3 method overwritten by 'printr':
## method from
## knit_print.data.frame rmarkdown
Matrices/data frames/tables
Matrices and data frames are printed as tables using the
kable() function in knitr:
options(digits = 4)
set.seed(123)
x = matrix(rnorm(40), 5)
x
| -0.5605 |
1.7151 |
1.2241 |
1.7869 |
-1.0678 |
-1.6867 |
0.4265 |
0.6886 |
| -0.2302 |
0.4609 |
0.3598 |
0.4979 |
-0.2180 |
0.8378 |
-0.2951 |
0.5539 |
| 1.5587 |
-1.2651 |
0.4008 |
-1.9666 |
-1.0260 |
0.1534 |
0.8951 |
-0.0619 |
| 0.0705 |
-0.6869 |
0.1107 |
0.7014 |
-0.7289 |
-1.1381 |
0.8781 |
-0.3060 |
| 0.1293 |
-0.4457 |
-0.5558 |
-0.4728 |
-0.6250 |
1.2538 |
0.8216 |
-0.3805 |
# with colunm names
dimnames(x) = list(NULL, head(LETTERS, ncol(x)))
x
| -0.5605 |
1.7151 |
1.2241 |
1.7869 |
-1.0678 |
-1.6867 |
0.4265 |
0.6886 |
| -0.2302 |
0.4609 |
0.3598 |
0.4979 |
-0.2180 |
0.8378 |
-0.2951 |
0.5539 |
| 1.5587 |
-1.2651 |
0.4008 |
-1.9666 |
-1.0260 |
0.1534 |
0.8951 |
-0.0619 |
| 0.0705 |
-0.6869 |
0.1107 |
0.7014 |
-0.7289 |
-1.1381 |
0.8781 |
-0.3060 |
| 0.1293 |
-0.4457 |
-0.5558 |
-0.4728 |
-0.6250 |
1.2538 |
0.8216 |
-0.3805 |
# further customization via kable(), e.g. digits and captions
knitr::kable(x, digits = 2, caption = 'A table produced by printr.')
A table produced by printr.
| -0.56 |
1.72 |
1.22 |
1.79 |
-1.07 |
-1.69 |
0.43 |
0.69 |
| -0.23 |
0.46 |
0.36 |
0.50 |
-0.22 |
0.84 |
-0.30 |
0.55 |
| 1.56 |
-1.27 |
0.40 |
-1.97 |
-1.03 |
0.15 |
0.90 |
-0.06 |
| 0.07 |
-0.69 |
0.11 |
0.70 |
-0.73 |
-1.14 |
0.88 |
-0.31 |
| 0.13 |
-0.45 |
-0.56 |
-0.47 |
-0.63 |
1.25 |
0.82 |
-0.38 |
| Mazda RX4 |
21.0 |
6 |
160 |
110 |
3.90 |
2.620 |
16.46 |
0 |
1 |
4 |
4 |
| Mazda RX4 Wag |
21.0 |
6 |
160 |
110 |
3.90 |
2.875 |
17.02 |
0 |
1 |
4 |
4 |
| Datsun 710 |
22.8 |
4 |
108 |
93 |
3.85 |
2.320 |
18.61 |
1 |
1 |
4 |
1 |
| Hornet 4 Drive |
21.4 |
6 |
258 |
110 |
3.08 |
3.215 |
19.44 |
1 |
0 |
3 |
1 |
| Hornet Sportabout |
18.7 |
8 |
360 |
175 |
3.15 |
3.440 |
17.02 |
0 |
0 |
3 |
2 |
| Valiant |
18.1 |
6 |
225 |
105 |
2.76 |
3.460 |
20.22 |
1 |
0 |
3 |
1 |
| 5.1 |
3.5 |
1.4 |
0.2 |
setosa |
| 4.9 |
3.0 |
1.4 |
0.2 |
setosa |
| 4.7 |
3.2 |
1.3 |
0.2 |
setosa |
| 4.6 |
3.1 |
1.5 |
0.2 |
setosa |
| 5.0 |
3.6 |
1.4 |
0.2 |
setosa |
| 5.4 |
3.9 |
1.7 |
0.4 |
setosa |
| 4.6 |
3.4 |
1.4 |
0.3 |
setosa |
| 5.0 |
3.4 |
1.5 |
0.2 |
setosa |
| 4.4 |
2.9 |
1.4 |
0.2 |
setosa |
| 4.9 |
3.1 |
1.5 |
0.1 |
setosa |
For contingency tables, 1-d tables are printed as a 1-row matrix, 2-d
tables are printed an n × m matrix, and tables of
higher dimensions are printed as data frames with frequencies.
x1 = sample(letters[1:3], 1000, TRUE)
x2 = sample(letters[1:3], 1000, TRUE)
x3 = sample(letters[1:3], 1000, TRUE)
table(x1)
| a |
103 |
109 |
108 |
| b |
108 |
115 |
108 |
| c |
123 |
103 |
123 |
| a |
a |
a |
41 |
|
|
b |
26 |
|
|
c |
36 |
|
b |
a |
34 |
|
|
b |
31 |
|
|
c |
44 |
|
c |
a |
34 |
|
|
b |
33 |
|
|
c |
41 |
| b |
a |
a |
37 |
|
|
b |
36 |
|
|
c |
35 |
|
b |
a |
40 |
|
|
b |
31 |
|
|
c |
44 |
|
c |
a |
36 |
|
|
b |
38 |
|
|
c |
34 |
| c |
a |
a |
31 |
|
|
b |
46 |
|
|
c |
46 |
|
b |
a |
25 |
|
|
b |
35 |
|
|
c |
43 |
|
c |
a |
46 |
|
|
b |
46 |
|
|
c |
31 |
Search results from help.search()
Here are some examples demonstrating the results of
help.search(), or you can also use ?? to
search for a string.
| grDevices |
xyTable |
Multiplicities of (x,y) Points, e.g., for a Sunflower
Plot |
| graphics |
sunflowerplot |
Produce a Sunflower Scatter Plot |
help.search('contourplot')
| graphics |
filled.contour |
Level (Contour) Plots |
| lattice |
levelplot |
Level plots and contour plots |
| lattice |
panel.levelplot |
Panel Functions for levelplot and contourplot |
help.search('foo', package = 'base')
| base |
is.things |
Explore some properties of R objects and is.FOO()
functions. Not for newbies! |
help.search('foooooooo', package = 'utils')
## No results found
In a normal R session, the results will be displayed as an HTML page
by default, but normally these functions are meant to be called in an
interactive R session, and knitr documents are often
compiled in non-interactive R sessions, so we changed the printing
behavior of these results, and readers will get the basic idea of these
functions when reading the knitr output. If they want
to run these functions by themselves, they can do it in an interactive R
session.
Help pages
When you want to read the help page of a certain R object, you
normally use ? or help(), which will launch a
separate help page from the R session, and require human interaction.
Again, we may not desire human interactions in knitr
documents, so the help pages are printed as static documents here.
Extract Model Coefficients
Description
coef is a generic function which extracts model coefficients
from objects returned by modeling functions. coefficients is
an alias for it.
Usage
coef(object, ...)
coefficients(object, ...)
## Default S3 method:
coef(object, complete = TRUE, ...)
## S3 method for class 'aov'
coef(object, complete = FALSE, ...)
Arguments
object |
an object for which the extraction of model coefficients is
meaningful.
|
complete |
for the default (used for lm, etc) and
aov methods:
logical indicating if the full coefficient vector should be returned
also in case of an over-determined system where some coefficients
will be set to NA, see also alias. Note
that the default differs for lm() and
aov() results.
|
... |
other arguments.
|
Details
All object classes which are returned by model fitting functions
should provide a coef method or use the default one.
(Note that the method is for coef and not coefficients.)
The "aov" method does not report aliased coefficients (see
alias) by default where complete = FALSE.
The complete argument also exists for compatibility with
vcov methods, and coef and aov methods for
other classes should typically also keep the complete = *
behavior in sync. By that, with p <- length(coef(obj, complete = TF)),
dim(vcov(obj, complete = TF)) == c(p,p) will be fulfilled for both
complete settings and the default.
Value
Coefficients extracted from the model object object.
For standard model fitting classes this will be a named numeric vector.
For "maov" objects (produced by aov) it will be a matrix.
References
Chambers, J. M. and Hastie, T. J. (1992)
Statistical Models in S.
Wadsworth & Brooks/Cole.
See Also
fitted.values and residuals for related methods;
glm, lm for model fitting.
Examples
x <- 1:5; coef(lm(c(1:3, 7, 6) ~ x))
When help pages are really long, we can use the chunk option
printr.help.sections to select a few sections to display,
e.g. we only show the sections description and
usage of the paste() function:
Concatenate Strings
Description
Concatenate vectors after converting to character.
Concatenation happens in two basically different ways, determined by
collapse being a string or not.
Usage
paste (..., sep = " ", collapse = NULL, recycle0 = FALSE)
paste0(..., collapse = NULL, recycle0 = FALSE)
Vignette/dataset lists
We can print the lists of vignettes and datasets in packages using
vignette() and data(), respectively.
vignette(package = 'rpart')
Vignettes in rpart
| longintro |
Introduction to Rpart (source, pdf) |
| usercode |
User Written Split Functions (source, pdf) |
vignette(package = c('rpart', 'knitr'))
Vignettes
| rpart |
longintro |
Introduction to Rpart (source, pdf) |
| rpart |
usercode |
User Written Split Functions (source, pdf) |
| knitr |
knitr-html |
An R HTML Vignette with knitr (source, html) |
| knitr |
knit_print |
Custom Print Methods (source, html) |
| knitr |
datatables |
Display Tables with the JavaScript Library DataTables
(source, html) |
| knitr |
knitr-intro |
Not an Introduction to knitr (source, html) |
| knitr |
knitr-markdown |
R Markdown Vignettes with litedown (source, html) |
| knitr |
docco-classic |
R Markdown with the Docco Classic Style (source,
html) |
| knitr |
docco-linear |
R Markdown with the Docco Linear Style (source,
html) |
| knitr |
knit_expand |
Templating with knit_expand() (source, html) |
| knitr |
knitr-refcard |
knitr Reference Card (source, html) |
data(package = 'lattice')
Data sets in lattice
| barley |
Yield data from a Minnesota barley trial |
| environmental |
Atmospheric environmental conditions in New York
City |
| ethanol |
Engine exhaust fumes from burning ethanol |
| melanoma |
Melanoma skin cancer incidence |
| singer |
Heights of New York Choral Society singers |
| USMortality |
Mortality Rates in US by Cause and Gender |
| USRegionalMortality |
Mortality Rates in US by Cause and Gender |
data(package = c('rpart', 'lattice'))
Data sets
| rpart |
car.test.frame |
Automobile Data from ‘Consumer Reports’ 1990 |
| rpart |
car90 |
Automobile Data from ‘Consumer Reports’ 1990 |
| rpart |
cu.summary |
Automobile Data from ‘Consumer Reports’ 1990 |
| rpart |
kyphosis |
Data on Children who have had Corrective Spinal
Surgery |
| rpart |
solder |
Soldering of Components on Printed-Circuit Boards |
| rpart |
solder.balance (solder) |
Soldering of Components on Printed-Circuit Boards |
| rpart |
stagec |
Stage C Prostate Cancer |
| lattice |
barley |
Yield data from a Minnesota barley trial |
| lattice |
environmental |
Atmospheric environmental conditions in New York
City |
| lattice |
ethanol |
Engine exhaust fumes from burning ethanol |
| lattice |
melanoma |
Melanoma skin cancer incidence |
| lattice |
singer |
Heights of New York Choral Society singers |
| lattice |
USMortality |
Mortality Rates in US by Cause and Gender |
| lattice |
USRegionalMortality |
Mortality Rates in US by Cause and Gender |
data(package = 'knitr') # no datasets here
## Data sets not found
browseVignettes(package = 'knitr')
| knitr-html.html |
An R HTML Vignette with knitr |
| knit_print.html |
Custom Print Methods |
| datatables.html |
Display Tables with the JavaScript Library
DataTables |
| knitr-intro.html |
Not an Introduction to knitr |
| knitr-markdown.html |
R Markdown Vignettes with litedown |
| docco-classic.html |
R Markdown with the Docco Classic Style |
| docco-linear.html |
R Markdown with the Docco Linear Style |
| knit_expand.html |
Templating with knit_expand() |
| knitr-refcard.html |
knitr Reference Card |
Package info
A description of a package can be printed via
library(help = 'foo'):
Information on package 'printr'
Description:
Package: printr
Type: Package
Title: Automatically Print R Objects to Appropriate Formats According to the
'knitr' Output Format
Version: 0.3.1
Authors@R: c( person("Yihui", "Xie", role = c("aut", "cre"), email =
"[email protected]", comment = c(ORCID = "0000-0003-0645-5666")) )
Description: Extends the S3 generic function knit_print() in 'knitr' to
automatically print some objects using an appropriate format such as
Markdown or LaTeX. For example, data frames are automatically printed
as tables, and the help() pages can also be rendered in 'knitr'
documents.
Imports: knitr (>= 1.31)
Suggests: tools, rmarkdown
License: GPL
URL: https://yihui.org/printr/
BugReports: https://github.com/yihui/printr/issues
VignetteBuilder: knitr
RoxygenNote: 7.2.3
Encoding: UTF-8
Repository: https://yihui.r-universe.dev
RemoteUrl: https://github.com/yihui/printr
RemoteRef: HEAD
RemoteSha: a2b5b84ba8be8903e7da6ebec96aa9e15b95f6ca
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>)
Maintainer: Yihui Xie <[email protected]>
Built: R 4.4.2; ; 2024-11-21 04:35:28 UTC; unix
Index:
printr Print R objects in 'knitr' documents nicely