yihui / printr

Some (magical) printing methods for knitr

printr

This is a companion package to knitr. Its main purpose is to extend the S3 generic function knit_print() in knitr, which is the default value of the chunk option render, as explained in the vignette knit_print.html.

You can install the stable version from CRAN or the development version from my personal repo:

# CRAN version
install.packages('printr')

# or the dev version
install.packages(
  'printr',
  repos = c('https://yihui.r-universe.dev', 'https://cran.rstudio.com')
)

To enable the printing methods defined in this package, just library(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

For more information, please check out the package vignette:

vignette('printr', package = 'printr')

You are welcome to contribute more S3 methods to this package, and you may want to read the existing methods in this package before you get started. In most cases, I guess you will end up rendering either plain text (see knit_print.packageInfo for example) or tables (see knit_print.matrix) in the output.

printr's Issues

Response.name for high-dimensional tables

Thanks for the useful package. I'm printing a 3-dimensional table as the result of prop.table() call. In the code, as.data.table() is called for high-dimensional tables, which uses response.name= "Freq" by default. "Freq" response name is misleading in my case, but I don't think there is a way to change it.

Support for matrices

I can't seem to get matrices to print with this package. Everything works fine for dataframes, ?foo, etc, but not matrices. The screenshot summarizes the situation.

support for multiway table?

printr gives beautiful output for table(). Is there any plan for supporting multi-way table generated by ftable()?

An RMD example:

---
title: "Untitled"
author: ""
date: ""
output: pdf_document

---


```{r, echo=FALSE}
library(knitr)
library(printr)
table(mtcars[c("cyl", "vs", "am", "gear")])
ftable(mtcars[c("cyl", "vs", "am", "gear")],
       row.vars = 1:3)
```  ```

knit_print is not the default currently

This is just a minor note, but render currently defaults to NULL, not to knit_print as you say here and in the vignette. You do a bit of black magic for htmlwidgets, before passing things along to knit_print. Or maybe it's not black magic, but it tripped me up when I tried to handle things with pander where possible.

support for DT

It would be great to have printr's magic work with the elegant jquery tables from the DT package for HTML documents...

http://rstudio.github.io/DT/

vignette not included

I know where to find the vignette, but it is not included in the distribution (0.0.6). So the mentioned

vignette('printr', package = 'printr')

does not work

Use repr instead

Instead of reproducing everything repr has been doing for a long time, knit_print should use repr instead of this.

knit_print.help_files_with_topic

see http://www.noamross.net/blog/2013/6/18/helpconsoleexample.html

also help.search()

also http://stackoverflow.com/q/24146843/559676

Offer a way to use paged_table() feature from R Markdown within Quarto

See this discussion: quarto-dev/quarto-cli#933 (reply in thread)

df_print is not a Quarto feature. But while writing an example on how it would work, I am wondering if we should not adapa printr package to allow opt-in some mechanism for chunk.

Currently printr only modifies by default the method knit_print but we could offer other mechanism.

For example this is an example of creating a df_print chunk option

```{r}
kable_print <- function(x, options) {
  knitr::asis_output(
    paste(c("", "", knitr::kable(x)), collapse = "\n")
  )
}

paged_print <- function(x, options) {
  knitr::asis_output(
    rmarkdown:::paged_table_html(x, options = attr(
      x,
      "options"
    )),
    meta = list(dependencies = rmarkdown::html_dependency_pagedtable())
  )
}

knitr::opts_hooks$set(df_print = function(options) {
  if (options$df_print == "paged") {
    options$render = paged_print
  } else if (options$df_print == "kable") {
    options$render = kable_print
  }
  options
})

```

```{r, df_print = "paged"}
iris
```

```{r, df_print = "kable"}
head(iris)
```

```{r}
head(iris)
```

This works well within Quarto. As other option described in quarto-dev/quarto-cli#933 (reply in thread)

This is to share some thoughts and idea. I think there is some useful change we could do.

Anyway, main addition in printr would be a knit_print method for paged_df maybe.

Make functionality modular

Thanks for this nice package. I am a teacher mainly interested in including sections of help pages in my xaringan presentations so that I can explain functions to students. However, I still want my tibbles printed in the regular way. Could you make the functionality modular so that we can choose what gets pretty-printed?

error installing printr on R 3.3.0

Hi, after upgrading from R 3.2 to 3.3.0 I am no longer able to install your readr.
Is there any workaround this?

install.packages('printr')
Installing package into ‘C:/Users/lucas_000/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘printr’ is not available (for R version 3.3.0)

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252   
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_3.3.0

compatibility with microbenchmark

I cannot make printr and microbenchmark work well together. For example:

---
title: "test"
author: "Ignacio"
output: html_document

---

```{r}
library(printr)
library(microbenchmark)
a1 <- a2 <- a3 <- a4 <- numeric(0)

res <- microbenchmark(a1 <- c(a1, 1),
                      a2 <- append(a2, 1),
                      a3[length(a3) + 1] <- 1,
                      a4[[length(a4) + 1]] <- 1,
                      times=100L)
tbl<-print(res)
tbl
```

Prints the table twice, once with good formatting and one without. If i change

tbl<-print(res)
tbl

to just

print(res)

I get the table without formatting.

Thanks!

named index of data.frame

---
title: "Untitled"
author: "Andrew Tang"
date: "2016/10/4"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(printr)
```

```{r}
iris['Sepal.Length']
```

In the knit HTML result, Sepal.Length will be a title.

Unable to successfully utilize the help method in printr -- clarification appreciated

code.txt
code.pdf

Plan to upload printr to CRAN?

Is there a plan to upload the printr package to CRAN?

Add GHA workflow for testing

With Quarto it is possible that this package will be used more (to replace df_print for example).
quarto-dev/quarto-cli#933 (comment)

I forgot to add the usual infrastructure in this one, so Travis is failing and needs to be replaced.

format 1-dim table in multiple lines

How to fit the table output according to the page width when using printr table function?

table(sample(stringi::stri_rand_strings(20, 3), 200, replace = TRUE))

The output of the above code exceeds the page width. How to print the table into multiple lines if the width is exceeding the page width?

• setting the width options(width = 10) did not help either.

Limit table size in latex

I would like an option to limit the maximum rows/cols for latex output. An option similar to options(dplyr.print_max = 10) would be good. There should be some indication of how many rows & columns are omitted, similar to the tibble string output.

I have a few tables with hundreds of rows and columns. In the notebook preview these print nicely as tibble truncated tables (10 rows max), but when rendered to PDF I get pages of tables which also overflow the right margin.

Error when printing summary for a data frame variable

my.data <- data.frame(a= 1:3, b= 4:6)

summary(my.data$a)

I'm getting this error when running the above code:

'dimnames' applied to non-array

Running summary on the data frame itself works properly.

Markdown violation

As I mentioned in another Issue, I don't like the TOC at the very vignette beginning.

To circumvent that, I am customizing the style sheet and using the following markup pattern where I want the TOC:

<div id="TOC">
<div class="toctitle">Table of Contents </div>
- [Digesting the Image Samples](#digest)
- [Getting the Computed Values](#result)
  * [Variance Result](#var)
  * [Covariance Result](#cov)
- [Introduction to Model Fitting](#intro-fit)  
</div>

However , the inner list (with the "Variance.." and "Covariance..." items), is ignored in the final html. They appear at the same level as the other LI items and not inside their own UL tag list.

I have to add "manual" UL tags to circumvent his:

<div id="TOC">
<div class="toctitle">Table of Contents </div>
- [Digesting the Image Samples](#digest)
- [Getting the Computed Values](#result)
<ul>
  * [Variance Result](#var)
  * [Covariance Result](#cov)
</ul>
- [Introduction to Model Fitting](#intro-fit)  
</div>

Thanks in advance.

kable() and the margin of the page

Hy all!

I want to control the way the table is printed using the kable function().

Instead of printing like this: (Because I don't like the extra space between columns)

I would like to print like this:

I saw that depending on the template, the output of kable is different. How can I control it?

Thanks in advance,
Guilherme

automatic table numbering does not work for default html format

Table numbering with table caption works for PDF and html_vignette format, but not for default html format. Also, the table caption is some light grey color, instead of black as in html_vignette format.

1-dim table with caption

I have seen #15 how to print a caption with table, but I did not find a solution how to add a caption to a simple 1-dim table when printr is loaded.

This gives a subscript error

x1 = sample(letters[1:3], 1000, TRUE)
kable(table(x1), caption = "...")
table(x1)  # nice printout with knitr, but no caption

Help pages rendered as code block in knit to pdf

Help pages are rendered as a code block in knit to pdf, whereas for knit to html, the proper page is displayed. Is there any way to get similar result in pdf ?

print.summary.lm method

Hi,

A print.summary.lm method would be amazing.

I am using summary(x)$coef right now, which also works nicely, just as with kable but much cleaner!

However, eventually there might be value in creating a specific method method such that you could simple enter:

<<model1>>=
summary(lm(y ~ X, data=df))
@

Which would then print a formatted table.

Thanks!

Positioning the TOC

It would be great if it were possible to select were the TOC will appear.

I like to show the TOC after a brief introduction, the same style used by wikipedia. That way, the items in the TOC makes more sense to the primer.

This post is about an enhancement, but I don't know how to classify it that way.

package ‘printr’ is not available (for R version 3.0.2)

How can I install the package printr for R version 3.0.2?

prints complete table with data.table when update by reference

---
title: "copy this into a Rmd"
author: "Henk Harmsen"
date: "September 10, 2015"
output: html_document

---

```{r}
library(data.table)

data(mtcars)
df = data.table(mtcars)
```

this works, no intention to print/head table:

```{r}
df[, mpg2 := mpg * 2]
```

but after loading printr, update by reference prints out the whole table:

```{r}
library(printr)
df[, mpg3 := mpg2 / 2]
```

printr doesn't work when used outside RStudio

If I run this from the terminal

curl https://raw.githubusercontent.com/yihui/printr/master/vignettes/printr.Rmd > /tmp/printr.Rmd; Rscript -e 'library(knitr); library(printr); knit2html("/tmp/printr.Rmd")'

the file produced doesn't have the pretty tables

However, I knit the vignette in RStudio it works fine.

Grouped tibble (`grouped_df`) is not handled by printr

Tibbles do not render correctly all the time when printr is used. If they are grouped, they are rendered as plain text.

Versions:

• printr 0.1
• knitr 1.20

Below is a reproducible example:

library(dplyr)
library(printr)

Normal tibble is rendered as table

mtcars %>% head

	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

Grouped tibble is rendered as text

mtcars %>% group_by(cyl)  %>% head

## # A tibble: 6 x 11
## # Groups:   cyl [3]
##     mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
##   <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1  21.0    6.  160.  110.  3.90  2.62  16.5    0.    1.    4.    4.
## 2  21.0    6.  160.  110.  3.90  2.88  17.0    0.    1.    4.    4.
## 3  22.8    4.  108.   93.  3.85  2.32  18.6    1.    1.    4.    1.
## 4  21.4    6.  258.  110.  3.08  3.22  19.4    1.    0.    3.    1.
## 5  18.7    8.  360.  175.  3.15  3.44  17.0    0.    0.    3.    2.
## 6  18.1    6.  225.  105.  2.76  3.46  20.2    1.    0.    3.    1.

Removing the class "grouped_df" leads to correct rendering again

class(x) <- setdiff(class(x),"grouped_df")
x %>% head

mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
21.0	6	160	110	3.90	2.620	16.46	0	1	4	4
21.0	6	160	110	3.90	2.875	17.02	0	1	4	4
22.8	4	108	93	3.85	2.320	18.61	1	1	4	1
21.4	6	258	110	3.08	3.215	19.44	1	0	3	1
18.7	8	360	175	3.15	3.440	17.02	0	0	3	2
18.1	6	225	105	2.76	3.460	20.22	1	0	3	1

printr labels + kable caption

I cannot get both printr and kable's caption option working together. This might be a bug or I am missing something simple. An example, not sure how to format it to be more readable, so a .txt and .pdf with printed .html attached:
printr_test.pdf
printr_test.txt

r global options, packages etc. (as text)

{r global_options, include = FALSE}
knitr::opts_chunk$set(fig.width = 6, fig.height = 4, fig.path = 'Figs/',
echo = TRUE, warning = FALSE, message = FALSE,
cache = TRUE, tidy = FALSE, size = "small")
options(width = 10000)

{r load packages, cache = FALSE}
library(printr)
library(knitr)

{r session, cache = FALSE}
sessionInfo()

## R version 3.2.4 Revised (2016-03-16 r70336)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 7 x64 (build 7601) Service Pack 1
## 
## locale:
## [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] knitr_1.12.3 printr_0.0.5
## 
## loaded via a namespace (and not attached):
##  [1] magrittr_1.5    formatR_1.3     tools_3.2.4     htmltools_0.3.5 yaml_2.1.13     Rcpp_0.12.4     stringi_1.0-1   rmarkdown_0.9.5 stringr_1.0.0   digest_0.6.9    evaluate_0.8.3

printr (labels)

set.seed(2016)
x1 = sample(letters[1:3], 1000, TRUE)
x2 = sample(letters[1:3], 1000, TRUE)
t <- table(x1, x2, dnn = c("Sample A", "Sample B"))
t

printr + kable (caption, NO labels...)

set.seed(2016)
x1 = sample(letters[1:3], 1000, TRUE)
x2 = sample(letters[1:3], 1000, TRUE)
t <- table(x1, x2, dnn = c("Sample A", "Sample B"))
kable(t, caption = "kable table title")

something weird

When echo = false labels on first table, caption from second table before first.

set.seed(2016)
x1 = sample(letters[1:3], 1000, TRUE)
x2 = sample(letters[1:3], 1000, TRUE)
table(x1, x2, dnn = c("Sample A", "Sample B"))
kable(table(x1, x2, dnn = c("Sample A", "Sample B")), caption = "kable table title")

With kable(NULL, ...) and echo = false this kinda looks allright...

set.seed(2016)
x1 = sample(letters[1:3], 1000, TRUE)
x2 = sample(letters[1:3], 1000, TRUE)
table(x1, x2, dnn = c("Sample A", "Sample B"))
kable(NULL, caption = "kable table title")

Any idea how to get them both (labels and caption) working together?

Problem when using ***

I was working with a series of tables and had put a *** between them to get a horizontal line. However this seemed to really destroy the LaTex rendering if there was not a blank line between the preceding code chunk and the ***. (Maybe there is an rmarkdown rule I am unaware of about this?) I just wanted to note it since someone else may come across it.

Missing style?

When knitting the vignette to html, the table formatting is absent (except for the bold text in the table header). Is there supposed to be an additional style sheet?

Rmd partials

I like the concept of Rmd partials for repetitive things I do (like summaries of models, robustness checks, making a codebook for the items in a survey).

But I'm not sure I'm using them right, because it seems a bit hacky at times.

To give an example: here, you can see where I used one to summarise a regression with some plots and headlines (this is a simplified example, it's usually a bit more involved).

The partial itself: https://rubenarslan.github.io/repro_web_stack/_regression_summary.html
Used: https://rubenarslan.github.io/repro_web_stack/3_analyses.html

Here are things that felt a bit hacky:

• I needed to set options(knitr.duplicate.label = 'allow') globally if I want named chunks.
• I "needed" this convenience function: https://github.com/rubenarslan/formr/blob/master/R/rmarkdown_options.R#L234 so that it's rendered "asis" and so that the environment is the calling environment for knit_child.
• I wanted to call the partials from a function (could simply be knit_print.lm or something more "custom" like I use now). So it takes arguments from the calling environment, but I cannot specify these in the Rmd file. I tried using parameters, but I think knitr:knit_child does not support them.

I was thinking of packaging some partials that I've made for myself, but wanted to collect your opinion on best practices first. Should I maybe use an htmlwidget-style approach for this as this is more "standard"? I like about the knit_child approach that I can treat it like text, concatenate several etc.

Error when using summary()

base::summary() causes a fatal error when present in a markdown file with printr.

Reproducible example

     library(printr)  
     summary(iris$Sepal.Length)

generates
Error in provideDimnames(x, sep = sep, base = base) : 'dimnames' applied to non-array Calls: <Anonymous> ... eval -> eval -> data.frame -> do.call -> provideDimnames

dimnames(summary(iris$Sepal.Length)) is NULL

Using as.array(summary(iris$Sepal.Length)) solves it, but it was definitely unexpected by me at least.

Consider the option rmarkdown.pandoc.to

See rstudio/rmarkdown@e6f8a77

When printing an object, we need to consider two types of output formats:

1. opts_knit$get('out.format') is for general document formats, e.g. Rnw, Rhtml, Rmd, Rrst, ...
2. opts_knit$get('rmarkdown.pandoc.to') is for R Markdown only

LaTeX tables using array

See this example by @Thell http://rpubs.com/Thell/xtable

"[" trips up printing

```{r help page,  render.args=list(help=list(sections=c('description', 'format')))}
?ToothGrowth
```

produces: