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The write2 function

Ethan Heinzen

Introduction

The write2*() functions were designed as an alternative to SAS’s ODS procedure for useRs who want to save R Markdown tables to separate Word, HTML, or PDF files without needing separate R Markdown programs.

There are three shortcut functions for the most common output types: HTML, PDF, and Word. Each of these three functions calls write2(), an S3 function which accepts many file output types (see the help pages for rmarkdown::render()). Methods have been implemented for tableby(), modelsum(), and freqlist(), but also knitr::kable(), xtable::xtable(), and pander::pander_return().

The two most important things to recognize with write2() are the following:

Which function is being used to output the object. Sometimes the write2 functions use summary(), while other times they will use print(). The details for each object specifically are described below.
How the ... arguments are passed. To change the options for the summary-like or print-like function, you can pass named arguments which will in turn get passed to the appropriate function. Details for each object specifically are described below.

A note on piping

arsenal is piping-compatible!

The write2*() functions are probably the most useful place to take advantage of the magrittr package’s piping framework, since commands are often nested several functions deep in the context of write2*(). Piping also allows the arsenal package to become a part of more standard analysis pipelines; instead of needing to write separate R Markdown programs, intermediate analysis tables and output can be easily incorporated into piped statements.

This vignette will sprinkle the foward pipe (%>%) throughout as a hint at the power and flexibility of arsenal and piping.

Examples Using `arsenal` Objects

library(arsenal)
library(magrittr)
data(mockstudy)
tmpdir <- tempdir()

`tableby`

For tableby objects, the output function in write2() is summary(). For summary.tableby objects, the output function is print(). For available arguments, see the help pages for summary.tableby(). Don’t use the option text = TRUE with the write2 functions.

mylabels <- list(sex = "SEX", age ="Age, yrs")
tab1 <- tableby(arm ~ sex + age, data=mockstudy)

write2html(
  tab1, paste0(tmpdir, "/test.tableby.html"), quiet = TRUE,
  title = "My test table",      # passed to summary.tableby
  labelTranslations = mylabels, # passed to summary.tableby
  total = FALSE                 # passed to summary.tableby
)

`modelsum`

For modelsum objects, the output function in write2() is summary(). For summary.modelsum objects, the output function is print(). For available arguments, see the help pages for summary.modelsum(). Don’t use the option text = TRUE with the write2 functions.

tab2 <- modelsum(alk.phos ~ arm + ps + hgb, adjust= ~ age + sex, family = "gaussian", data = mockstudy)

write2pdf(
  tab2, paste0(tmpdir, "/test.modelsum.pdf"), quiet = TRUE,
  title = "My test table", # passed to summary.modelsum
  show.intercept = FALSE,  # passed to summary.modelsum
  digits = 5               # passed to summary.modelsum
)

`freqlist`

For freqlist objects, the output function in write2() is summary(). For summary.freqlist objects, the output function is print(). For available arguments, see the help pages for summary.freqlist().

mockstudy[, c("arm", "sex", "mdquality.s")] %>% 
  table(useNA = "ifany") %>% 
  freqlist(groupBy = c("arm", "sex")) %>% 
  write2word(
    paste0(tmpdir, "/test.freqlist.doc"), quiet = TRUE,
    single = FALSE,         # passed to summary.freqlist
    title = "My cool title" # passed to summary.freqlist
  )

`comparedf`

For comparedf objects, the output function in write2() is summary(). For summary.comparedf objects, the output function is print().

Examples Using Other Objects

`knitr::kable()`

For objects resulting from a call to kable(), the output function in write2() is print(). There aren’t any arguments to the print.knitr_kable() function.

mockstudy %>% 
  head() %>% 
  knitr::kable() %>% 
  write2html(paste0(tmpdir, "/test.kable.html"), quiet = TRUE)

`xtable::xtable()`

For xtable objects, the output function in write2() is print(). For available arguments, see the help pages for print.xtable().

mockstudy %>% 
  head() %>% 
  xtable::xtable(caption = "My xtable") %>% 
  write2pdf(
    paste0(tmpdir, "/test.xtable.pdf"), quiet = TRUE,
    comment = FALSE, # passed to print.xtable to turn off the default message about xtable version
    include.rownames = FALSE, # passed to print.xtable
    caption.placement = "top" # passed to print.xtable
  )

To make an HTML document, use the print.xtable() option type = "html".

mockstudy %>% 
  head() %>% 
  xtable::xtable(caption = "My xtable") %>% 
  write2html(
    paste0(tmpdir, "/test.xtable.html"), quiet = TRUE,
    type = "html",            # passed to print.xtable
    comment = FALSE, # passed to print.xtable to turn off the default message about xtable version
    include.rownames = FALSE, # passed to print.xtable
    caption.placement = "top" # passed to print.xtable
  )

User beware! xtable() is not compatible with write2word().

`pander::pander_return()`

Pander is a little bit more tricky. Since pander::pander() doesn’t return an object, the useR should instead use pander::pander_return(). For this (and for all character vectors), the the output function in write2() is cat(sep = '\n').

write2word(pander::pander_return(head(mockstudy)), file = paste0(tmpdir, "/test.pander.doc"), quiet = TRUE)

Output Multiple Tables to One Document

To output multiple tables into a document, simply make a list of them and call the same function as before.

mylist <- list(
  tableby(sex ~ age, data = mockstudy),
  freqlist(table(mockstudy[, c("sex", "arm")])),
  knitr::kable(head(mockstudy))
)

write2pdf(mylist, paste0(tmpdir, "/test.mylist.pdf"), quiet = TRUE)

One neat side-effect of this function is that you can output text and headers, etc. The possibilities are endless!

mylist2 <- list(
  "# Header 1",
  "This is a small paragraph introducing tableby.",
  tableby(sex ~ age, data = mockstudy),
  "<hr>",
  "# Header 2",
  "<font color='red'>I can change color of my text!</font>"
)
write2html(mylist2, paste0(tmpdir, "/test.mylist2.html"), quiet = TRUE)

In fact, you can even recurse on the lists!

write2pdf(list(mylist2, mylist), paste0(tmpdir, "/test.mylists.pdf"), quiet = TRUE)

Output Other Objects Monospaced (as if in a terminal)

It may be useful at times to write output that would normally be copied from the terminal. The default method for write2() does this automatically. To output the results of summary.lm(), for example:

lm(age ~ sex, data = mockstudy) %>% 
  summary() %>% 
  write2pdf(paste0(tmpdir, "/test.lm.pdf"), quiet = TRUE)

The verbatim() function is another option to explicitly alert write2() to do this. This becomes particularly helpful to overrule existing S3 methods.

For example, suppose you wanted to just print a tableby object (as if it were to print in the terminal):

tab4 <- tableby(arm ~ sex + age, data=mockstudy)
write2html(verbatim(tab4), paste0(tmpdir, "/test.print.tableby.html"), quiet = TRUE)

Or suppose you wanted to print a character vector (as if it were to print in the terminal):

chr <- paste0("MyVector", 1:10)
write2pdf(verbatim(chr), paste0(tmpdir, "/test.character.pdf"), quiet = TRUE)

Note that you can combine multiple objects in one call:

write2pdf(verbatim(tab4, chr), paste0(tmpdir, "/test.verbatim.pdf"), quiet = TRUE)

Add a YAML Header to the Output

You can add a YAML header to write2() output using the yaml() function.

mylist3 <- list(
  yaml(title = "Test YAML Title", author = "My cool author name"),
  "# Header 1",
  "This is a small paragraph introducing tableby.",
  tableby(sex ~ age, data = mockstudy)
)
write2html(mylist3, paste0(tmpdir, "/test.yaml.html"), quiet = TRUE)

In fact, all detected YAML pieces will be moved as the first output, so that the above code chunk gives the same output as this one:

mylist4 <- list(
  "# Header 1",
  "This is a small paragraph introducing tableby.",
  yaml(title = "Test YAML Title"),
  tableby(sex ~ age, data = mockstudy),
  yaml(author = "My cool author name")
)
write2html(mylist4, paste0(tmpdir, "/test.yaml2.html"), quiet = TRUE)

Add a Code Chunk to the Output

It is now possible to add code chunks to the output .Rmd:

mylist5 <- list(
  "# What is 1 + 2?",
  code.chunk(a <- 1, b <- 2),
  code.chunk(a + b, chunk.opts = "r echo=FALSE, eval=TRUE")
)
write2html(mylist5, paste0(tmpdir, "/test.code.chunk.html"), quiet = TRUE)

This allow flexibility to create objects on-the-fly, to read in saved objects to the temporary .Rmd, etc. The possibilities are endless!

FAQs

How do I suppress the note about my document getting rendered?

This is easily accomplished by using the argument quiet = TRUE (passed to the rmarkdown::render() function).

write2html(
  knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.quiet.html"),
  quiet = TRUE # passed to rmarkdown::render
)

How do I look at the temporary `.Rmd` file?

This is easily accomplished by using the option keep.rmd = TRUE.

write2html(
  knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.keep.rmd.html"),
  quiet = TRUE, # passed to rmarkdown::render
  keep.rmd = TRUE
)

How do I prevent my document from being rendered?

This is easily accomplished by using the option render. = FALSE. Note that this will then default to keep.rmd = TRUE.

write2html(
  knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.dont.render.html"),
  render. = FALSE
)

How do I output headers, raw HTML/LaTeX, paragraphs, etc.?

One can simply abuse the list S3 method for write2()!

mylist2 <- list(
  "# Header 1",
  "This is a small paragraph introducing tableby.",
  tableby(sex ~ age, data = mockstudy),
  "<hr>",
  "# Header 2",
  "<font color='red'>I can change color of my text!</font>"
)
write2html(mylist2, paste0(tmpdir, "/test.mylist2.html"), quiet = TRUE)

How do I tweak the default format from `write2word()`, `write2html()`, or `write2pdf()`?

You can pass arguments to the format functions used behind the scenes.

write2html(
  knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.theme.html"),
  quiet = TRUE,  # passed to rmarkdown::render
  theme = "yeti" # passed to rmarkdown::html_document
)

See the help pages for rmarkdown::word_document(), rmarkdown::html_document(), and rmarkdown::pdf_document().

How do I output to a file format other than word, HTML, and PDF?

This can be done using the generic write2() function. The last argument in the function can be another format specification. For details on the acceptable inputs, see the help page for write2().

write2(
  knitr::kable(head(mockstudy[, 1:4])), paste0(tmpdir, "/test.kable.rtf"),
  quiet = TRUE,  # passed to rmarkdown::render
  output_format = rmarkdown::rtf_document
)

How do I avoid prefixes on my table captions in PDF?

You can do this pretty easily with the yaml() function:

mylist5 <- list(
  yaml("header-includes" = list("\\usepackage[labelformat=empty]{caption}")),
  "# Header 1",
  "This is a small paragraph introducing tableby.",
  tableby(sex ~ age, data = mockstudy)
)
write2pdf(mylist5, paste0(tmpdir, "/test.noprefixes.pdf"), title = "My tableby")

How do I output multiple tables with different titles?

There are now write2() methods for the summary objects of arsenal functions. This allows you to specify a title for each table:

mylist6 <- list(
  summary(tableby(sex ~ age, data = mockstudy), title = "A Title for tableby"),
  summary(modelsum(age ~ sex, data = mockstudy), title = "A Title for modelsum"),
  summary(freqlist(~ sex, data = mockstudy), title = "A Title for freqlist")
)
write2pdf(mylist6, paste0(tmpdir, "/test.multiple.titles.pdf"))

Why is `write2()` not working in R Markdown/R Studio?

It’s possible that a global option in R Studio is preventing the tables from rendering. Consider turning off (i.e., unchecking) the option Tools > Global Options > R Markdown > Show output inline for all R Markdown documents.

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