Building standalone Rmarkdown documents using the data language engine

David M. Kaplan

2020-12-02

This document provides a brief introduction to how to use the knitrdata package to create standalone Rmarkdown documents. For examples of Rmarkdown documents using the package, please consult the examples directory provided with the package. There is also an instructional video for how to use the package.

Overview

Sometimes it would be useful to make completely standalone Rmarkdown documents that do not depend on data in external files. One important example of this is scientific publications written in Rmarkdown for which we often would like to supply the source document with the data to ensure results are reproducible. The knitrdata package addresses this need by creating a mechanism for incorporating arbitrary text and binary data in Rmarkdown documents. It works conceptually and technically in a manner that is very similar to how images and other binary data are incorporated into standalone HTML web pages and email attachments: data are incorporated into specially delimited chunks that consist of the data themselves plus a small bit of header information explaining how the data are to be processed. Text data (e.g., CSV data tables, BibTeX references, LaTeX style files) is typically incorporated in chunks as is, whereas binary data (e.g., RDS files, images, NetCDF files) is encoded as text using one of two standard encoding schemes. During knitting of the Rmarkdown document, chunk data is decoded if necessary, after which it can either be loaded into the Rmarkdown R session or saved to an external file.

knitrdata achieves this by extending knitr to provide a new data language engine (i.e., a new chunk type). Instead of putting code inside data chunks, one puts the contents of the data file that one wishes to use in your Rmarkdown document. For binary data, the package currently supports two standard encoding formats: base64, the standard binary encoding format used (behind the scenes) for things like email attachments and standalone HTML web pages; and gpg, a well-known encryption algorithm that prevents data from being accessed by users without the appropriate decryption key. The latter option requires that a GPG keyring for managing encryption keys be installed and properly configured.

data chunks do not produce output in the form of text or figures as most code chunks do. Instead, the decoded contents of the chunk are either returned as a variable in the R workspace or saved to an external file.

Instructional video

There is an instructional video screencast demonstrating the use of knitrdata in Rstudio. It is available on youtube or by clicking the video insert below.

Installation & getting started

knitrdata can be installed from its github repository using the package remotes:

remotes::install_github("dmkaplan2000/knitrdata",build_vignettes=TRUE)

Once the package is installed, it needs to be loaded in the Rmarkdown script before the first data chunk, typically in the setup chunk at the start of the document:

library(knitrdata)

To ensure that your document is as standalone as possible, you can combine these two steps in the setup chunk (though this may install packages without asking the user):

# If package not installed, install it
if (!requireNamespace("knitrdata")) {
  if (!requireNamespace("remotes"))
    install.packages("remotes")
  remotes::install_github("dmkaplan2000/knitrdata",build_vignettes = TRUE)  
}

library(knitrdata) # load package

After the package is installed, data chunks can be incorporated in the document. The precise format for data chunks is described in the “Data chunks” Section, but beforehand encoding of binary data is presented. If you are only interested in incorporating text data in your Rmarkdown document, then you can safely skip directly to the “Data chunks” Section.

Encoding data

Both text and binary data files can be encoded, but encoding is only required for binary data. Two encoding formats are currently implemented: base64, used for non-sensitive data; and gpg, allowing one to encrypt data so that only users with the decryption key have access. The latter option requires that a GPG keyring be installed and properly configured.

Two helper functions, data_encode and data_decode, are included in the package to facilitate encoding and decoding of data files. These are basically wrapper functions for functionality provided by the xfun and gpg packages for base64 and gpg encoding, respectively. To demonstrate their use, we will use the following simple data frame that exists in both text (CSV) and binary (RDS) formats:

D = data.frame(a=1:3,b=letters[1:3])
write.csv(D,"test.csv", row.names = FALSE, quote = FALSE)
saveRDS(D,"test.RDS")
D
#>   a b
#> 1 1 a
#> 2 2 b
#> 3 3 c

The contents of the CSV file are as follows:

a,b
1,a
2,b
3,c

This CSV text will be used as is in data chunks (see “Data chunks” Section for details).

Base64

Base64 encoding is a widely-used, standard encoding to be used for all non-sensitive binary data. It is based on translating 6-bits of information into one of 64 alphanumeric and symbolic characters.

Encoding in base64 using the data_encode function works as follows:

b64 = knitrdata::data_encode("test.RDS","base64")

By default this function will silently return the encoded data as a character string. This character string can then be visualized using the cat function so that it can be copied and pasted directly into a data chunk:

cat(b64)
#> H4sIAAAAAAAAA4vgYmBgYGZgAWJmViCTgTU0xE3XAigmDOQwAfE7KM0IVMQJpPmS
#> 83MLEpNL4jPzSopTC9FkWZISi1OhYrxgcQj9D6QTZJUDBwMY2H9ApaFqBKDOAZnF
#> mAhjJMEYyUAbkK1jzUvMTS2G6mPCog9NeXJOYjFMOUyQKyWxJFEvrQhoEppyzqL8
#> cj2YDSBfMDUAif////8FuRYAeDNrwDsBAAA=

This is only practical for relatively small data files, so for larger files, one can place the output in a file:

data_encode("test.RDS","base64",output="test.RDS.base64")
cat(readLines("test.RDS.base64"),sep="\n")
#> H4sIAAAAAAAAA4vgYmBgYGZgAWJmViCTgTU0xE3XAigmDOQwAfE7KM0IVMQJpPmS
#> 83MLEpNL4jPzSopTC9FkWZISi1OhYrxgcQj9D6QTZJUDBwMY2H9ApaFqBKDOAZnF
#> mAhjJMEYyUAbkK1jzUvMTS2G6mPCog9NeXJOYjFMOUyQKyWxJFEvrQhoEppyzqL8
#> cj2YDSBfMDUAif////8FuRYAeDNrwDsBAAA=

Though it is rarely necessary to call the data_decode function directly when working with the data chunks in Rmarkdown documents, base64 encoded data can be decoded as follows:

rds = data_decode(b64,"base64",as_text=FALSE)
writeBin(rds,"test_output.RDS")
y = readRDS("test_output.RDS")
y
#>   a b
#> 1 1 a
#> 2 2 b
#> 3 3 c

GPG

Ecryption of data using GPG requires a properly configured GPG keyring. The functioning of GPG and GPG keyrings is beyond the scope of this document, but numerous websites explain how GPG works and how to install a GPG keyring, including the main gpg website.

For the purposes of this vignette, I will generate a test GPG private-public key pair using the gpg package, however in real use scenarios proper keys would typically be generated using the gpg command line tool (or an equivalent alternative) with appropriate options.

id = gpg::gpg_keygen("test","test@test.org")

Next one uses this key to encode a data file:

enc = data_encode("test.RDS","gpg",options = list(receiver=id))
cat(enc)

Note that the ID of the desired encryption key must be supplied as the receiver in the options list input argument.

Decoding works as follows:

rds = data_decode(enc,"gpg")
writeBin(rds,"test_output.RDS")
y = readRDS("test_output.RDS")
y

Note that there is no need to supply the receiver ID when decoding because the appropriate private key is in the keyring. When decoding, the gpg package or keyring may prompt for a password to unlock the decryption key if the key is password protected.

We can delete the public-private key pair we created for this exercise from our keyring as follows:

gpg::gpg_delete(id,secret=TRUE)

Data chunks

Data is incorporated into Rmarkdown documents using data chunks that consist of the data themselves preceded by a header containing a set of special chunk options describing how the data is to be processed.

Text data chunks

The simplest possible data chunk is a text data chunk containing plain text. Textual data can be directly placed into a data chunk in an Rmarkdown document as follows:

```{data output.var="d"}
a,b
1,a
2,b
3,c
```

When the Rmarkdown document is knitted, this chunk will put the text contents of the chunk into the variable d, which will then contain the chunk contents as a character string. For the example CSV data above, the character string can then be converted into a data.frame using read.csv:

read.csv(text=d)
#>   a b
#> 1 1 a
#> 2 2 b
#> 3 3 c

One can also load the data directly into a data.frame using the loader.function chunk option. The loader.function should be a function (or a character string containing the name of a function) whose first input argument will be the name of a file. A file containing the (decoded) data chunk contents will be passed to this function and the output will be assigned to the variable name contained in output.var.

```{data output.var="d",loader.function=read.csv}
a,b
1,a
2,b
3,c
```

This will assign to d the output of read.csv applied to the CSV data in the chunk.

d
#>   a b
#> 1 1 a
#> 2 2 b
#> 3 3 c

Additional input arguments can be passed to loader.function by supplying a list as the loader.ops chunk option:

```{data output.var="d",loader.function=read.csv,loader.ops=list(header=FALSE)}
a,b
1,a
2,b
3,c
```
d
#>   V1 V2
#> 1  a  b
#> 2  1  a
#> 3  2  b
#> 4  3  c

Note that in this case the first line of the CSV data has been treated as data instead of as a header because we supplied the header=FALSE optional argument.

Text documents in data chunks

The data inside a text data chunk does not have to be scientific data. It can be any textual information, including the contents of formatting files used by Rmarkdown to generate final output documents. These include BibTeX files with references, LaTeX style files (.cls) and bibliography style files (.csl). For example, if we include the following in a Rmarkdown document:

```{data output.file="references.bib",echo=FALSE}
@article{MeynardTestingmethodsspecies2019,
  ids = {MeynardTestingmethodsspecie,MeynardTestingmethodsspeciesinpress},
  title = {Testing Methods in Species Distribution Modelling Using Virtual Species: What Have We Learnt and What Are We Missing?},
  shorttitle = {Testing Methods in Species Distribution Modelling Using Virtual Species},
  author = {Meynard, Christine N. and Leroy, Boris and Kaplan, David M.},
  year = {2019},
  month = dec,
  volume = {42},
  pages = {2021--2036},
  issn = {0906-7590, 1600-0587},
  doi = {10.1111/ecog.04385},
  file = {/home/dmk/papers/meynard.et.al.2019.testing_methods_in_species_distribution_modelling_using_virtual_species.pdf},
  journal = {Ecography},
  keywords = {artificial species,environmental niche models,niche,simulations,species distribution modelling,virtual ecologist},
  language = {en},
  number = {12}
}

@article{SantosConsequencesdriftcarcass2018,
  title = {Consequences of Drift and Carcass Decomposition for Estimating Sea Turtle Mortality Hotspots},
  author = {Santos, Bianca S. and Kaplan, David M. and Friedrichs, Marjorie A. M. and Barco, Susan G. and Mansfield, Katherine L. and Manning, James P.},
  year = {2018},
  month = jan,
  volume = {84},
  pages = {319--336},
  issn = {1470-160X},
  doi = {10.1016/j.ecolind.2017.08.064},
  copyright = {All rights reserved},
  file = {/home/dmk/papers/santos.et.al.2018.consequences_of_drift_and_carcass_decomposition_for_estimating_sea_turtle.pdf},
  journal = {Ecological Indicators},
  keywords = {Carcass decomposition,Chesapeake bay,Conservation,Drift leeway,Drift simulations,Endangered species,Sea turtle mortality,Sea turtle strandings}
}
```

This will generate the file references.bib from the chunk contents. Note that one uses output.file instead of output.var to save the contents to a file. Textual output to a file can also be achieved using the cat language environment as described in the R Markdown Cookbook here, though the data language engine provides more options for the handling of chunk contents (for example, one can use base64 encoding to embed Rmarkdown documents within Rmarkdown documents).

As style files like the BibTeX file described above are only used by knitr/pandoc in the final formatting phase of generating an output document, these files can be generated from data chunks during the initial phases of the knitting. This allows them to be stored inside the Rmarkdown document itself, with no need for the external file prior to knitting.

Base64-encoded binary data chunks

Base64 encoded binary data is incorporated into a chunk by copying the output of the data_encode function into the chunk and supplying the format="binary" chunk option:

```{data output.var="b",format="binary",echo=FALSE}
H4sIAAAAAAAAA4vgYmBgYGZgZgNiViCTgTU0xE3XAigmDOQwAfE7KM3IwMLACaT5
kvNzCxKTS+Iz80qKUwvRZFmSEotToWK8YHEI/Q+kE2SVAwcDGNh/QKUhaph5wc6B
6GOCsFmQzWfLSS1LzSkGsgTAshBRxkQYIwnGSEbTyJqck1gM0wc3LQ3okfwiiN2o
yvMSc1NhypmwWANWzvIfzUCulMSSRL20IqBmNAM5i/LL9WCGgnzJ1AAk/v///xdk
OwBVQunahwEAAA==
```

This will place the decoded contents of the chunk into a raw vector b. Note that format must be specified as 'binary' and that we have chosen echo=FALSE to avoid including lots of ugly encoded content in our formatted document. By default, when format="binary", it is assumed that encoding="base64", but this can also be supplied as a chunk option for additional clarity.

The contents of the raw vector b must be written to a file before they can be read back into the Rmarkdown session:

writeBin(b,"test_output.RDS")

We can combine the decoding and the writing steps by specifying the output.file chunk option instead of output.var:

```{data output.file="test_output.RDS",format="binary",echo=FALSE}
H4sIAAAAAAAAA4vgYmBgYGZgZgNiViCTgTU0xE3XAigmDOQwAfE7KM3IwMLACaT5
kvNzCxKTS+Iz80qKUwvRZFmSEotToWK8YHEI/Q+kE2SVAwcDGNh/QKUhaph5wc6B
6GOCsFmQzWfLSS1LzSkGsgTAshBRxkQYIwnGSEbTyJqck1gM0wc3LQ3okfwiiN2o
yvMSc1NhypmwWANWzvIfzUCulMSSRL20IqBmNAM5i/LL9WCGgnzJ1AAk/v///xdk
OwBVQunahwEAAA==
```

This will save the decoded data to the filename given by output.file. Then this file can be read back into the Rmarkdown session:

readRDS("test_output.RDS")
#>   a b
#> 1 1 a
#> 2 2 b
#> 3 3 c

Finally, we can combine all three steps (decoding, writing to disk, reading back into R) using the loader.function chunk option:

```{data output.var="b",format="binary",echo=FALSE,loader.function=readRDS}
H4sIAAAAAAAAA4vgYmBgYGZgZgNiViCTgTU0xE3XAigmDOQwAfE7KM3IwMLACaT5
kvNzCxKTS+Iz80qKUwvRZFmSEotToWK8YHEI/Q+kE2SVAwcDGNh/QKUhaph5wc6B
6GOCsFmQzWfLSS1LzSkGsgTAshBRxkQYIwnGSEbTyJqck1gM0wc3LQ3okfwiiN2o
yvMSc1NhypmwWANWzvIfzUCulMSSRL20IqBmNAM5i/LL9WCGgnzJ1AAk/v///xdk
OwBVQunahwEAAA==
```

Given these options, during knitting, the contents of the data chunk will be decoded, written to a temporary file as binary data and then read back into the R session using the readRDS function. In the end, the variable whose name is given by output.var will be assigned the output of readRDS:

b
#>   a b
#> 1 1 a
#> 2 2 b
#> 3 3 c

GPG-encoded data chunks

GPG chunks work similar to base64 chunks except that one must specify encoding="gpg". To demonstrate this functionality, we first import into the GPG keyring the private key previously used to encode some data. We would never include the private key in an Rmarkdown document in a real use case, but this is practical for this vignette and it demonstrates another use of text data chunks.

```{data key,output.file="key",include=FALSE}
-----BEGIN PGP PRIVATE KEY BLOCK-----

lQVYBF6A3p8BDADcaf7tveXZUpi0IfEpmYrPP8/OSXSh3iBkd5bdTvbq/FwLGIsD
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RkF8ZbRCPRk4Vl2DYM/rXC2VGCFZ6OeJAbYEGAEKACAWIQTvl6O3A7Tx/z8NeR/q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=C6UF
-----END PGP PRIVATE KEY BLOCK-----
```

This key then needs to be imported into the keyring:

gpg::gpg_import("key")

Now that we have this private key, we can decode some binary data encrypted using this key:

```{data t3,format="binary",encoding="gpg",output.var="d",loader.function=readRDS}
-----BEGIN PGP MESSAGE-----
Version: GnuPG v2
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=m4sT
-----END PGP MESSAGE-----
```
d

Helper functions for creating and inserting data chunks

For small data chunks, one can copy-paste the (encoded) data from the command line or from a file into a Rmarkdown document. For larger data chunks, this can be awkward, so knitrdata includes two command-line helper functions for creating and inserting data chunks into Rmarkdown documents, as well as 3 RStudio Addins that facilitate creating data chunks. The command-line functions are create_chunk and insert_chunk. We can combine these functions with data_encode to generate the base64 data chunk described above. First, we use create_chunk to generate the chunk:

library(magrittr) # For pipe operator

chunk = data_encode("test.RDS","base64") %>%
  create_chunk(chunk_label="mydata",output.var="d",format="binary",echo=FALSE,
               loader.function=readRDS)

cat(chunk,sep="\n")
#> ```{data mydata, output.var = "d", format = "binary", echo = FALSE, loader.function = readRDS}
#> H4sIAAAAAAAAA4vgYmBgYGZgAWJmViCTgTU0xE3XAigmDOQwAfE7KM0IVMQJpPmS
#> 83MLEpNL4jPzSopTC9FkWZISi1OhYrxgcQj9D6QTZJUDBwMY2H9ApaFqBKDOAZnF
#> mAhjJMEYyUAbkK1jzUvMTS2G6mPCog9NeXJOYjFMOUyQKyWxJFEvrQhoEppyzqL8
#> cj2YDSBfMDUAif////8FuRYAeDNrwDsBAAA=
#> ```

Note that with the exception to the chunk label, chunk contents and other named arguments to this function, all the other arguments are not evaluated, so they can be given exactly as they should appear in the Rmarkdown document regardless of whether the chunk options make sense in the current context.

Next, we can use insert_chunk to place this chunk at a given line number in a Rmarkdown file (here taken to be example.Rmd):

rmd = insert_chunk(chunk,11,rmd.file="example.Rmd")
writeLines(rmd,"example_with_data_chunk.Rmd")

This will insert the new data chunk at line 11 in the Rmarkdown document.

knitrdata also includes the list_rmd_chunks and splice_rmd_by_chunk functions for identifying and potentially removing or working with the chunks in a Rmarkdown document. See the documentation and examples for these functions for more details on their use.

Data integrity checks using md5sum

Using the procedures above should assure that data inside data chunks do not have errors. Nevertheless, there is always the possibility that a stray keystroke would modify the data, particularly for binary data encoded as text. To protect against this, data chunks can have a md5sum chunk option that will be used to test if the decoded data matches expectations. A MD5 sum is essentially a very large number (typically encoded in hexadecimal) derived from a file’s contents that has a vanishingly small probability of being equal to the equivalent number derived from a different file’s contents. If two files have the same MD5 sum, they are almost certainly identical.

To use the md5sum chunk option, one must first determine the MD5 sum of the decoded source data:

tools::md5sum("test.RDS")
#>                           test.RDS 
#> "c5c4292e64e0536e69fd24862128e82d"

If this character string is given as the md5sum chunk option to a data chunk, then the MD5 sum of the decoded data of that chunk will be calculated and checked against this character string. If the two do not match, an error will be generated.

We can add a MD5 sum check to the data chunk generated in the previous section as follows:

md5 = tools::md5sum("test.RDS")
chunk = data_encode("test.RDS","base64") %>%
  create_chunk(chunk_label="mydata",output.var="d",format="binary",
               echo=FALSE,loader.function=readRDS,
               chunk_options_string = paste0("md5sum='",md5,"'"))

cat(chunk,sep="\n")
#> ```{data mydata, output.var = "d", format = "binary", echo = FALSE, loader.function = readRDS, md5sum='c5c4292e64e0536e69fd24862128e82d'}
#> H4sIAAAAAAAAA4vgYmBgYGZgAWJmViCTgTU0xE3XAigmDOQwAfE7KM0IVMQJpPmS
#> 83MLEpNL4jPzSopTC9FkWZISi1OhYrxgcQj9D6QTZJUDBwMY2H9ApaFqBKDOAZnF
#> mAhjJMEYyUAbkK1jzUvMTS2G6mPCog9NeXJOYjFMOUyQKyWxJFEvrQhoEppyzqL8
#> cj2YDSBfMDUAif////8FuRYAeDNrwDsBAAA=
#> ```

md5sum can be used on all data chunk types, including text data chunks that are not encoded in any special way.

Reading a data chunk from an external file

One disadvantage of using data chunks is that it can make Rmarkdown files long and difficult to navigate if you use lots of data. Rstudio can help with this problem by allowing one to hide the contents of a chunk and by using navigation tools to jump between sections. In addition, using insert_chunk or the RStudio Addins to place a data chunk inside a document as the last step before public diffusion may avoid having to work extensively with the large file. Nevertheless, large file size can still be a problem. To facilitate the initial construction of standalone Rmarkdown documents, data chunks can be read from external files using the external.file chunk option. The external file must contain the encoded chunk contents exactly as they would appear in a data chunk. The intended use of this option is that large data chunks would be placed initially in external files, but the contents of these files would be placed directly in the data chunks before sharing the document with others.

writeLines(c("This is from an external file.","It has two lines."),
           "test_external.txt")
```{data ext,output.var="ext",external.file="test_external.txt"}
Content will be ignored with a warning!
```
cat(ext)
#> This is from an external file.
#> It has two lines.

Extra language engines for CSV and RDS data

As it is very common for data chunks to be used for CSV or RDS data, additional shorthand language engines are included in the knitrdata package for working with these data. These chunks types are csv, csv2 and rds for working with comma-separated CSV data, semicolon-separated CSV data and RDS data, respectively. These language engines are implemented as wrappers for the standard data language engine, but with the loader.function option predefined to be read.csv, read.csv2 and readRDS, respectively. Extra parameters for these loader functions can be given directly as chunk options, as well as via the loader.ops chunk option.

As an example, one could load CSV data that has no header and that uses a non-standard delimiter and comma as the decimal point indicator as follows:

```{csv2 output.var = "d", sep="|", header=FALSE}
a|1,1
b|2,2
c|3,3
```
d
#>   V1  V2
#> 1  a 1.1
#> 2  b 2.2
#> 3  c 3.3

Rstudio Addins for working with data chunks

The steps described above for encoding data, creating data chunks and inserting them in Rmarkdown documents have been combined into a set of GUI Shiny applications that assist in creating and/or removing data chunks:

The last two of these, insert_data_chunk_dialog() and remove_chunks_dialog(), are accessible in the Rstudio Addins menu under the knitrdata heading with titles Insert filled data chunk and Remove chunks, respectively. There is also a non-interactive addin entitled Insert empty data chunk that inserts an empty data chunk template in the active source document.

Before using these tools, first install all the additional packages suggested by knitrdata: shiny, miniUI, DT, rstudioapi.

The use of these tools is generally self explanatory and is explained in greater detail in the instructional video. The chunk creation apps ask for the name of the data file to be incorporated into the chunk, as well as a standard set of other chunk options, such as data format and encoding and output options. The app will attempt to suggest sensible options based on the input data file, though these can be changed afterward. For example, if a binary file is selected, then the format and encoding options will be set to binary and base64 respectively. GPG encoding of data using the app is supported and will prompt the user to select the key ID(s)s of the key(s) to be used to encrypt the data. By default, md5sum checks of all binary data chunks will be included.

The chunk removal addin presents a searchable list of all chunks in the source document. To eliminate a set of chunks, one just selects the corresponding rows and clicks the Remove chunks button.

Note that these tools do not try to determine if the active source document is a Rmarkdown document. If undesired changes are made to a document, then one can undo (ctrl-z) those changes afterward.

Use cases

There are many potential scenarios where including data inside Rmarkdown documents can be useful. The most obvious is to render a document fully standalone, perhaps for creating a single document that reproduces an entire publication or report or to make life as simple as possible for collaborators that are not comfortable managing complex Rmarkdown documents requiring multiple files. To do this, one would place not only data inside chunks in the Rmarkdown document, but also ancillary files associated with the document, such as CSS, LaTeX and CSL (bibliography) style files, and BibTeX files. These latter chunks would typically recreate these external files using the output.file chunk option.

knitrdata also has uses in cases where the objective is not necessarily to render a document fully standalone. One can use it as a convenient way to input small data tables and data vectors (e.g., see Numeric vector data below) into an Rmarkdown document. For example, the data chunk syntax combined with CSV data may be simpler and cleaner than creating a data.frame or tibble directly in R code. Furthermore, though markdown allows one to create small tables by hand, it is difficult or impossible to reproduce the sophisticated tables that knitr::kable and kableExtra are capable of creating, and tables created in markdown may not float as other tables do, potentially an issue for producing scientific publications with Rmarkdown. knitrdata can be used as a simple way to input these tables into R, which can then be used as input to kable and other tools. Finally, data chunks provide a convenient system for making certain Rmarkdown document text conditional on parameter values or results (see Conditional text in Rmarkdown using knitrdata).

One knitrdata feature that may at first glance seem to be of little value is the possibility to gpg encrypt data chunks. Why would one want to encrypt just the data when one can encrypt the entire Rmarkdown document? However, there are many cases where the data themselves are confidential (e.g., economically important data, confidential medical information), but the methods used to analyze and synthesize those data can and should be publicly available. Furthermore, it is increasingly common to share code and documents on public collaboration websites, such as github or slack, but one may not have sufficient confidence in the privacy protections of these websites to give them access to the data themselves.

When not to use data chunks

Though the knitrdata package can be a powerful tool, it can also be abused by placing very large amounts of data inside Rmarkdown files. This will make the documents very large and difficult to navigate. The options to collapse data chunks in Rstudio, use Rstudio’s navigation tools, use knitrdata’s helper functions for data chunk creation and the use of the external.file chunk option all can reduce the importance of these issues, but including very large amounts of data in Rmarkdown documents is unlikely to be optimal. In particular, Rstudio currently will not open Rmarkdown documents larger than 5 MB in size, though larger documents can still be opened by other editors and rendering from the command line using rmarkdown::render is always possible. Basic prudence should be used when deciding what and how much data to include in Rmarkdown documents.

Tips & tricks

Numeric vector data

You can use a data chunk to load numeric vector data as follows:

```{data output.var="v",line.sep=""}
1.2,3.4,5.6,
7.8,9.0
```

```{r}
f = function(v) as.numeric(strsplit(v,",")[[1]])
v=f(v)
v
```
#> [1] 1.2 3.4 5.6 7.8 9.0

Conditional text in Rmarkdown with missing values

One way to create large amounts of text in an Rmarkdown document that is only included in the document if certain conditions are met is with the asis language engine. For example, if one creates an input parameter in the YAML header of an Rmarkdown document:

params:
  cond: TRUE

Then one could include content in the document based on this parameter as follows:

```{asis eval=params$cond}
# A conditional section

This **will not** be evaluated: $5+4=9$
```

This will add a section and a paragraph with one sentence. One disadvantage of this approach is that the content of an asis chunk is never evaluated so one cannot use inline R code.

This limitation can be overcome with knitrdata by pushing the content of the chunk into a text variable with conversion specifications that can be replaced using the sprintf function. For example, placing the following in the document:

```{data include=FALSE,output.var="cond_text"}
# A conditional section

This **will** be evaluated: $5+4=%d$
```

```{r results='asis',echo=FALSE,eval=params$cond}
cat(sprintf(cond_text,5+4))
```

Will lead to %d being replaced with 9.

Unencoded text chunks and md5sum

Using md5sum checks on text chunks that are not encoded (i.e., 'asis') can be tricky because when the chunk is processed, an operating-system-dependent newline character will be added to each line, including the final line, and character encoding (i.e., UTF-8, latin1, etc.) translation might be carried out. This will potentially make the md5sum check fail if the file was created on a different operating system or the final line lacks a newline character. To have the best possible chances of success when using md5sum checks with unencoded text files, follow these steps:

If you follow these steps, md5sum checks of text chunk contents should work. The Insert filled data chunk RStudio addin will attempt to set the line.sep chunk option to match that of the incoming text file so that one normally should not need to worry about the text file format.

If for some reason these steps are impractical or are not sufficient (e.g., due to differences in character encodings between operating systems), one can always use a different method to check the validity of chunk contents. For example, the following would do a post hoc check of the validity of loaded data using a SHA1 hash:

```{data output.var="d",loader.function=read.csv}
a,b
1,a
2,b
3,c
```

```{r checkdata}
if (digest::sha1(d) != "a5918a84b39f0b6f42e9ab4a19771a7d6a5777a0")
  stop("data corrupted!")
```

These concerns do not apply to base64 or gpg encoded text files as the exact text file contents are encoded in the chunk contents.

Workarounds for GPG data chunk error: Password callback did not return a string value

If one includes in a Rmarkdown document a GPG-encoded data chunk that uses a password-protected GPG key, then knitting may fail with the error Password callback did not return a string value. This is because knitting of an Rmarkdown document takes place in a non-interactive R session and, therefore, gpg::gpg_decrypt is unable to open the password entry dialog during the knitting process. The gpg package does not currently include another mechanism for providing the key password, but one can work around this problem by using any mechanism to temporarily store the key password in the GPG keyring manager. This can generally be achieved by decrypting something that was encrypted by the same key that was used to encrypt the chunk. This normally leads to the GPG key password being temporarily stored in the keyring so that gpg::gpg_decrypt will not attempt to open the password entry dialog, thereby avoiding the problem.

As a workaround for this problem, knitrdata includes the unlock_gpg_key_passphrase that when run from the command line with identifying information regarding the key needed to decrypt the data chunks in the Rmarkdown document will attempt to unlock the key.

knitrdata::unlock_gpg_key_passphrase(name="David M. Kaplan")

It achieves this by encrypting and then immediately decrypting a small amount of data with the given key.

Full list of data chunk options

In addition to the standard eval and echo chunk options, data chunks supports the following chunk options:

Full list of knitrdata chunk options.
Chunk option Description
format One of 'text' or 'binary'. Defaults to 'text'.
encoding One of 'asis', 'base64' or 'gpg'. Defaults to 'asis' for format='text' and 'base64' for format='binary'.
decoding.ops A list with additional arguments for data_decode. Currently only useful for passing the verify argument to gpg::gpg_decrypt for gpg encrypted chunks.
external.file A character string with the name of a file whose text contents will be used as if they were the contents of the data chunk.
md5sum A character string giving the correct md5sum of the decoded chunk data. If supplied, the md5sum of the decoded data will be calculated and compared to the supplied value, returning an error if the two do not match.
output.var A character string with the variable name to which the chunk output will be assigned. At least one of output.var or output.file must always be supplied.
output.file A character string with the filename to which the chunk output will be written. At least one of output.var or output.file must always be supplied.
loader.function A function that will be passed (as the first argument) the name of a file containing the (potentially decoded) contents of the data chunk.
loader.ops A list of additional arguments to be passed to loader.function.
line.sep Only used when encoding='asis'. In this cases, specifies the character string that will be used to join the lines of the data chunk before export to an external file, further processing or returning the data. Defaults to platform.newline().
max.echo An integer specifying the maximum number of lines of data to echo in the final output document. Defaults to 20. If the data exceeds this length, only the first 20 lines will be shown and a final line indicating the number of ommitted lines will be added.

csv, csv2 and rds chunks support these same options, but format and loader.function are typically not used and additional arguments to the predefined loader functions can be passed directly as chunk options.