R – YAML current date in rmarkdown

knitrrr-markdownyaml

I'm wondering if there's a trick to put the current date in the YAML front-matter of a .rmd document to be processed by knitr and the rmarkdown package. I used to have the following line at the top of my wiki pages,

   _baptiste, `r format(Sys.time(), "%d %B, %Y")`_

and it would get converted to baptiste, 03 May, 2014 in the html output. Now, I would like to take advantage of the advanced pandoc wrapper provided by rmarkdown, but having r code in the YAML header doesn't seem to work:

---
title: "Sample Document"
output:
  html_document:
    toc: true
    theme: united
date: `r format(Sys.time(), "%d %B, %Y")`
author: baptiste
---

Error in yaml::yaml.load(front_matter) : 
  Scanner error: while scanning for the next token at line 6, column 7
 found character that cannot start any token at line 6, column 7
Calls: <Anonymous> ... output_format_from_yaml_front_matter -> 
       parse_yaml_front_matter -> <Anonymous> -> .Call

Any workaround?

Best Answer

This is a little bit tricky, but you just need to make the date field valid in YAML by quoting the inline R expression, e.g.

date: "`r format(Sys.time(), '%d %B, %Y')`"

Then the parsing error will be gone, and the date will be generated in the markdown output so Pandoc can use the value from Sys.time().

Related Solutions

Json – the difference between YAML and JSON

Technically YAML is a superset of JSON. This means that, in theory at least, a YAML parser can understand JSON, but not necessarily the other way around.

See the official specs, in the section entitled "YAML: Relation to JSON".

In general, there are certain things I like about YAML that are not available in JSON.

As @jdupont pointed out, YAML is visually easier to look at. In fact the YAML homepage is itself valid YAML, yet it is easy for a human to read.
YAML has the ability to reference other items within a YAML file using "anchors." Thus it can handle relational information as one might find in a MySQL database.
YAML is more robust about embedding other serialization formats such as JSON or XML within a YAML file.

In practice neither of these last two points will likely matter for things that you or I do, but in the long term, I think YAML will be a more robust and viable data serialization format.

Right now, AJAX and other web technologies tend to use JSON. YAML is currently being used more for offline data processes. For example, it is included by default in the C-based OpenCV computer vision package, whereas JSON is not.

You will find C libraries for both JSON and YAML. YAML's libraries tend to be newer, but I have had no trouble with them in the past. See for example Yaml-cpp.

Python – How to parse a YAML file in Python

The easiest and purest method without relying on C headers is PyYaml (documentation), which can be installed via pip install pyyaml:

#!/usr/bin/env python

import yaml

with open("example.yaml", "r") as stream:
    try:
        print(yaml.safe_load(stream))
    except yaml.YAMLError as exc:
        print(exc)

And that's it. A plain yaml.load() function also exists, but yaml.safe_load() should always be preferred unless you explicitly need the arbitrary object serialization/deserialization provided in order to avoid introducing the possibility for arbitrary code execution.

Note the PyYaml project supports versions up through the YAML 1.1 specification. If YAML 1.2 specification support is needed, see ruamel.yaml as noted in this answer.

Also, you could also use a drop in replacement for pyyaml, that keeps your yaml file ordered the same way you had it, called oyaml. View synk of oyaml here

Best Answer

Related Solutions

Json – the difference between YAML and JSON

Python – How to parse a YAML file in Python

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