The DataPackageR YAML configuration file."

In DataPackageR: Construct Reproducible Analytic Data Sets as R Packages

Configuring and controlling DataPackageR builds.

Data package builds are controlled using the datapackager.yml file.

This file is created in the package source tree when the user creates a package using datapackage_skeleton().

It is automatically populated with the names of the code_files and data_objects the passed in to datapackage_skeleton.

The datapackager.yml file.

The structure of a correctly formatted datapackager.yml file is shown below:

library(DataPackageR)
library(yaml)
yml <- DataPackageR::construct_yml_config(code = "subsetCars.Rmd", data = "cars_over_20")

cat(yaml::as.yaml(yml))

YAML config file properties.

The main section of the file is the configuration: section.

It has three properties:

• files:

The files (R or Rmd) to be processed by DataPackageR. They are processed in the order shown. Users running multi-script workflows with dependencies between the scripts need to ensure the files are processed in the correct order.

Here subsetCars.Rmd is the only file to process. The name is transformed to an absolute path within the package.

Each file itself has just one property:

• enabled: A logical yes, no flag indicating whether the file should be rendered during the build, or whether it should be skipped. This is useful for 'turning off' long running processing tasks if they have not changed. Disabling processing of a file will not overwrite existing documentation or data objecs created during previous builds.

• objects:

The names of the data objects created by the processing files, to be stored in the package. These names are compared against the objects created in the render environment by each file. They names must match. - render_root:

The directory where the Rmd or R files will be rendered. Defaults to a randomly named subdirectory of tempdir(). Allows workflows that use multiple scripts and create file system artifacts to function correctly by simply writing to and reading from the working directory.

Editing the YAML config file.

The structure of the YAML is simple enough to understand but complex enough that it can be a pain to edit by hand.

DataPackageR provides a number of API calls to construct, read, modify, and write the yaml config file.

API calls

construct_yml_config

Make an r object representing a YAML config file.

Example

The YAML config shown above was created by:

# Note this is done by the datapackage_skeleton. 
# The user doesn't usually need to call 
# construct_yml_config()
yml <- DataPackageR::construct_yml_config(
  code = "subsetCars.Rmd",
  data = "cars_over_20"
  )

yml_find

Read a yaml config file from a package path into an r object.

Example

Read the YAML config file from the mtcars20 example.

# returns an r object representation of
# the config file.
mtcars20_config <- yml_find(
  file.path(tempdir(),"mtcars20")
  )

yml_list_objects

List the objects in a config read by yml_find.

Example

  yml_list_objects(yml)

yml_list_files

List the files in a config read by yml_find.

Example

  yml_list_files(yml)

yml_disable_compile

Disable compilation of named files in a config read by yml_find.

Example

yml_disabled <- yml_disable_compile(
    yml,
    filenames = "subsetCars.Rmd")
cat(as.yaml(yml_disabled))

yml_enable_compile

Enable compilation of named files in a config read by yml_find.

Example

yml_enabled <- yml_enable_compile(
    yml,
    filenames = "subsetCars.Rmd")
cat(as.yaml(yml_enabled))

yml_add_files

Add named files to a config read by yml_find.

Example

yml_twofiles <- yml_add_files(
    yml,
    filenames = "anotherFile.Rmd")
# cat(as.yaml(yml_twofiles))

yml_add_objects

Add named objects to a config read by yml_find.

Example

yml_twoobj <- yml_add_objects(
    yml_twofiles,
    objects = "another_object")
# cat(as.yaml(yml_twoobj))

yml_remove_files

Remove named files from a config read by yml_find.

Example

yml_twoobj <- yml_remove_files(
    yml_twoobj,
    filenames = "anotherFile.Rmd")
# cat(as.yaml(yml_twoobj))

yml_remove_objects

Remove named objects from a config read by yml_find.

Example

yml_oneobj <- yml_remove_objects(
    yml_twoobj,
    objects = "another_object")
# cat(as.yaml(yml_oneobj))

yml_write

Write a modified config to its package path.

Example

yml_write(yml_oneobj, path = "path_to_package")

The yml_oneobj read by yml_find() carries an attribute that is the path to the package. The user doesn't need to pass a path to yml_write if the config has been read by yml_find.

DataPackageR documentation built on March 17, 2021, 5:07 p.m.