library(yspec)2.1 Introduction
The yspec package will read your data specification file when it is written in a specific yaml format. Using the object created from this file, you can validate data assembly outputs, label the data frame to be written in sas xport format, create a define.pdf document, and more.
For each data set in your project that needs documentation, create a yaml file that lists the columns in the data set along with details about the data in that column. This yaml file can be loaded into your R session into an object that you can work with. This is referred to as a spec object. The term spec refers to a single documented data object / data file.
Once all of your data sets have been documented with their own yaml file, you can create another object called a yproj objects. This is used to template the rendering of a single integrated data definitions file for your entire project.
Keep reading the vignette to see how it works.
2.2 Example spec file
An example specification file looks like:
specfile <- ys_help$file()SETUP__:
description: Example PopPK analysis data set
sponsor: example-project
projectnumber: EXAMPK1011F
use_internal_db: true
glue:
bmiunits: "kg/m$^2$"
flags:
covariate: [AGE:SCR, HT, AST:ALT]
lookup_file: "look.yml"
extend_file: "analysis1-ext.yml"
C:
NUM:
ID:
SUBJ: !look
TIME: !look
label: time after first dose
unit: hour
SEQ:
label: data type
values: {observation: 0, dose: 1}
CMT:
EVID:
make_factor: trueOnce the data specification yaml file is written, it can be loaded in R
spec <- ys_load(specfile)
head(spec) name info unit short source
1 C cd- . comment character ysdb_internal
2 NUM --- . record number ysdb_internal
3 ID --- . subject identifier ysdb_internal
4 SUBJ c-- . subject identifier ysdb_internal
5 TIME --- hour TIME look
6 SEQ -d- . SEQ .
7 CMT --- . compartment number ysdb_internal
8 EVID -d- . event ID ysdb_internal
9 AMT --- mg dose amount ysdb_internal
10 DV --- micrograms/L dependent variable ysdb_internalData from specific columns can be printed
spec$WT name value
col WT
type numeric
short weight
unit kg
range 40 to 100spec$EVID name value
col EVID
type numeric
short event ID
value 0 : observation
1 : dose 2.2.1 Items that you should be including for most columns
short: a short name for the column (e.gweight); this will default to the column name (col) … sometimes that makes senselabel: to be used to label the data set and to populate thedefine.pdfdocument (e.g.patient weight at baseline)unit: when it’s appropriate (e.g.kg)decode: for discrete data items (e.g. if SEX isvalues: [0,1]then then usedecode: [male, female]; or include themake_factor: truefield
2.3 Check a data set against the spec
Use the ys_check() function, with the data frame as the first argument and the spec object as the second argument
data <- ys_help$data()
ys_check(data, spec)2.4 Example to render spec
The specification object can be rendered to a specification file with the ys_document function
ys_document(spec, stem = "working_document")ys_document will pass along arguments to rmarkdown::render so that you can control those aspects of how the document is rendered. You can also create custom output formats to get the data table to render in the way that you like.
2.5 Example project object
To create an project-wide listing of documented data sets, we create a yproj or project object. We create this from the spec objects that we read about in the previous section. Let’s load another object to use along with the object loaded in the previous section.
pdspec <- load_spec_ex("DEM104101F_PKPD.yml")Now, we have two objects to work with:
head(spec) name info unit short source
1 C cd- . comment character ysdb_internal
2 NUM --- . record number ysdb_internal
3 ID --- . subject identifier ysdb_internal
4 SUBJ c-- . subject identifier ysdb_internal
5 TIME --- hour TIME look
6 SEQ -d- . SEQ .
7 CMT --- . compartment number ysdb_internal
8 EVID -d- . event ID ysdb_internal
9 AMT --- mg dose amount ysdb_internal
10 DV --- micrograms/L dependent variable ysdb_internalhead(pdspec) name info unit short source
1 C c-- . C .
2 MDV --- . MDV .
3 SEQ -d- . SEQ .
4 AMT --- mg AMT .
5 II --- hours II .
6 CMT --- . Compartment .
7 TAFD --- hours TAFD .
8 WT --- kg Weight .
9 EGFR --- ml/min/1.73 m2 eGFR .
10 SEX -d- . SEX .We can create a project object from both objects
proj <- ys_project(spec,pdspec)
projprojectnumber: EXAMPK1011F
sponsor: example-project
--------------------------------------------
datafiles:
name description data_stem
analysis1 Example PopPK analysis data set analysis1
DEM104101F_PKPD Population PKPD analysis data set DEM104101F_PKPD2.6 Render a project file
2.6.1 Working document
To render the project file we’ll use the same ys_document() function.
This time, we’ll add some extra (optional) arguments that will help us get the document to look the way we want:
ys_document(
proj,
stem = "project_document",
build_dir = definetemplate(),
author = "Michelle Johnson",
title = "Analysis data specification"
)Using the build_dir argument gets us the document rendered with Metrum Research Group branding. Also, author and title are passed into the configuration fields for this document.
2.6.2 Regulatory document
To get a document that is formatted according to FDA requirements, use:
ys_document(
proj,
type = "regulatory",
stem = "fda_document",
build_dir = definetemplate(),
author = "Michelle Johnson",
title = "Analysis data specification"
)