In metrumresearchgroup/yspec: Data Specification for Pharmacometrics

Introduction

This vignette shows you how to gather the specifications for all of your analysis project data sets, assemble into a single object, and use that object to render a project-wide define document.

Set up

library(yspec)

Load specification objects for all data sets

If my project had 3 analysis data sets, one for PK, one for PKPD, and one for AEs, we create a specification object for each one. Here, we're using load_spec_ex() because we're using example material from the package. You should use ys_load() for your project and give the full path to the yaml specification file.

sp1 <- load_spec_ex("DEM104101F_PK.yml")
sp2 <- load_spec_ex("DEM104101F_PKPD.yml")
sp3 <- load_spec_ex("DEM104101F_AE.yml")

Each object looks something like

sp1

This includes our usual information about the columns in the data set.

Create a project object

We take these specification objects and create a project object from them.

proj <- ys_project(sp1,sp2,sp3)

proj

Now, for each specification object, we have a data / specification name as well as a description (along with some other information).

This file is by default saved to a temporary location. But you can also save it locally and keep it as a part of the project.

```{txt, code = readLines(get_meta(proj)[["spec_file"]])}

To do this, we tucked some additional information into the data set 
specification file. For example, the specification file for the first spec 
object (`sp1`) looks like this:
```{txt, code = readLines(yspec_yml_file(sp1))}

In the SETUP__ block, we included a description; this is required to make a project object from data objects. There also is a name that defaults to the stem of the data specification file. We also optionally included projectnumber and sponsor. These will get inserted into the define document when the MetrumRG Rmarkdown template is used.

Render a define file

Now, we have an object with the project information put together. The essential contents of that object have been written to a project spec file and can be used to template the creation of a project data specification file.