Defining a data set

Data set structure

The data set structure contains for each subject measurements, dose regimen, covariates etc … i.e. all collected information. The data must be in the long format, i.e each line corresponds to one individual and one time point. Different type of information (dose, observation, covariate, etc) are recorded in different columns, which must be tagged with a column type (see below). The column types are very similar and compatible with the structure used by the Nonmem software (the differences are listed here). This is specified when the user defines each column type in the data set as in the following picture.

Notice that Monolix often provides an initial guess of the type of the column depending on the name.
In addition, we have a button DATA VIEWER that allows to explore the data set as Datxplore.

Description of column-types

The first line of the data set must be a header line, defining the names of the columns. The columns names are completely free. In the MonolixSuite applications, when defining the data, the user will be asked to assign each column to a column-type (see here for an example of this step). The column type will indicate to the application how to interpret the information in that column. The available column types are given below:

Column-types used for all types of lines:

Column-types used for response-lines:

Column-types used for dose-lines:

Loading a new data set

To load a new data set, you have to go to “Browse” your data set (green frame), tag all the columns (purple frame), define the observation types, and click on the blue button ACCEPT  as on the following.

Observation type

There are three types of observations

  • continuous: The observation is continuous with respect to time. For example, a concentration is a continuous observation.
  • count/categorical: The observation values takes place in a finite categorical space. For example, the observation can be a categorical observation (an effect can be observed as low, medium, high) or a count observation over a defined time (the number of epileptic crisis in a defined time).
  • event: The observation is an event, for example the occurring of an epileptic crisis.

The type of observations can be specified by the user in the interface.

Labeling

The name proposed in the figure and in the data choice is the one defined in the label. The user can modify it. By default, the label used is the one defined in the data set.
Starting from the 2019 version, it is possible to change your preferences. By clicking on Settings>Preferences, the following windows pops up.

In the DATA frame, you can add or remove preferences for each column.
To remove a preference, double-click on the preference you would like to remove. A confirmation window will be proposed.
To add a preference, click on the header type you consider, add a name in the header name and click on “ADD HEADER” as on the following figure.


Notice that all the preferences are shared between Monolix, Datxplore, and PKanalix.

Filtering

Starting from the 2019 version, we added the possibility to graphically filter the data set using the filters at the bottom of the page.

Notice that this is only a graphical filtering action, it does not filter the data set used by Monolix. The user can propose filter on any column and on any combination of column. It allows a very interesting shortcut to see directly in your data set without directly reopening it.
In addition, each contiguous information of a subject is linked and a summary of the covariate is displayed along with the id value. Moreover, it is possible to expand or retract all the information of a subject.

Importing a project from Datxplore or PKanalix

It is possible to import a project from Datxplore or PKanalix. For that, go to Project>New project for Datxplore/PKanalix (as in the green box of the following figure). In that case, a new project will be created and all the DATA frame will already be filled by the information from the Datxplore or PKanalix project.