You can import tabular data to the SimBiology Model Analyzer app or to the MATLAB® Workspace. The supported file types are Excel® files (.xls, .xlsx), text files (.csv, .txt), and SAS® XPORT files (.xpt). You can also specify that the data is in a NONMEM® formatted file. The import process interprets the columns according to the NONMEM definitions. For more information see Support for Importing NONMEM Formatted Files.
If your data set contains dosing information that is infusion data, the data set must contain the rate and not an infusion duration.
Regardless of whether unit conversion functionality is on or
off, dosing in the data file must be expressed in amounts (or as
infusion rate). By default Unit Conversion is
off, so you must ensure that units for the data are consistent with
each other. If you want to turn on unit conversion, see Unit Conversion for Imported Data .
If you are creating a file containing time course data that you want to import into SimBiology for fitting, create the data file with the following columns:
Group column — Specify text, numeric, or categorical values. For instance, you can use this column to group multiple individuals into separate groups. You can then use this grouping or categorical information for hierarchical fits. This column is optional.
ID column — Specify text, numeric, or categorical values. The rows in the file that have the same ID column value are for the same individual. This column is optional if the measurement data comes from just one individual.
Time column — Specify monotonically increasing positive values within each ID that define the time of the dose, observation measurements, and covariate measurements.
Zero or more dosing columns — Create one dosing column for each compartment
being dosed. In each column, specify positive values representing dose amounts that
are added to a species. Use
NaN (not a number) to specify that no
dose was applied at the specified time. In other words, specify the dose amount as
NaN when an observation was recorded but no dose was
Zero or more rate columns — Specify positive values, zero, or
NaN. Zero specifies an infinite rate and
specifies that no rate applies. The rate column is associated with a dosing column and
defines the rate at which the dose is administered. For example, if you can specify an
infusion dose in the
Dose1 column, specify its rate in the
Zero or more observation columns — Specify numeric values or
NaN values define that no observation was
recorded at the specified time. Use
NaN for times when a dose was
applied but no observation was recorded. You can specify one observation value at a
particular time for each ID. When you have replicates, specify multiple observation
values for the same time point by adding more rows with the same time value. For an
example, see rows 2 and 3 in the screen shot below, where
CentralConc has two measurements at time = 0.
Zero or more covariate columns — Specify text, numeric, or categorical
NaN. Each value defines the covariate value at the
NaN values indicate that no covariate observation
was recorded at the specified time. SimBiology supports only covariates that are not
time varying. For instance, see the Sex and Age
columns in the example below. For an example that shows how to use categories for
fitting, see Estimate Category-Specific PK Parameters for Multiple Individuals.
A screen shot of a sample data file follows.
You can download the sample Excel file from the following location:
matlabroot is the root directory where you installed MATLAB. You can
matlabroot at the command line to see the
file path of the root directory.
You can specify that the data is in a NONMEM formatted file. The following table highlights the interpretation of this data in SimBiology® software.
Text (character vector), numeric, or categorical values
that identify the record or group. The import process assumes that
contiguous data with the same value contains data from one individual.
If the data contains non-contiguous references to the same value,
the import process assigns the second ID encountered an indexed valued
derived from the group first encountered. For example, if the ID columns
Monotonically increasing positive values within each
group, indicating time of observation or dose or text (character vector).
The data file can specify clock (
The following table is an example of how the import process interprets the clock values as decimal values.
data file also contains a
Defines the day of the observation or the dose. The column
can contain the month as a number (
|Numeric value of an observation. Column cannot contain |
|Defines whether a row describes an observation: |
|Defines the type of event described for the row in the record:|
If a column contains values for dose, but
The import process does
not support values
|Indicates which compartment is used for observation value or
for dose received. The interpretation also depends on |
SimBiology numbers compartments starting with 1, while NONMEM
numbers them starting with 0. For instance, if a NONMEM data file
contains doses and measurements for
|Positive number indicating dose. |
|Positive number indicating rate of infusion. |
|Positive number defining the time between doses.|
|When the data specifies a number of identical serial doses
at specific intervals (defined by |
The import process does not support (and therefore ignores) the rows containing the following values or definitions:
EVID values 3 and 4
SS column for specifying steady
PCMT column to define whether to
compute a prediction for the row
CALL column for calling the ERROR
or the PK subroutine
If rate is specified as being less than zero, it is assumed to be zero
When you are importing data from a table using SimBiology Model Analyzer, the
app supports the following column data types:
string, cell array of character vectors,
When you import a multidimensional
SimData array to the app, the app
SimData array and uses a single index (linear indexing) in the
corresponding datasheet. For example, if you import a
2x2x2 SimData array
A, the app creates a datasheet with 8 groups (one for each
SimData object), indexing from 1 to 8. The app still displays the
original size of the
SimData array in the