Importing Data — Supported Files and Data Types

Supported Files and Data Types

You can import tabular data to the SimBiology® desktop or to the MATLAB® Workspace. The supported file types are .xls, .csv, and .txt. You can 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.

From the SimBiology desktop, you can filter the raw data to suppress outliers, visualize data using common plots (such as plot, semilog, scatter, or stairs), and perform basic statistical analysis. You also can use functions to process and visualize the data at the command line.

    Note:   If your data set contains dosing information that is infusion data, the data set must contain the rate and not an infusion duration.

Unit Conversion

Regardless of whether unit conversion functionality is on or off, dosing in the data file must be expressed in amounts (or as amount/time for 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 .

Support for Importing NONMEM Formatted Files

You can specify that the data is in a NONMEM formatted file. The following table highlights the interpretation of this data in SimBiology software.

Column HeaderInterpretation
ID

Text or numeric values that identify the record. 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 contains [1 1 1 2 2 2 1 1 1], the IDs assigned are 1, 2, 1_1.

TIME

Monotonically increasing positive values within each group, indicating time of observation or dose. The data file can specify clock (2:30) or decimal values (6.25). The import process assigns a value of 0 to the first TIME value in the data file. The import process assigns subsequent values relative to the first value. For example the import process interprets [10:05 10:30 11 12:30 21.3] as: [0 0.25 0.95 2.25 14.2].

If the data file also contains a DATE column, the import process uses it with the TIME column in calculating the relative TIME values. The column cannot contain Inf.

DATE, DAT1, DAT2, or DAT3

Defines the day of the observation or the dose. The column can contain the month as a number (9) or a string (Sep). Specify date in the following formats:

  • DATE — The column can specify month/day/year or month-day-year. If you specify two numbers, the import process assumes they are month and day.

  • DAT1 — The column can specify day/month/year or day-month-year. If you specify two numbers, the import process assumes they are day and month.

  • DAT2 — The column can specify year/month/day or year-month-day. If you specify two numbers, the import process assumes they are month and day.

  • DAT3 — The column can specify year/day/month or year-day-month. If you specify two numbers, the import process assumes they are day and month.

Note the following additional assumptions:

  • If you specify only one number, the import process assumes it is the day

  • You can omit the year or specify 1, 2, 3, or 4 digits. If you specify two-digit years, it is assumed to be in the 1900s.

DVNumeric value of an observation. Column cannot contain Inf or –Inf.
MDVDefines whether a row describes an observation:
  • Row contains 0 — Observation event

  • Row contains 1 — Not an observation event

EVIDDefines the type of event described for the row in the record:
  • 0 — Observation event; row contains an observed value.

  • 1 — Dose event; row describes a dose.

  • 2 — Other event; row describes some other event such as measurement of a covariate.

If a column contains values for dose, but EVID is not 1, the import process ignores the value. You see a warning and the value is ignored.

If EVID is set to 2, then only those specified row data are imported as covariate data. However, if you have an EVID column as well as one or more covariate columns, but do not specify a value of 2 anywhere in the EVID column, then SimBiology imports all the row data as covariate values.

The import process does not support values 3 and 4. You see a warning and the value is ignored.

CMTIndicates which compartment is used for observation value or for dose received. The interpretation also depends on EVID:
  • Observation event (EVID = 0 ) — CMT column indicates which compartment was used for observation value.

  • Dose Event (EVID = 1) — CMT column indicates which compartment received the dose.

    Note:   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 CMT = 0, SimBiology generates data columns named Dose1 and Response1 respectively.

AMTPositive number indicating dose. 0 or NaN specifies no dose administered. The column cannot contain Inf.
RATEPositive number indicating rate of infusion. 0 specifies an infinite rate (equivalent to a bolus dose), and NaN specifies no rate. The column cannot contain Inf.
IIPositive number defining the time between doses.
ADDLWhen the data specifies a number of identical serial doses at specific intervals (defined by II), ADDL specifies the number of doses in the series excluding the initial dose. If the data specifies II but not ADDL, then SimBiology assumes that the dosing occurs for the duration of that data record.

Unsupported NONMEM Definitions

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 state doses

  • 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

Creating a Data File with SimBiology Definitions

If you are creating a file containing population data that you want to later import into SimBiology, create the data file with the following columns:

  • Group column — Specify text or numeric values. The rows in the file that have the same Group column value are for the same individual.

  • Time column — Specify monotonically increasing positive values within each group that define the time of the dose, observation and/or covariate measurements.

  • Zero or more dosing columns — Create one dosing column for each compartment being dosed. In each column, specify positive values representing doses in amount that are added to a species. Use 0 or NaN to specify that no dose was applied at the specified time. This is useful for times when an observation was recorded but no dose was applied.

  • Zero, or more rate columns — Specify positive values. Zero specifies an infinite rate and NaN specifies that no rate applies. The rate column is associated with a dosing column and defines the rate at which the dose is administered.

  • Zero or more observation columns — Specify numeric values or NaNs. You can only specify one observation value at a particular time for each group. NaN values define that no observation was recorded at the specified time. This is useful for times when a dose was applied but no observation was recorded.

  • Zero or more covariate columns — Specify numeric values or NaNs. Each value defines the covariate value at the specified time. NaN values define that no covariate observation was recorded at the specified time.

    If you set an EVID value of 2 for some rows, then SimBiology imports only those rows as covariate data. If you do not mention an EVID value of 2 anywhere and have one or more covariate columns, then SimBiology imports all the row data as covariate data.

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