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.
Note
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 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 .
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 Header | Interpretation | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
ID | 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
contains | ||||||||||
TIME | 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.
If the
data file also contains a | ||||||||||
DATE , DAT1 , DAT2 ,
or DAT3 | Defines the day of the observation or the dose. The column
can contain the month as a number (
Note
| ||||||||||
DV | Numeric value of an observation. Column cannot contain Inf or –Inf . | ||||||||||
MDV | Defines whether a row describes an observation:
| ||||||||||
EVID | Defines the type of event described for the row in the record:
If a column contains values for dose, but If The import process does
not support values | ||||||||||
CMT | Indicates which compartment is used for observation value or
for dose received. The interpretation also depends on EVID :
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 | ||||||||||
AMT | Positive number indicating dose. 0 or NaN specifies
no dose administered. The column cannot contain Inf . | ||||||||||
RATE | Positive 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 . | ||||||||||
II | Positive number defining the time between doses. | ||||||||||
ADDL | When 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. |
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
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, numeric, or categorical 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 NaN
s. 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 NaN
s. 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.
When you are importing data from a table using SimBiology Model Analyzer, the
app supports the following column data types: double
,
char
, cell array of character vectors, categorical
,
duration
, and datetime
.
When you import a multidimensional SimData
array to the app, the app
flattens the 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
Browser.