FAQ

Evolution

  • What are the evolution in this version compared to the previous version (2016R1)? All the evolution can be found here.
  • Can I get the documentation for the data set associated with the 2016R1 version? Of course, you can download it here.

Questions about format

  • Which file formats are supported? Text and comma-separated values file are allowed. The file extension should preferably be .txt or .csv.
  • Should I have a header line? Yes, having a header line is mandatory.
  • Are there restrictions on header names? No, there is no limitation in terms of names nor on character number. However, some characters are not allowed as in the rest of the data file (see here).
  • Which column types are mandatory? The ID, and OBSERVATION column-types are mandatory. All others are optional.
  • Which column-types are possible? The complete list of supported column-types can be found here.
  • Which separators are allowed? The supported separators are comma (“,”), semicolon (“;”), space (” “), and tab (“\t”).
  • Which characters are allowed in strings? The list of allowed characters can be found here.
  • What does “.” mean? The “.” can be used in almost all the lines of the data set but has several meaning depending on the context. A summary can be found here.
  • How can I ignore some response-lines of my data set? Use IGNORED OBSERVATION=1 for that.
  • How can I ignore some dose-lines of my data set? Use EVENT ID=2
  • Can I specify time in hour or in days? Yes, all the possible formats are defined here.
  • Can the data be split into several files (for instance one file for dosing and one for observations)? No. All the data must be grouped into a single file.

Questions about units

  • How are units handled? Units are free but must be consistent. For instance TIME, INFUSION RATE, INFUSION DURATION, INTERDOSE INTERVAL must have the same TIME units. With models from the libraries, no unit conversion is done. Thus, if in the data set TIME is in hours, rate constant parameters will be /hours. If in the data set the AMOUNT is in mmol and the concentration in mM, then the volume parameter will be in L.
  • Is it possible to automatically convert units? No.
  • Are the units visible in the graphical user interface of Monolix? No.

Questions about format difference with NONMEM

  • What are the differences between Monolix and Nonmem in terms of data set? The few differences are listed here.
  • What is the equivalent of the NONMEM CMT column? Depending on the usage of the CMT column, it can correspond to the OBSERVATION ID column-type, or the ADMINISTRATION ID column-type. All differences between NONMEM and the MonolixSuite are listed here.

Questions about subjects and occasions

  • Must all lines corresponding to the same individual be grouped? No, this is not necessary. All lines with the same ID will be assigned to the same individual, whatever their order or grouping.
  • How can I define occasions? For that, you can use the OCCASION column-type as explained here.

Questions about time

  • Must the times be in ascending order? For a given individual, the times do not need to be in order. The sorting will be done automatically.
  • Can I specify time in hour or in days? Yes, all the possible formats are defined here.
  • Can time have negative values? Yes.
  • For time-to-event data, do I have to indicate the start time? Yes, it must be explicitly stated, for instance with TIME=0 and OBSERVATION=0. Guidelines for data set formatting for time-to-event data are given here.

Questions about responses and observations

  • Are non-continuous data types (such as count, time-to-event and categorical data) supported? Yes. Exemples of data set for non-continuous data types are presented here.
  • Which value should I enter in the OBSERVATION column-type for BLQ values? In the OBSERVATION column-type, give the limit of quantification (LOQ). To mark the observations as being BLQ, use the CENSORED column-type. To indicate a censoring interval, use the LIMIT column-type in addition.
  • Can my data set contain different types of observations? Yes, use the OBSERVATION ID column to define to which type of data the line corresponds. An example data set with different types of observations is presented here.
  • What happen if I define both a dose and a response in the same line? Depending on the values, it can be a dose, a response. To see all the configurations, see here.

Questions about dose regimen

  • How are steady-state doses handled? In case of a steady-state dose, 5 additional doses are added before the steady-state dose, in order to reach steady-state. More details can be found here.
  • What happen if I define both a dose and a response in the same line? Depending on the values, it can be a dose, a response. To see all the configurations, see here.
  • For dose-lines, should I specify the compartment into which the dose is introduced? No. In the MonolixSuite, the matching between the data (dose and observation lines) and the model (administrations and predictions) is done using identifiers, not based on compartment numbers. To assign a dose to a specific administration of the model (oral or iv macros for classical PK models, depot macro for more complex ODEs), the column ADMINISTRATION ID is used. The identifier in the ADMINISTRATION ID column should match the “adm=” field of the macro.
  • If I have several outputs, should I duplicate the dosing information? No.
  • If a dose is split in two absorption routes, should I duplicate the dosing information? No. The same dose line can be split in different fractions using the bioavaila

Questions about covariates

  • Can I have time-varying covariates? Continuous (CONTINUOUS COVARIATE) and categorical (CATEGORICAL COVARIATE) covariates must be contant within a subject-occasion. If a continuous covariate varies with respect to time, the first value in time will be used for the entire subject-occasion. Time-varying continuous covariates can be tagged as regressors (column-type REGRESSOR) to be used as such.

Questions about controls and events

  • How can I ignore certain response-lines of my data set? Use IGNORED OBSERVATION=1 for that.
  • Are the MDV and EVID columns necessary? These columns are not mandatory and most of the time not necessary.
  • How can I define a time at which I which the output the predictions, even if I have no observation? No, use Simulx for simulations.