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PEtab NMLE extension

Note

An NLME extension will be most useful in conjunction with a dosing or time-course extension.

This is a draft for a PEtab NLME extension. It adds the following to the existing PEtab specification.

Individual table

This table is an addition to the existing PEtab format. It introduces a classification of individuals (most fine grained grouping) into several (more coarse grained) groups. Random effects can be specific to each individual or to the groups they belong to.

Detailed field description

  • individualId [STRING]

  • ${groupId} [STRING, OPTIONAL]

    Further columns may be used to group individuals into different categories.

Parameter table

In addition to the existing descriptions of fixed effects, the NLME extension adds the following columns to describe random effects.

Detailed field description

  • randomVariableId [STRING]

    ID of the random variable. If left empty, there is no random effect defined on the parameter of this row.

  • randomEffectFormula [STRING]

    Random effect function as plain text formula expression. Must contain the parameterId and the randomVariableId and must not contain any other symbols (or should we allow that???).

  • distributionType [STRING: 'normal' or 'laplace', OPTIONAL]

    Assumed random effect distribution. Only normal and laplace distributions are currently allowed (but we could allow any term in some ontology for distributions). Defaults to normal. Distributions are assumed to be zero-centered. Covariances are defined in the covariance table.

  • groupType [STRING]

    Defines how random effects are grouped together. Any column name from the individual table is allowed, except for covariate (i.e. numeric) columns.

Covariance tables

These tables are an addition to the existing PEtab format to describe the covariances of the random effects. Each groupType for which covariances are estimated has its own table. Four formats are allowed

  • Matrix format

    All random effects occur in columns and rows. Covariances that are estimate contain the value 1, covariances that are assumed to be zero contain the value 0, or are left blank.

  • Sparse matrix format

    This format contains two columns, randomEffect1 and randomEffect2 to list pairs of random effects for which covariances shall be estimated. Variances are estimated for all random effects. No duplicate sets are allowed (e.g. if one row specifies u1, u2, there must not be a u2, u1 row).

  • Single cell format

    If the covariance table only contains a single cell, this cell must contain the string full to specify that all (co)variances are estimated.

  • No table

    If no table is provided, only the variances, but no covariances are estimated.