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Reserved keywords

Reserved keywords

Some keywords are used in Mlxtran for dedicated purposes. Thus these keywords are not available for re-definition or overloading.

Time-related keyword

The reserved keyword for the time is t. It corresponds to the time defined in the TIME column in Monolix, and the times defined in the treatment, observation and regressor elements in Simulx.

Example:

The keyword time can be used to define a time-varying clearance for instance:

CODE
[LONGITUDINAL]
input = {V, CLini, CLss, T12}

EQUATION:
Cl = CLss - (CLss-CLini)*exp(-t/T12)
Cc = pkmodel(V,Cl)

Administration-related keywords

Information related to the doses defined in the data set or in the Simulx treatment elements are available in the structural model via several keyword. They are piece-wise constant functions which value is updated each time there is a dose. Before the first dose, their value is zero.

The value of the keyword are directly related to the design, they are unaffected by the absorption/depot macros  arguments such as Tlag or p. Note that doses are not discriminated according to their administration types.

  • tDose: holds the time of the last administered dose.

  • amtDose: holds the amount of the last administered dose.

  • inftDose: holds the infusion duration of the last administered dose.

Example:

The keyword amtDose can be used to define a dose-dependent absorption for instance:

CODE
[LONGITUDINAL]
input = {ka, V, Cl, D50}

EQUATION:
F = D50/(amtDose+D50)
Cc = pkmodel(ka, V, Cl, p=F)

https://www.youtube.com/watch?v=9gy1JLfDssI

Full list of keywords

Reserved keywords

Here is the full list of Mlxtran keywords to use in Simulx, except

  • the keywords used for distribution definition (that are listed here)

  • the keywords used for classical mathematical definition (that are listed here)

Name

   Meaning

where can it be used ?

link

absorption

Macro used for defining the absorption process in a longitudinal model

In subsection [LONGITUDINAL] after PK:

link

adm

Type of administration (type and adm are equivalent)

In argument of the following macros: absorption, depot, iv and oral

depot macroother macros

amount

Name of the variable defined as the dose amount within the compartment

In argument of the following macros: compartment and peripheral

link

amtDose

Amount of the last administered dose. This is a step function and is null before the first dose.

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

current page

bsmm

Mixture of continuous observations. It is a mixture between subjects model mixtures (BSMM). It assumes no inter individual variabilities for the proportions of each group (ı.e. the probabilities to belong to the different groups). It is relevant only for Monolix.

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

see Monolix doc

categorical

Type of observation model

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: after a type=

link

categories

List of the available ordered categories for a categorical observation. They are usually represented by increasing successive integers.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is a category

link

cmt

Label of the compartment

In argument of the following macros: absorption, compartment, depot, effect, elimination, iv, oral

link

coefficient

Coefficient under consideration for a distribution definition depending on covariates

In any distribution definition in a block DEFINITION:

link

combined1

Combined error model latex-1-20240607-151033.png

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

combined1c

Corresponds to a combined error model latex-20240607-151046.png

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

combined2

Combined error model latex-1-20240607-151117.png

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

combined2c

Combined error model latex-20240607-151132.png

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

compartment

Macro used for defining a compartment

In subsection [LONGITUDINAL] after PK:

link

concentration

Name of the variable defined as the concentration within the compartment

In argument of the following macros: compartment, effect, peripheral

link

constant

Constant error model latex-1-20240607-151204.png

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

continuous

Type of observation model.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: after a type=

link

count

Type of observation model.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: after a type=

link

covariate

Covariate under consideration for a distribution definition

In any distribution definition in a block DEFINITION:

link

delay

It corresponds to delay function to define DDE.

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

link

dependence

It corresponds to the label used to defined that an observation variable for ordered categorical data modelled as a Markov chain.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is categorical

link

depot

It corresponds to an absorption targeting a depot. A component of an ODE system is defined as the target depot for the doses.

In subsection [LONGITUDINAL] after PK:

link

effect

This macro defines an effect compartment. It is linked to a simple compartment and used through the variable for its effect concentration.

In subsection [LONGITUDINAL] after PK:

link

elimination

This macro defines an elimination process.

In subsection [LONGITUDINAL] after PK:

link

else

It is part of a conditional statement. A conditional statment can be built by combining the keywords if, elseif, else and end.

In a block EQUATION:

 link

elseif

It is part of a conditional statement. A conditional statment can be built by combining the keywords if, elseif, else and end.

In a block EQUATION:

link

end

It is part of a conditional statement. A conditional statment can be built by combining the keywords if, elseif, else and end.

In a block EQUATION:

link

errorModel

It corresponds to the label to define an error model for a continuous observation model

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

event

Type of observation model.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: after a type=

link

eventType

Label to define the event type for an event observation model. It allows to define if the exact time of the events or censored per interval is observed.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is an event

link

from

Label of the source compartment for the transfer.

In argument of the following macro: transfer

link

hazard

Hazard function

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is an event

link

if

It is part of a conditional statement. A conditional statment can be built by combining the keywords if, elseif, else and end.

In a block EQUATION:

link

inftDose

The keyword inftDose defines the infusion time of the last administered dose. This is a step function. The rate of the final absorption can be different from the rate of the administration process. It is null before the first dose.

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

current page

input

It corresponds to the definition of the inputs in a subsection

In subsections [LONGITUDINAL], [INDIVIDUAL], and [COVARIATE]

link

intervalCensored

Argument of eventType.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is an event

link

intervalLength

Label to length of censoring intervals in an event observation model. It is useful for simulation only,

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is an event

link

iv

The macro iv defines an absorption for intravenous doses. Doses without an administration rate or infusion time are instantaneously absorbed within the associated compartment, as an IV bolus.

In subsection [LONGITUDINAL] after PK:

link

linear

It is an argument of odeType= and allows to define the dynamical system as linear

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

link

Markov

It corresponds to the dependence of a categorical observation model. It allows to define that the observation model is based on a Markov chain

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: after a dependence=

link

maxEventNumber

Maximum number of events in an event observation model. It is useful for simulation only

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is an event

link

mean

Mean of the associated normal distribution.

In any distribution definition in a block DEFINITION:

link

nonStiff

It is an argument of odeType= and allows to define the dynamical system is nonStiff and thus yields to an adapted numerical scheme for the resolution

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

link

odeType

It is the label that allows to define the type of ODE.

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

link

oral

It is a macro used for defining the absorption process in a longitudinal model

In subsection [LONGITUDINAL] after PK:

link

output

It allows to define the outputs of a structural model

In the longitudinal model, in subsection [LONGITUDINAL], in a block OUTPUT:

link

P

The majuscule P corresponds to the definition of a probability

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION:

link

p

It corresponds to the bio availability in an absorption process

In argument of the following macro: absorption, depot, iv, and oral

link

peripheral

The macro peripheral defines a peripheral compartment. It is equivalent to a simple compartment with two transfers of amount towards and from another compartment.

In subsection [LONGITUDINAL] after PK:

link

PK

It defines where the macros are defined

In subsection [LONGITUDINAL]

link

pkmodel

It defines the macro pkmodel

In subsection [LONGITUDINAL], in a block PK: or in a block EQUATION:

link 

prediction

It corresponds to the name of the base prediction variable

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

proportional

Corresponds to proportional error model latex-1-20240607-151236.png

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

proportionalc

Corresponds to proportional error model latex-20240607-151256.png

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is continuous

link

regressor

It declares the input regression values.

In the longitudinal model, in subsection [LONGITUDINAL], after the input definition

link 

rightCensoringTime

Right censoring time of events. It is useful for simulation only

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION: when the type of observation is an event

link 

sd

Standard deviation of the associated normal distribution (standardDeviation and sd are synonymous keywords)

In any distribution definition in a block DEFINITION:

link

standardDeviation

Standard deviation of the associated normal distribution (standardDeviation and sd are synonymous keywords)

In any distribution definition in a block DEFINITION:

link 

stiff

It is an argument of odeType= and allows to define the dynamical system is nonStiff and thus yields to an adapted numerical scheme for the resolution

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

link 

t

time

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION:

Current page 

t_0

Initialization time for the equations

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION:

link

t0

Initialization time for the equations

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION:

link

table

This keywords declares the variables to record in tables.

In the longitudinal model, in subsection [LONGITUDINAL], in a block OUTPUT:

link

target

Name of the component of an ODE system that is shifted by the absorption.

In argument of the following macro: depot

 link

tDose

The keyword tDose defines the time of the last administered dose. This is a step function. Its value is unaffected by any lag time Tlag. Indeed, a lag time targets the dose absorption. It is null before the first dose.

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

Current page

to

Label of the target compartment for the transfer

In argument of the following macro: transfer

link

transfer

The macro transfer defines a transfer of amount from a first compartment to a second one.

In subsection [LONGITUDINAL] after PK:

link

transitionRate

Transition rate departing from a given category to another one. It is used in the definition of a categorical observation model.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION:

link

type

It allows the type of observation model. It can be continuous, count, categorical, or event.

In the longitudinal model, in subsection [LONGITUDINAL], in a block DEFINITION:

link

typical

It corresponds to the typical value during a distribution definition

In any distribution definition in a block DEFINITION:

link

use

It allows to define the regressor in the longitudinal subsection. Regressors are defined as inputs at the beginning and thus are specified as regressors using use=

In the longitudinal model, in subsection [LONGITUDINAL], after the input definition

link

var

Variance of the associated normal distribution (variance and var are synonymous keywords)

In any distribution definition in a block DEFINITION:

link

variance

Variance of the associated normal distribution (variance and var are synonymous keywords)

In any distribution definition in a block DEFINITION:

link

volume

It corresponds to the name of predefined variable to use as the volume of the compartment

In argument of the following macros: compartment, effect, peripheral

 link

wsmm

Mixture of continuous observations. It is a mixture within subjects.

In the longitudinal model, in subsection [LONGITUDINAL], in a block EQUATION:

see Monolix doc

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