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Create an ODE-based model specification

Source: R/rxode2.R
rxode2.Rd

Create a dynamic ODE-based model object suitably for translation into fast C code

Usage

rxode2(
  model,
  modName = basename(wd),
  wd = getwd(),
  filename = NULL,
  extraC = NULL,
  debug = FALSE,
  calcJac = NULL,
  calcSens = NULL,
  collapseModel = FALSE,
  package = NULL,
  ...,
  linCmtSens = c("linCmtA", "linCmtB", "linCmtC"),
  indLin = FALSE,
  verbose = FALSE,
  fullPrint = getOption("rxode2.fullPrint", FALSE)
)

RxODE(
  model,
  modName = basename(wd),
  wd = getwd(),
  filename = NULL,
  extraC = NULL,
  debug = FALSE,
  calcJac = NULL,
  calcSens = NULL,
  collapseModel = FALSE,
  package = NULL,
  ...,
  linCmtSens = c("linCmtA", "linCmtB", "linCmtC"),
  indLin = FALSE,
  verbose = FALSE,
  fullPrint = getOption("rxode2.fullPrint", FALSE)
)

rxode(
  model,
  modName = basename(wd),
  wd = getwd(),
  filename = NULL,
  extraC = NULL,
  debug = FALSE,
  calcJac = NULL,
  calcSens = NULL,
  collapseModel = FALSE,
  package = NULL,
  ...,
  linCmtSens = c("linCmtA", "linCmtB", "linCmtC"),
  indLin = FALSE,
  verbose = FALSE,
  fullPrint = getOption("rxode2.fullPrint", FALSE)
)

Arguments

model

This is the ODE model specification. It can be:

  • a string containing the set of ordinary differential equations (ODE) and other expressions defining the changes in the dynamic system.

  • a file name where the ODE system equation is contained

An ODE expression enclosed in \{\}

(see also the filename argument). For details, see the sections “Details” and rxode2 Syntax below.

modName

a string to be used as the model name. This string is used for naming various aspects of the computations, including generating C symbol names, dynamic libraries, etc. Therefore, it is necessary that modName consists of simple ASCII alphanumeric characters starting with a letter.

wd

character string with a working directory where to create a subdirectory according to modName. When specified, a subdirectory named after the “modName.d” will be created and populated with a C file, a dynamic loading library, plus various other working files. If missing, the files are created (and removed) in the temporary directory, and the rxode2 DLL for the model is created in the current directory named rx_????_platform, for example rx_129f8f97fb94a87ca49ca8dafe691e1e_i386.dll

filename

A file name or connection object where the ODE-based model specification resides. Only one of model or filename may be specified.

extraC

Extra c code to include in the model. This can be useful to specify functions in the model. These C functions should usually take double precision arguments, and return double precision values.

debug

is a boolean indicating if the executable should be compiled with verbose debugging information turned on.

calcJac

boolean indicating if rxode2 will calculate the Jacobain according to the specified ODEs.

calcSens

boolean indicating if rxode2 will calculate the sensitivities according to the specified ODEs.

collapseModel

boolean indicating if rxode2 will remove all LHS variables when calculating sensitivities.

package

Package name for pre-compiled binaries.

...

ignored arguments.

linCmtSens

The method to calculate the linCmt() solutions

indLin

Calculate inductive linearization matrices and compile with inductive linearization support.

verbose

When TRUE be verbose with the linear compartmental model

fullPrint

When using printf within the model, if TRUE print on every step (except ME/indLin), otherwise when FALSE print only when calculating the d/dt

Value

An object (environment) of class rxode2 (see Chambers and Temple Lang (2001)) consisting of the following list of strings and functions:

* `model` a character string holding the source model specification.
* `get.modelVars`a function that returns a list with 3 character
    vectors, `params`, `state`, and `lhs` of variable names used in the model
    specification. These will be output when the model is computed (i.e., the ODE solved by integration).

  * `solve`{this function solves (integrates) the ODE. This
      is done by passing the code to [rxSolve()].
      This is as if you called `rxSolve(rxode2object, ...)`,
      but returns a matrix instead of a rxSolve object.

      `params`: a numeric named vector with values for every parameter
      in the ODE system; the names must correspond to the parameter
      identifiers used in the ODE specification;

      `events`: an `eventTable` object describing the
      input (e.g., doses) to the dynamic system and observation
      sampling time points (see  [eventTable()]);

      `inits`: a vector of initial values of the state variables
      (e.g., amounts in each compartment), and the order in this vector
      must be the same as the state variables (e.g., PK/PD compartments);


      `stiff`: a logical (`TRUE` by default) indicating whether
      the ODE system is stiff or not.

      For stiff ODE systems (`stiff = TRUE`), `rxode2` uses
      the LSODA (Livermore Solver for Ordinary Differential Equations)
      Fortran package, which implements an automatic method switching
      for stiff and non-stiff problems along the integration interval,
      authored by Hindmarsh and Petzold (2003).

      For non-stiff systems (`stiff = FALSE`), `rxode2` uses `DOP853`,
      an explicit Runge-Kutta method of order 8(5, 3) of Dormand and Prince
      as implemented in C by Hairer and Wanner (1993).

      `trans_abs`: a logical (`FALSE` by default) indicating
      whether to fit a transit absorption term
      (TODO: need further documentation and example);

      `atol`: a numeric absolute tolerance (1e-08 by default);

      `rtol`: a numeric relative tolerance (1e-06 by default).e

      The output of \dQuote{solve} is a matrix with as many rows as there
      are sampled time points and as many columns as system variables
      (as defined by the ODEs and additional assignments in the rxode2 model
          code).}

  * `isValid` a function that (naively) checks for model validity,
      namely that the C object code reflects the latest model
      specification.
  * `version` a string with the version of the `rxode2`
      object (not the package).
  * `dynLoad` a function with one `force = FALSE` argument
      that dynamically loads the object code if needed.
  * `dynUnload` a function with no argument that unloads
      the model object code.
  * `delete` removes all created model files, including C and DLL files.
      The model object is no longer valid and should be removed, e.g.,
      `rm(m1)`.
  * `run` deprecated, use `solve`.
  * `get.index` deprecated.
  * `getObj` internal (not user callable) function.

Details

The Rx in the name rxode2 is meant to suggest the abbreviation Rx for a medical prescription, and thus to suggest the package emphasis on pharmacometrics modeling, including pharmacokinetics (PK), pharmacodynamics (PD), disease progression, drug-disease modeling, etc.

The ODE-based model specification may be coded inside a character string or in a text file, see Section rxode2 Syntax below for coding details. An internal rxode2 compilation manager object translates the ODE system into C, compiles it, and dynamically loads the object code into the current R session. The call to rxode2 produces an object of class rxode2 which consists of a list-like structure (environment) with various member functions (see Section Value below).

For evaluating rxode2 models, two types of inputs may be provided: a required set of time points for querying the state of the ODE system and an optional set of doses (input amounts). These inputs are combined into a single event table object created with the function eventTable() or et().

An rxode2 model specification consists of one or more statements optionally terminated by semi-colons ; and optional comments (comments are delimited by # and an end-of-line).

A block of statements is a set of statements delimited by curly braces, { ... }.

Statements can be either assignments, conditional if/else if/else, while loops (can be exited by break), special statements, or printing statements (for debugging/testing)

Assignment statements can be:

  • simple assignments, where the left hand is an identifier (i.e., variable)

  • special time-derivative assignments, where the left hand specifies the change of the amount in the corresponding state variable (compartment) with respect to time e.g., d/dt(depot):

  • special initial-condition assignments where the left hand specifies the compartment of the initial condition being specified, e.g. depot(0) = 0

  • special model event changes including bioavailability (f(depot)=1), lag time (alag(depot)=0), modeled rate (rate(depot)=2) and modeled duration (dur(depot)=2). An example of these model features and the event specification for the modeled infusions the rxode2 data specification is found in rxode2 events vignette.

  • special change point syntax, or model times. These model times are specified by mtime(var)=time

  • special Jacobian-derivative assignments, where the left hand specifies the change in the compartment ode with respect to a variable. For example, if d/dt(y) = dy, then a Jacobian for this compartment can be specified as df(y)/dy(dy) = 1. There may be some advantage to obtaining the solution or specifying the Jacobian for very stiff ODE systems. However, for the few stiff systems we tried with LSODA, this actually slightly slowed down the solving.

Note that assignment can be done by =, <- or ~.

When assigning with the ~ operator, the simple assignments and time-derivative assignments will not be output.

Special statements can be:

  • Compartment declaration statements, which can change the default dosing compartment and the assumed compartment number(s) as well as add extra compartment names at the end (useful for multiple-endpoint nlmixr models); These are specified by cmt(compartmentName)

  • Parameter declaration statements, which can make sure the input parameters are in a certain order instead of ordering the parameters by the order they are parsed. This is useful for keeping the parameter order the same when using 2 different ODE models. These are specified by param(par1, par2,...)

An example model is shown below:

   # simple assignment
   C2 = centr/V2;

   # time-derivative assignment
   d/dt(centr) = F*KA*depot - CL*C2 - Q*C2 + Q*C3;

Expressions in assignment and if statements can be numeric or logical.

Numeric expressions can include the following numeric operators +, -, *, /, ^ and those mathematical functions defined in the C or the R math libraries (e.g., fabs, exp, log, sin, abs).

You may also access the R’s functions in the R math libraries, like lgammafn for the log gamma function.

The rxode2 syntax is case-sensitive, i.e., ABC is different than abc, Abc, ABc, etc.

Identifiers

Like R, Identifiers (variable names) may consist of one or more alphanumeric, underscore _ or period . characters, but the first character cannot be a digit or underscore _.

Identifiers in a model specification can refer to:

  • State variables in the dynamic system (e.g., compartments in a pharmacokinetics model).

  • Implied input variable, t (time), tlast (last time point), and podo (oral dose, in the undocumented case of absorption transit models).

  • Special constants like pi or R’s predefined constants.

  • Model parameters (e.g., ka rate of absorption, CL clearance, etc.)

  • Others, as created by assignments as part of the model specification; these are referred as LHS (left-hand side) variable.

Currently, the rxode2 modeling language only recognizes system state variables and “parameters”, thus, any values that need to be passed from R to the ODE model (e.g., age) should be either passed in the params argument of the integrator function rxSolve() or be in the supplied event data-set.

There are certain variable names that are in the rxode2 event tables. To avoid confusion, the following event table-related items cannot be assigned, or used as a state but can be accessed in the rxode2 code:

  • cmt

  • dvid

  • addl

  • ss

  • rate

  • id

However the following variables are cannot be used in a model specification:

  • evid

  • ii

Sometimes rxode2 generates variables that are fed back to rxode2. Similarly, nlmixr generates some variables that are used in nlmixr estimation and simulation. These variables start with the either the rx or nlmixr prefixes. To avoid any problems, it is suggested to not use these variables starting with either the rx or nlmixr prefixes.

Logical Operators

Logical operators support the standard R operators ==, != >= <= > and <. Like R these can be in if() or while() statements, ifelse() expressions. Additionally they can be in a standard assignment. For instance, the following is valid:

cov1 = covm*(sexf == "female") + covm*(sexf != "female")

Notice that you can also use character expressions in comparisons. This convenience comes at a cost since character comparisons are slower than numeric expressions. Unlike R, as.numeric or as.integer for these logical statements is not only not needed, but will cause an syntax error if you try to use the function.

References

Chamber, J. M. and Temple Lang, D. (2001) Object Oriented Programming in R. R News, Vol. 1, No. 3, September 2001. https://cran.r-project.org/doc/Rnews/Rnews_2001-3.pdf.

Hindmarsh, A. C. ODEPACK, A Systematized Collection of ODE Solvers. Scientific Computing, R. S. Stepleman et al. (Eds.), North-Holland, Amsterdam, 1983, pp. 55-64.

Petzold, L. R. Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations. Siam J. Sci. Stat. Comput. 4 (1983), pp. 136-148.

Hairer, E., Norsett, S. P., and Wanner, G. Solving ordinary differential equations I, nonstiff problems. 2nd edition, Springer Series in Computational Mathematics, Springer-Verlag (1993).

Plevyak, J. dparser, https://dparser.sourceforge.net/. Web. 12 Oct. 2015.

See also

eventTable(), et(), add.sampling(), add.dosing()

Author

Melissa Hallow, Wenping Wang and Matthew Fidler

Examples

# \donttest{
# Step 1 - Create a model specification
ode <- "
   # A 4-compartment model, 3 PK and a PD (effect) compartment
   # (notice state variable names 'depot', 'centr', 'peri', 'eff')

   C2 = centr/V2;
   C3 = peri/V3;
   d/dt(depot) =-KA*depot;
   d/dt(centr) = KA*depot - CL*C2 - Q*C2 + Q*C3;
   d/dt(peri)  =                    Q*C2 - Q*C3;
   d/dt(eff)  = Kin - Kout*(1-C2/(EC50+C2))*eff;
"

m1 <- rxode(model = ode)
#>  
#>  
print(m1)
#> rxode2 2.0.11.9000 model named rx_e8357cab04a27df7a76366ceeca0a34c model (✔ ready). 
#> $state: depot, centr, peri, eff
#> $params: V2, V3, KA, CL, Q, Kin, Kout, EC50
#> $lhs: C2, C3

# Step 2 - Create the model input as an EventTable,
# including dosing and observation (sampling) events

# QD (once daily) dosing for 5 days.

qd <- eventTable(amount.units = "ug", time.units = "hours")
qd$add.dosing(dose = 10000, nbr.doses = 5, dosing.interval = 24)

# Sample the system hourly during the first day, every 8 hours
# then after

qd$add.sampling(0:24)
qd$add.sampling(seq(from = 24 + 8, to = 5 * 24, by = 8))

# Step 3 - set starting parameter estimates and initial
# values of the state

theta <-
  c(
    KA = .291, CL = 18.6,
    V2 = 40.2, Q = 10.5, V3 = 297.0,
    Kin = 1.0, Kout = 1.0, EC50 = 200.0
  )

# init state variable
inits <- c(0, 0, 0, 1)
# Step 4 - Fit the model to the data

qd.cp <- m1$solve(theta, events = qd, inits)
#> Warning: Assumed order of inputs: depot, centr, peri, eff

head(qd.cp)
#>      time       C2        C3     depot    centr      peri      eff
#> [1,]    0  0.00000 0.0000000 10000.000    0.000    0.0000 1.000000
#> [2,]    1 43.99334 0.9113641  7475.157 1768.532  270.6751 1.083968
#> [3,]    2 54.50866 2.6510696  5587.797 2191.248  787.3677 1.179529
#> [4,]    3 51.65163 4.4243597  4176.966 2076.396 1314.0348 1.227523
#> [5,]    4 44.37513 5.9432612  3122.347 1783.880 1765.1486 1.233503
#> [6,]    5 36.46382 7.1389804  2334.004 1465.845 2120.2772 1.214084

# This returns a matrix.  Note that you can also
# solve using name initial values. For example:

inits <- c(eff = 1)
qd.cp <- solve(m1, theta, events = qd, inits)
print(qd.cp)
#> ── Solved rxode2 object ──
#> ── Parameters ($params): ──
#>      V2      V3      KA      CL       Q     Kin    Kout    EC50 
#>  40.200 297.000   0.291  18.600  10.500   1.000   1.000 200.000 
#> ── Initial Conditions ($inits): ──
#> depot centr  peri   eff 
#>     0     0     0     1 
#> ── First part of data (object): ──
#> # A tibble: 37 × 7
#>   time    C2    C3  depot centr  peri   eff
#>    [h] <dbl> <dbl>  <dbl> <dbl> <dbl> <dbl>
#> 1    0   0   0     10000     0     0   1   
#> 2    1  44.0 0.911  7475. 1769.  271.  1.08
#> 3    2  54.5 2.65   5588. 2191.  787.  1.18
#> 4    3  51.7 4.42   4177. 2076. 1314.  1.23
#> 5    4  44.4 5.94   3122. 1784. 1765.  1.23
#> 6    5  36.5 7.14   2334. 1466. 2120.  1.21
#> # … with 31 more rows

plot(qd.cp)


# You can also directly simulate from a nlmixr model
 f <- function() {
   ini({
     KA <- .291
     CL <- 18.6
     V2 <- 40.2
     Q <- 10.5
     V3 <- 297.0
     Kin <- 1.0
     Kout <- 1.0
     EC50 <- 200.0
   })
   model({
     # A 4-compartment model, 3 PK and a PD (effect) compartment
     # (notice state variable names 'depot', 'centr', 'peri', 'eff')
     C2 <- centr/V2
     C3 <- peri/V3
     d/dt(depot) <- -KA*depot
     d/dt(centr) <- KA*depot - CL*C2 - Q*C2 + Q*C3
     d/dt(peri)  <-                    Q*C2 - Q*C3
     d/dt(eff)   <- Kin - Kout*(1-C2/(EC50+C2))*eff
     eff(0) <- 1
   })
 }

 u <- f()

 # this pre-compiles and displays the simulation model
 u$simulationModel
#>  
#>  
#> rxode2 2.0.11.9000 model named rx_b811189e58df77727a5f17bde5f3141f model (✔ ready). 
#> $state: depot, centr, peri, eff
#> $params: KA, CL, V2, Q, V3, Kin, Kout, EC50
#> $lhs: C2, C3

 qd.cp <-solve(u, qd)
#>  
#>  

 print(qd.cp)
#> ── Solved rxode2 object ──
#> ── Parameters ($params): ──
#>      KA      CL      V2       Q      V3     Kin    Kout    EC50 
#>   0.291  18.600  40.200  10.500 297.000   1.000   1.000 200.000 
#> ── Initial Conditions ($inits): ──
#> depot centr  peri   eff 
#>     0     0     0     1 
#> ── First part of data (object): ──
#> # A tibble: 37 × 7
#>   time    C2    C3  depot centr  peri   eff
#>    [h] <dbl> <dbl>  <dbl> <dbl> <dbl> <dbl>
#> 1    0   0   0     10000     0     0   1   
#> 2    1  44.0 0.911  7475. 1769.  271.  1.08
#> 3    2  54.5 2.65   5588. 2191.  787.  1.18
#> 4    3  51.7 4.42   4177. 2076. 1314.  1.23
#> 5    4  44.4 5.94   3122. 1784. 1765.  1.23
#> 6    5  36.5 7.14   2334. 1466. 2120.  1.21
#> # … with 31 more rows

# }