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Translate structural models between rxode2 and MLXTRAN syntax

Source: R/sg-translator.R
sg_translator.Rd

Converts structural pharmacometric model files between rxode2 (R package) and MLXTRAN (Monolix) syntax. Supports ODE-based models and Monolix pkmodel macros.

Usage

sg_translator(
  input_path,
  to,
  output_path,
  dm_list = NULL,
  regressors = NULL,
  output_vars = NULL,
  macros = TRUE,
  stiff = TRUE
)

Arguments

input_path

Character string. Path to the input structural model file (.txt).

to

Character string. Target format: "mlxtran" or "rxode".

output_path

Character string. Path to write the translated model file (.txt).

dm_list

List of dosing macros with cmt and adm vectors. For example, list(cmt = 2, adm = 1) or list(cmt = c(2, 1), adm = c(1, 2)). Used to generate iv() dosing macros in MLXTRAN output.

regressors

Character vector of regressor variable names. For example, c("WTBL", "ADAN") generates WTBL = {use = regressor} in MLXTRAN.

output_vars

Character vector of output variable names for the MLXTRAN OUTPUT: section. For example, c("Cc_mgL", "CSF1_ngmL") generates output = {Cc_mgL, CSF1_ngmL}. Required when to = "mlxtran"; ignored when to = "rxode".

macros

Logical. If TRUE, attempt to convert rxode2 model to pkmodel macro format in MLXTRAN (only for simple 1- or 2-compartment oral PK models). Default TRUE.

stiff

Logical. If TRUE, add odeType = stiff to the MLXTRAN EQUATION section. Default TRUE.

Value

Invisibly returns the translated model as a character string. The translated model is also written to output_path.

Details

The function detects the source format automatically from file content.

rxode2 format uses # [INPUT], # [MODEL], # [OUTPUT] section markers, d/dt(X) ODE notation, f(X) for bioavailability, and alag(X) for lag time.

MLXTRAN format uses [LONGITUDINAL], PK:/EQUATION:/OUTPUT: sections, ddt_X ODE notation, compartment()/iv() dosing macros, and optionally pkmodel() macros.

When converting rxode2 to MLXTRAN with macros = TRUE, the function checks if the model structure matches a simple pkmodel() pattern (1- or 2-compartment with first-order oral absorption). If not, it falls back to full ODE format with compartment()/iv() macros.

MLXTRAN models using absorption()/elimination()/peripheral() macros (type 2) are expanded to explicit ODEs when converted to rxode2.

Examples

# \donttest{
# Convert rxode2 model to MLXTRAN ODE format
rxode_model_hv_iv <- system.file("extdata", "models", "rxode",
                                 "model_PK_hv_iv.txt", package = "SimuRg")
#> Warning: cannot open compressed file '/tmp/RtmpLedq7K/temp_libpath8b6abff614d/SimuRg/DESCRIPTION', probable reason 'No such file or directory'
rxode_model_1c <- system.file("extdata", "models", "rxode",
                              "model_PK_1c.txt", package = "SimuRg")
#> Warning: cannot open compressed file '/tmp/RtmpLedq7K/temp_libpath8b6abff614d/SimuRg/DESCRIPTION', probable reason 'No such file or directory'
monolix_model_hv_iv <- system.file("extdata", "models", "monolix",
                                   "model_PK_hv_iv.txt", package = "SimuRg")
#> Warning: cannot open compressed file '/tmp/RtmpLedq7K/temp_libpath8b6abff614d/SimuRg/DESCRIPTION', probable reason 'No such file or directory'
monolix_model_1c <- system.file("extdata", "models", "monolix",
                                "model_PK_1c.txt", package = "SimuRg")
#> Warning: cannot open compressed file '/tmp/RtmpLedq7K/temp_libpath8b6abff614d/SimuRg/DESCRIPTION', probable reason 'No such file or directory'

path_to_save <- tempdir()

sg_translator(rxode_model_hv_iv, to = "mlxtran",
              output_path = normalizePath(file.path(path_to_save,
                                                    "model_PK_hv_iv_mlx.txt"),
                                          mustWork = FALSE),
              output_vars = "Cc_mgL",
              dm_list = list(cmt = 1, adm = 1), stiff = TRUE)
#> Error: cannot open file '/tmp/RtmpLedq7K/temp_libpath8b6abff614d/SimuRg/R/SimuRg.rdb': No such file or directory

# Convert rxode2 model to MLXTRAN with pkmodel macros
sg_translator(rxode_model_1c, to = "mlxtran",
              output_path = normalizePath(file.path(path_to_save,
                                                    "model_PK_1c_mlx.txt"),
                                          mustWork = FALSE),
              output_vars = "Cc_nM", macros = TRUE)
#> Warning: restarting interrupted promise evaluation
#> Error: cannot open file '/tmp/RtmpLedq7K/temp_libpath8b6abff614d/SimuRg/R/SimuRg.rdb': No such file or directory

# Convert MLXTRAN model to rxode2
sg_translator(monolix_model_hv_iv, to = "rxode",
              output_path = normalizePath(file.path(path_to_save,
                                                    "model_PK_hv_iv_rx.txt"),
                                           mustWork = FALSE))
#> Warning: restarting interrupted promise evaluation
#> Error: cannot open file '/tmp/RtmpLedq7K/temp_libpath8b6abff614d/SimuRg/R/SimuRg.rdb': No such file or directory
# }