Interoperability

PyMixEF translates only constructs whose meaning it can describe. Every import or export returns an InterchangeResult containing both the translated value and a CompatibilityReport.

Compatibility statuses

Status

Meaning

exact

represented without a known semantic change in the documented subset

transformed

normalized into an equivalent PyMixEF form, with the change reported

approximated

represented by an explicit approximation and rationale

unsupported

preserved or identified for review but not silently executed/translated

 
translated = pymixef.interoperability.translate_r_formula(
    "response ~ treatment * time + (1 | subject)"
)

print(translated.value)
print(translated.report.supported)
for issue in translated.report.issues:
    print(issue.to_dict())

translated.require_supported()

Call require_supported() before consuming the value when a workflow must refuse any unsupported construct.

Format matrix

Format

Direction

Initial supported subset

NONMEM-style data

import

column normalization, required ID/TIME check

NONMEM output table

import

comma/whitespace table with preamble handling

NM-TRAN control stream

import/inspect

record preservation; structural code explicitly unsupported

R/lme4 formula

translate

shared fixed/random operators; arbitrary R evaluation refused

PharmML

import/export

named declarations / parameter declarations

SBML L3V2 Core

import/export

compartments, species, parameters, states

SED-ML L1V4

import/export

uniform time-course grid and KiSAO algorithm

These are conservative subsets, not full implementations of their external standards.

NONMEM

import_nonmem_data uppercases or explicitly maps columns and reports duplicate targets or missing ID/TIME. Canonical event processing remains a separate, auditable step.

import_nonmem_table removes repeated TABLE NO. preambles, requires one unique header row, refuses ragged records, and parses numeric columns where possible.

parse_control_stream preserves NM-TRAN records. $INPUT, $DATA, $SUBROUTINES, $MODEL, $THETA, $OMEGA, $SIGMA, $ESTIMATION, $SIMULATION, and $TABLE are normalized for inspection. $PK, $DES, and $ERROR text is retained but marked unsupported because arbitrary structural code is not executed.

R formulas

translate_r_formula accepts shared fixed effects, interactions, nesting, and |/|| random operators. R environment access and function evaluation, including ::, $, [[, I(, poly(, ns(, and bs(, are reported as unsupported; create transformed columns explicitly.

The repository also contains an alpha reticulate wrapper. Its release gate and distribution status are described in interoperability and refusal policy.

PharmML

Import recognizes named population/individual parameters, random variables, derivative variables, variables, and symbols inside the initial container subset. Unknown elements, attributes, and mixed text receive occurrence-specific locations in the compatibility report.

Export writes minimal parameter declarations and reports model equations and unserialized properties as unsupported.

SBML

Import targets SBML Level 3 Version 2 Core declarations for compartments, species, and parameters. Reactions, kinetic laws, rate/assignment/algebraic rules, and general SBML events are not executed.

Export writes a reviewable declaration document containing a default compartment, state/species declarations, and parameters. Dosing belongs in the canonical event table.

SED-ML

Import/export covers a Level 1 Version 4 uniformTimeCourse: initial time, output start/end, number of points, and KiSAO algorithm identifier. One-step, steady-state, repeated-task, and functional-range experiments are outside the initial subset.

Comparing numerical results

Interchange asks whether model meaning can be represented. pymixef.compare asks whether fitted numerical output agrees with an explicitly mapped reference. Comparison requires coefficient mapping and compatible objective conventions; it does not infer whether another tool includes the same constants or uses the same conditional/marginal definition.

API reference