Fit SimBiology Models

Estimate parameters from data using fitproblem, fit population models with NLME, generate virtual patients, and compute NCA metrics.

When to Use

• "fit", "estimate", "calibrate" model parameters
• Parameter estimation from experimental/observed data
• Population PK/PD, NLME, mixed effects, inter-individual variability
• Virtual patients, virtual cohorts
• NCA, AUC, Cmax, Tmax, half-life, clearance
• Keywords: "fit", "estimate", "calibrate", "population", "NCA", "AUC"

When NOT to Use

• Model construction or diagram (use simbiology-build-model)
• Simulation without fitting (use simbiology-simulate-model)
• Sensitivity analysis (use simbiology-simulate-model)

Must-Follow Rules

1. Use fitproblem for parameter estimation

Always use fitproblem instead of calling sbiofit or sbiofitmixed directly. fitproblem provides a unified, declarative interface:

prob = fitproblem;
prob.Model = model;
prob.Data = data;
prob.ResponseMap = "Species = DataColumn";
prob.Estimated = estimatedInfo({'param'}, 'Bounds', [lo hi]);
results = fit(prob);

Do NOT call sbiofit(model, data, ...) or sbiofitmixed(model, data, ...) directly, their positional argument signatures are error-prone.

2. Fitting requires groupedData, NOT a plain table

Always wrap data:

data = groupedData(table(...));
data.Properties.IndependentVariableName = 'Time';

3. ResponseMap maps model outputs to data columns

Format is always "ModelOutput = DataColumnName":

% Single compartment, use species name on the left
prob.ResponseMap = "Drug = DrugConc";

% Multi-compartment, use qualified name to disambiguate
prob.ResponseMap = "Central.Drug = DrugConc";

% When species name matches data column name, still use the = format
prob.ResponseMap = "Drug = Drug";

Use the unqualified species name unless the same species name exists in multiple compartments (then qualify with Compartment.Species).