CLI Reference

All functionality is exposed via the tumorfits command.

tumorfits <subcommand> [options]

Run tumorfits --help or tumorfits <subcommand> --help for the full option listing.

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tumorfits extract-data

Extract patient CSVs from raw .RData files.

tumorfits extract-data [--data-root DIR] [--out-dir DIR]

Option	Default	Description
--data-root	data	Root directory containing .RData files
--out-dir	data/patient_data	Output directory

Example:

tumorfits extract-data \
    --data-root data/ \
    --out-dir   data/patient_data

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tumorfits ode

Fit the ODE model to one patient or a cohort.

tumorfits ode --data FILE (--patient ID | --flag FLAGS) [options]

Option	Default	Description
--data	(required)	Subclonal_ratio_estimates.extended.txt
--patient	—	Single patient ID (mutually exclusive with --flag)
--flag	—	Comma-separated Accept_estimate values, e.g. yes,maybe
--out_points	ode_gof_points.csv	Output long-table CSV
--diag_dir	results_ODE	Per-patient diagnostics directory
--time_unit	months	months or days
--n_starts	8	Number of optimiser restarts
--maxiter	1200	Max iterations per restart
--w_ca	0.5	Weight for CA125 term in likelihood
--n_jobs_patients	-1	Parallel workers for patients
--sample_list	None	Path to OV_patientDNA_sampleList.txt
--use_ca125_updated	false	Use revised CA125 values
--drop_failed	false	Exclude failed QC samples

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tumorfits pde

Run or fit the 1-D PDE reaction–diffusion model.

tumorfits pde --data FILE --ode_points FILE [--patient ID|ALL] [options]

Option	Default	Description
--data	(required)	Subclonal ratios file
--ode_points	(required)	ODE long-table CSV from tumorfits ode
--patient	ALL	Patient ID or ALL
--out_dir	results_pde_model	Output directory
--fit	false	Re-fit diffusion coefficients
--L	1.0	Domain length
--n_cells	200	Number of FEM cells
--dt	0.001	Time step
--DS, --DR	0.01	Diffusion coefficients
--n_starts	10	Optimiser restarts (if --fit)
--maxiter	150	Max iterations per restart

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tumorfits heatmap

Generate space-time heatmaps of S(x,t) and R(x,t) without re-fitting.

tumorfits heatmap --data FILE --ode_points FILE --patient ID [options]

Produces a single PNG file heatmap_<patient>.png in --out_dir.

Option	Default	Description
--data	(required)	Subclonal ratios file
--ode_points	(required)	ODE long-table CSV
--patient	(required)	Patient ID
--out_dir	results_pde_model	Output directory
--n_cells	100	Spatial resolution
--L	1.0	Domain length

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tumorfits mesh-view

Run a 2-D FEniCS simulation and produce PyVista visualisations.

tumorfits mesh-view --data FILE --ode-points FILE [options]

Saves three PNG files per patient: resistance zones, streamlines, drug efficacy.

Option	Default	Description
--data	(required)	Subclonal ratios file
--ode-points	(required)	ODE long-table CSV
--out-dir	results_pde_model	Output directory
--patient	ALL	Patient ID or ALL
--nx, --ny	50	FEniCS mesh resolution
--dt	0.5	Time step (months)
--sample-list	None	QC metadata file