METAMATS_SIZE
This software fits models of metastatic development to longitudinal data of metastatic sizes and provides simulation and visualization tools for metastatic modeling.
Language: Matlab
Dependencies: carcinom
, metamats_core
How to use it
- Data loaded in
import_data_<subject_ID>
- Fit launched in
./main_fit_separately.m
- Results (including parameter values) are exported in a file
/fit.mat - Birth times and growth curves of the metastases can be computed via
manips_birth_times
by informing the folder where results where exported - Example provided is a patient with non-small cell lung cancer developing brain metastases. Additional data for at least two other patients are available in
~/work/brain_metastases
(eithercode/
orB_MATEMATICS
)
Features
#### Model and fit
* For multiple subjects, fits can be performed either independently or jointly (i.e. with common parameters across subjects)
* Fit can be performed on either total number of visible metastases (not tested in details) or cumulative size distributions at possibly multiple time points
* Computes standard errors
* Allows different mechanistic models including: delay to metastasis, dormancy, secondary dissemination (metastases from metastases), equal or distinct growth functions and/or parameters between primary tumor and metastases
* Allows a multistart search for parameters’ estimation (to avoid local minima issues)
* Estimates PT growth parameters from size at diagnosis and doubling time (only available for lung ADK or squamous cell carcinoma and gompertz growth)
#### Simulation
* Estimation of mets birth times and growth kinetics
./manips_birth_times.m
* Movie with primary tumor growth curve and metastatic size distribution. Launched by setting output_s.hist_movie = 1 in
./main_fit_several_subjects_mets.m
(for instance)
* Movie with primary tumor and metastases sizes represented as disks is launched using
./plot_circles_for_movie.m
Abbreviations: PT = Primary tumor, mets = metastases