mechanisticModel R package

Date of Creation : december 18th, 2020

Description

This package implements a mechanistic model for the prediction of metastatic relapse proposed by S Benzekry (Modeling spontaneous metastasis following surgery: an in vivo-in silico approach doi:10.1158/0008-5472.CAN-15-1389) and used by chiara Nicolo (Machine Learning and Mechanistic Modeling for Predictionof Metastatic Relapse in Early-Stage Breast Cancer doi:10.1200/CCI.19.00133). Both the original python implementation and new c++ versions are available.

Authors

• Célestin BIGARRÉ celestin.bigarre@inria.fr [author, maintainer]
• Sébastien BENZEKRY sebastien.benzekry@inria.fr [maintainer]

Dependencies

R package

The following packages are required and will be installed alongside this package : - Rcpp - reticulate - saemix (>= 3.1.9000) from saemixdevelopment/saemixextension

Python module

THe python code is called using the reticulate package. Make sure a python version is available and configured with reticulate before using this package.

The python model relies on the scipy and numba python modules, make sure they are installed and available for reticulate. If not instlled use the following R command : ~~~R reticulate::py_install(“scipy”) reticulate::py_install(“numba”) ~~~

Usage

This package relies on a development version of the saemix package available at : https::github.com/saemixdevelopment/saemixextension, installing this package should install this new version of saemix but will REMOVE previously installed version of seamix. This developpement version includes the possibility to use a custom logpdf function in the saem algorithm instead of a MLXR model.

Patch Notes :

- 1.0.0 : First release of the package, the following functions are available :
    + mechanisticModel : fits the mechanistic model using one of the 3 implementation(original python, c++ reproducing python, c++ optimized)
    + test_saemx_iter : this run the first n iteration of saemix then auit and return internal variables. Tis is a test function that should not be called by a real user.
    + /!\ Note that a lot of documentation id lacking at the time, it will be added in a futur patch
- 1.1.0 : Major rebase of the source code
    + added a python version optimized with numba

Done

18/12/2020 : - package skeleton - added c++ code reproducing the python model