README.md

## Testing the Hidden Semi Markov Models (HSMM) software

This repository, developped during the HSMM-INCA ANR project,  contains scripts that test the functionnalities of HSMM simulation and estimation provided by different software identified on internet.
Especially, the scripts in deer and squirrel directories are developped for the software review chapter of a book on HSMM written by the members of the HSMM-INCA project. They target the testing of the edhsmm python and hhsmm R libraries for modeling guilding case studies (deers and squirrels) of the book.

## A docker image for testing the scripts

Docker is a platform designed to help developers build, share, and run container applications. A container is a bundle of application software with all the dependencies required for the applications to run. Since HSMM libraries evolved and can become unavailable, we decided to provide a docker image with snapshots of some HSMM libraries reviewed.

The container image can be found here: https://forgemia.inra.fr/inca-hsmm/software-review/container_registry.
The libraries installed are edhsmm (version 0.2.2), hhsmmlearn (commit version 69bc8aa), hhsmm (version 0.2.5), PHSMM (version 1.0).

To make it work, it is first required to install docker and then the container can be launched for example with the following command on a Linux device:
```
docker run --rm -it -p 8888:8888  \
  registry.forgemia.inra.fr/inca-hsmm/software-review:1.0
```

A new prompt indicates that one entered into the image. Then, depending on what we want to test, we can for example launch a pyhon and load the edhsmm library or launch R and load the hhsmm library :

```
python3
>>> from edhsmm.hsmm_multinom import MultinomialHSMM
```

```
R
> library(hhsmm)
```