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## Testing the Hidden Semi Markov Models (HSMM) software
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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.
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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.
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## A docker image for testing the scripts
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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.
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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).
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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:
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```
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docker run --rm -it -p 8888:8888  \
  registry.forgemia.inra.fr/inca-hsmm/software-review:1.0
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```

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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 :
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```
python3
>>> from edhsmm.hsmm_multinom import MultinomialHSMM
```
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```
R
> library(hhsmm)
```
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