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README.md

DOI

Optimal Binary Two-Stage Designs

Interactive Examples

All examples are available as jupyter notebooks in the folder /notebooks and can be explored interactively using binder. The free hosting service is run by https://mybinder.org. Since the instances are running on a free service, availibility and computing speed may vary.

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All links on this page point to release 0.2.2 of this repository. To run an other version, simply modify the binder link accordingly. The newest version of the 'introduction' notebook would be

https://mybinder.org/v2/gh/kkmann/optimal-binary-two-stage-designs/master?urlpath=lab/tree/notebooks/introduction.ipynb

and

https://mybinder.org/v2/gh/kkmann/optimal-binary-two-stage-designs/0.1.0?urlpath=lab/tree/notebooks/introduction.ipynb

would run version 0.1.0 of the introduction notebook.

Shiny App badge

A shiny app is available under this binder-link. The app showcases a few rudimentatry scenarios and does not require any programming experience. Note that the app is also hosted on the free https://mybinder.org service and the default settings for the optimisation are chosen conservatively to ensure proper solutions over a wide range of inputs. Depending on the user inputs, optimisation might thus take up to a few minutes.

Reproduce Locally

  1. install git, docker, python, and repo2docker
  2. execute git clone https://github.com/kkmann/optimal-binary-two-stage-designs to download the repository
  3. switch to the repository folder via cd optimal-binary-two-stage-designs
  4. [optionally] checkout a specific version tag using e.g. git checkout 0.2.2
  5. run jupyter-repo2docker . to build and start the container locally, this will start a Jupyter notebook server in you browser and you can navigate to the respective notebook in the notebooks/ subfolder.
  6. [optionally] the repository also contains a snakemake workflow to run all notebooks (and thus generate all plots) sequentially. This can be executed by opening a terminal window in Jupyter lab and running the command snakemake --cores 1 all.

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