Anaconda for R Users Christine Doig Oct 2015

2 • Industrial Engineer, UPC, Barcelona • Master Thesis - Voltage Stability Analysis, Aachen, Germany • Process Engineer - Operations Research, P&G • Business Analyst/Consultant, “La Caixa” • Quantitative Techniques for Finantial Markets, FME, UPC • Master in Data Mining and BI, FIB-UPC, Barcelona • Data Scientist, Continuum Analytics, Austin, Texas My background… Matlab C SAP SAS Excel VB Matlab SQL R Python R

3 • DARPA Memex - Human Trafficking • Python Advocate and Conference Speaker: PyCon Montreal, PyData Berlin, PyData Dallas, SciPy Austin, Europython Bilbao… • Blaze PM: http://blaze.pydata.org/ • Python Trainings • Blogs: • "Conda for Data Science" (https://www.continuum.io/content/conda-data-science) • "Jupyter and Conda for R" (https://www.continuum.io/blog/developer/jupyter-and-conda-r). at Continuum Analytics…

4 • Twitter: ch_doig • Github: chdoig • Site: chdoig.github.io • Email: [email protected] Keep in touch!

5 Continuum Analytics… …distributes Anaconda, an open source Python distribution that includes more than 300 packages for scientific computing and data science …provides enterprise ready products for data scientist through the Anaconda Platform …delivers Python trainings and offers consulting services …supports the development of open source technology: conda, blaze, dask, bokeh, numba… …sponsors Python conferences PyData, SciPy, PyCon, Europython, PySS… Learn more: https://www.continuum.io/

Agenda 6 • Anaconda and “R Essentials” • Conda: package and environment manager • Jupyter: collaborative notebooks • Bokeh: interactive data visualizations

CONDA, ANACONDA & R ESSENTIALS Introduction

8 Conda • Package and environment manager • Language angnostic (Python, R, Java…) • Cross-platform (Windows, OS X, Linux) $ conda install python=2.7 $ conda install pandas $ conda install -c r r $ conda install mongodb

9 Conda • Open source: BSD license • Docs: http://conda.pydata.org/docs/ • GH: https://github.com/conda

10 Conda vs Anaconda vs Miniconda vs R Essentials • Conda: package manager • Anaconda: Python + Conda + packages • Miniconda: Python + Conda • R Essentials: R + R packages

11 Language agnostic Python packages handles environments ! natively virtualenv installs binaries compiles from source general purpose ! envs python! envs Conda Pip

12 Conda + pip $ conda install pip $ pip install foo Conda skeleton pip $ conda skeleton pip foo $ conda build foo/

13 Why Conda? • Python with compiled, platform-dependent C, C++, or Fortran code • Seen this message too many times:“Storing debug log for failure in /.pip/pip.log” • Multi-language Data Science Projects

14 Anaconda Cloud ~ Github for binary packages

15 Anaconda Cloud $ conda build conda.recipe/ $ conda server upload my_foo_pkg $ conda install -c chdoig my_foo_pkg

16 Anaconda for R users $ conda install -c r r-foo

17 Mirror CRAN packages $ conda skeleton cran ldavis ! $ conda build r-ldavis/ ! $ conda server upload my_r_pkg ! $ conda install -c chdoig my_r_pkg

18 Conda environments name: myenv channels: - chdoig - r - foo dependecies: - python=2.7 - r - r-ldavis - pandas - mongodb - spark=1.5 - pip - pip: - flask-migrate - bar=1.4 environment.yml $ conda env create $ source activate myenv $ conda env export -n freeze.yml Create and activate Freeze versions Upload to anaconda.org $ conda server upload my_foo_env.yml $ conda env create chdoig/my_foo_env.yml

19 Conda auto env cdoig:~$ cd pygotham-topic-modeling/ discarding /anaconda/bin from PATH prepending /anaconda/envs/pygotham-topic/bin to PATH (pygotham-topic)cdoig:~/pygotham-topic-modeling$ https://github.com/chdoig/conda-auto-env

20 "R essentials" comes with IRKernel and over 80 of the most used R packages for data science like dplyr, shiny, ggplot2, tidyr, caret and nnet. $ conda install -c r r-essentials $ conda config --add channels r or $ conda install r-essentials R Essentials

21 or, alternatively, create an environment to isolate your "R essentials" packages from others: ! $ conda create -n r-essentials -c r r-essentials R Essentials environment

22 $ conda metapackage custom-r-bundle 0.1.0 --dependencies r-irkernel jupyter r-ggplot2 r-dplyr --summary "My custom R bundle” ! Custom metapackage to share

JUPYTER Introduction

24 http://jupyter.org/ https://try.jupyter.org/ The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text.

25 IPython IPython notebook nbviewer tmpnb binder Jupyter https://try.jupyter.org/ http://mybinder.org/

26 ! To start jupyter notebooks, simply run the following command: ! $ jupyter notebook http://nbviewer.ipython.org/github/chdoig/conda-jupyter-irkernel/blob/master/Jupyter%20and%20conda%20for%20R.ipynb

27 Jupyter and conda for R notebook demo

28 Slideshow

29

30 $ jupyter nbconvert my_r_notebook.ipynb --to slides --post serve

31

BOKEH Introduction

33 Custom visualizations Dashboards Streaming/ Animations Charts T ools Widgets Maps Hover Bokeh

34

35 http://hafen.github.io/rbokeh/ rbokeh

36 rbokeh demo

37 • Twitter: ch_doig • Github: chdoig • Site: chdoig.github.io • Email: [email protected] Keep in touch!

38 Q & A Thanks!