Computation

We will be using (I)Python as our programming language. In order to use some of the material available on this website and to share your material with others you should create a GitHub account for yourself. This will be useful to you in the future to keep track of changes when you are writing papers. I also recommend creating a Bitbucket account, which has similar functionality, but allows you to have unlimited private repositories for personal use. Additionally, I suggest you read Gentzkow & Shapiro's Code and Data for the Social Sciences: A Practitioner’s Guide to familiarize yourself with good practices in coding and statistical analysis. We will cover additional topics in class.


Text Editor

You should have a good text editor, which hopefully has syntax highlighting for various languages, especially for python, R and Stata. I personally recommend atom, which is free, custimizable and very flexible.


Installing (I)Python & Jupyter

The easiest and most convenient way to install a working version of IPython with all the required packages and tools is using Continuum's Anaconda Distribution. You can install following the instructions in that website, or if you can just run this script (Mac/Linux). After installing the latest version of Anaconda, add the Anaconda/bin directory to your PATH variable.

In Windows install Visual C++ 9.0, Visual C++ 14 and Microsoft MPI6.

In MACOS download and install XCode (from the Apple store) and command line tools (option within XCode or in a terminal execute xcode-select --install).

Then you can either:

A. download one of the following scripts

and execute

conda update conda
conda-env create -f GeoPython3env2019B_nobuilds.yml
# Or uncomment one of these if you want to install the older versions
#conda-env create -f GeoPython2env.yml
#conda-env create -f GeoPython3env.yml

This should create an environment with all the packages you will require for this course (and more!).

B. If A. fails, which seems to happen often due to version conflicts, execute

conda create --name GeoPython3env -c conda-forge -c numba -c rapidsai -c mro -c r -c defaults python=3.6 geopandas georasters pandas numpy matplotlib seaborn jupyter scikit-image scikit-learn scipy r rstudio r-irkernel ipykernel ipyparallel statsmodels pycountry networkx rpy2 rasterio r-tidyr r-tibble r-dplyr pandana urbanaccess dill xlrd pandas-datareader rise jupyterlab cython numba openpyxl scikit-bio geoplot wikipedia swifter pelican datashader 
conda activate GeoPython3env
pip install linearmodels isounidecode geonamescache geocoder

This should create an environment with most of the packages we need. We can always install others down the road.

To start using one of the environment you will need to exectute the following command

source activate GeoPython3env

or for Python 2.x

source activate GeoPython2env

I would suggest using GeoPython3env, since it is the latest and most up-to-date version (I'll try to keep adding new versions as time passes).

MacOS

Instead of the previous options, you can download this file and execute

conda create --name GeoPython3env --file GeoPython3env-spec-file.txt

Parallel Computing

One of the advantages of Jupyter Notebooks is that they allow you to work (very easily) with multiple processors using ipyparallel. Once you have ipyparallel installed (automatically done for you with the scritps above), you will need to execute the following code once

ipcluster nbextension enable

Stata Kernel

We can use Stata within Jupyter Notebooks with the Stata kernel. I recommend you make sure it is installed and you have highlighting. To install (in case you do not use the YAML environment file above), execute

pip install stata_kernel
python -m stata_kernel.install

and then

conda install -c conda-forge nodejs -y
jupyter labextension install jupyterlab-stata-highlight

R kernel

We can also use R within Jupyter Notebooks with the R kernel. The best way to install it (in case you do not use the YAML environment file above) is to use conda by executing

conda install -c r r-irkernel

You can also install R and R packages by using conda. Simply execute

conda install -c r r
conda install -c r r-PACKAGE_NAME

Running Stata or R in Python

We can also use Stata or R directly within Python. You only need to use the %magic for each after installing the required packages. For example for Stata you need ipystata. Install by executing

pip install ipystata

Then in jupyter execute

import ipystata 
from ipystata.config import config_stata
config_stata('Path to your Stata executable')

Once configured you can use the %%stata magic. E.g.

In[1]: import ipystata  
In[2]: %%stata  
        display "Hello, I am printed in Stata."

More info in the ipystata website.

Similarly, we can use R using rpy2. Install by executing

pip install rpy2

Then in jupyter execute

In [1]: %load_ext rpy2.ipython
In [2]: %%R

        R.version

More info in the rpy2 website.

Notebooks