refactor dynamics module

weikang9009 commented 5 years ago

This PR is to refactor dynamics module to mimic the cluster/analytics module. Major changes are:

rely on giddy's Sequence class for sequence analysis
sequence and transition as functions to be consistent with the rest of the analyze module.
input data set for sequence and transition is changed to Long-form (geo)DataFrame (Community.gdf) similar to the cluster function
these two functions are reused in the Community class as methods to operate on Community
- method transition
- method sequence
sequence function/method: extend giddy's Sequence functionality to further incorporate cluster analysis on sequences. Right now, ward clustering algorithm is the default option and the number of sequence clusters is requested from users.

The notebook 04_modeling_neighborhood_dynamics.ipynb is rewritten to demonstrate the usage of the refactored dynamics module.

knaaptime commented 5 years ago

this looks great, nice work. Since we're now depending on Transition and Sequence from the newest giddy, we should also pin that as the minimum compatible version.

I also renamed the notebooks in the last commit (because needed to insert harmonize in the middle), but it looks like maybe the dynamics notebook is still WIP?

weikang9009 commented 5 years ago

this looks great, nice work. Since we're now depending on Transition and Sequence from the newest giddy, we should also pin that as the minimum compatible version.

Set the constraints in https://github.com/spatialucr/geosnap/pull/125/commits/c3be3b049400bcd2640b9f67f3a98fc9039deeb5.

I also renamed the notebooks in the last commit (because needed to insert harmonize in the middle), but it looks like maybe the dynamics notebook is still WIP?

The notebook is ready https://github.com/weikang9009/geosnap/blob/sa/examples/05_modeling_neighborhood_dynamics.ipynb

oturns / geosnap

refactor dynamics module #125