4.2. Obtaining samples matrix and target values

In this notebook, we will show how CoPro reads the input data and derives the samples matrix and target values needed to establish a machine-learning model.

4.2.1. Preparations

Start with loading the required packages.

from copro import utils, pipeline, data

%matplotlib inline

import matplotlib.pyplot as plt
import pandas as pd
import geopandas as gpd
import os, sys
import warnings
from shutil import copyfile

For better reproducibility, the version numbers of all key packages used to run this notebook are provided.

Python version: 3.7.8 | packaged by conda-forge | (default, Jul 31 2020, 01:53:57) [MSC v.1916 64 bit (AMD64)]
copro version: 0.0.8
geopandas version: 0.9.0
xarray version: 0.15.1
rasterio version: 1.1.0
pandas version: 1.0.3
numpy version: 1.18.1
scikit-learn version: 0.23.2
matplotlib version: 3.2.1
seaborn version: 0.11.0
rasterstats version: 0.14.0

To be able to also run this notebooks, some of the previously saved temporary files need to be loaded.

conflict_gdf = gpd.read_file(os.path.join('temp_files', 'conflicts.shp'))
selected_polygons_gdf = gpd.read_file(os.path.join('temp_files', 'polygons.shp')) The configurations-file (cfg-file)

To be able to continue the simulation with the same settings as in the previous notebook, the cfg-file has to be read again and the model needs to be initialised subsequently. This is not needed if CoPro is run from command line. Please see the previous notebook for additional information.

settings_file = 'example_settings.cfg'
main_dict, root_dir = utils.initiate_setup(settings_file, verbose=False)

#### CoPro version 0.0.8 ####
#### For information about the model, please visit https://copro.readthedocs.io/ ####
#### Copyright (2020-2021): Jannis M. Hoch, Sophie de Bruin, Niko Wanders ####
#### Contact via: j.m.hoch@uu.nl ####
#### The model can be used and shared under the MIT license ####

INFO: reading model properties from example_settings.cfg
INFO: verbose mode on: False
INFO: saving output to main folder C:\Users\hoch0001\Documents\_code\copro\example\./OUT
config_REF = main_dict['_REF'][0]
out_dir_REF = main_dict['_REF'][1]

4.2.2. Reading the files and storing the data Background

This is an essential part of CoPro. For a machine-learning model to work, it requires a samples matrix (X), representing here the socio-economic and hydro-climatic ‘drivers’ of conflict, and target values (Y) representing the (observed) conflicts themselves. By fitting a machine-learning model, a relation between X and Y is established, which in turn can be used to make projections.

Additional information can be found on scikit-learn.

Since CoPro simulates conflict risk spatially explicit for each polygons (here water provinces), it is furthermore needed to be able to associate each polygon with the corresponding data points in X and Y. We therefore also keep a polygon-ID and its geometry, and track it throughout the modelling chain. Implementation

CoPro goes through all model years as specified in the cfg-file. Per year, CoPro loops over all polygons remaining after the selection procedure (see previous notebook) and does the following to obtain the X-data.

  1. Assign ID to polygon and retrieve geometry information;

  2. Calculate a statistical value per polygon from each input file specified in the cfg-file in section ‘data’. Which statistical value is ought to be computed needs to be specified in the cfg-file. In the cfg-file, it’s furthermore possible to specify whether values are ought to be log-transformed.

Note that CoPro applies a 1 year time-lag by default. That means that for a given year J, the data from year J-1 is read. This is to avoid issues with backwards reversibility, i.e. we assume that the driver results in conflict (or not) with one year delay and not immediately in the same year.

And to obtain the Y-data:

  1. Assign a Boolean value whether a conflict took place in a polygon or not - the number of casualties or conflicts per year is not relevant in thise case.

All information is stored in a X-array and a Y-array. The X-array has 2+n columns whereby n denotes the number of samples provided. The Y-array has obviously only 1 column, consisting of zeros and ones. In both arrays is the number of rows determined as number of years times the number of polygons. In case a row contains a missing value (e.g. because one input data does not cover this polygon), the entire row is removed from the XY-array.

Note that the sample values can still range a lot depending on their units, measurement, etc. In the next notebook, the X-data will be scaled to be able to compare the different values in the samples matrix.

X, Y = pipeline.create_XY(config_REF, out_dir_REF, root_dir, selected_polygons_gdf, conflict_gdf)
INFO: reading data for period from 2000 to 2012
INFO: skipping first year 2000 to start up model
INFO: entering year 2001
INFO: entering year 2002
INFO: entering year 2003
INFO: entering year 2004
INFO: entering year 2005
INFO: entering year 2006
INFO: entering year 2007
INFO: entering year 2008
INFO: entering year 2009
INFO: entering year 2010
INFO: entering year 2011
INFO: entering year 2012 Saving data to file

Depending on sample and file size, obtaining the X-array and Y-array can be time-consuming. Therefore, CoPro automatically stores a combined XY-array as npy-file to the output folder if not specified otherwise in the cfg-file. With this file, future runs using the same data but maybe different machine-learning settings can be executed in less time.

Let’s check if this files exists.

os.path.isfile(os.path.join(out_dir_REF, 'XY.npy'))

4.2.3. Temporary files

By default, a binary map of conflict per polygon for the last year of the simulation period is stored to the output directory. Since the output directory is created from scratch at each model initalisation, we need to temporarily store this map in another folder to be used in subsequent notebooks.


for root, dirs, files in os.walk(os.path.join(out_dir_REF, 'files')):
    for file in files:
        fname = file
        copyfile(os.path.join(out_dir_REF, 'files', str(fname)),
                 os.path.join('temp_files', str(fname)))