evalAIRR 0.0.7

Comparison of real and simulated AIRR datasets

evalAIRR

A tool that allows comparison of real and simulated datasets by providing different statistical indicators and dataset visualizations in one report.

Installation

It is recommended to use a virtual python environment to run evalAIRR if another python environment is used. Here is a quick guide on how you can set up a virtual environment:

https://docs.python.org/3/tutorial/venv.html#creating-virtual-environments

Install using pip

Run this command to install the evalAIRR package:

pip install evalairr

Quickstart

evalAIRR uses a YAML file for configuration. If you are unfamiliar with how YAML files are structured, read this guide to the syntax:

https://docs.fileformat.com/programming/yaml/#syntax

This is the stucture of a sample report configuration file you can use to start off with (it is included in the repository location ./yaml_files/quickstart.yaml):

datasets:
  real:
    path: ./data/encoded_real_1000_200.csv
  sim:
    path: ./data/encoded_sim_1000_200.csv
reports:
  feature_based:
    report1:
      features:
        - TGT
        - ANV
      report_types:
        - ks
        - distr_densityplot
output:
  path: './output/report.html'

This report will process the two provided datasets (real and simulated), and create an HTML report with feature-based report types - Kolmogorov–Smirnov test (indicated by ks) and a feature distribution density plot (indicated by distr_densityplot) for the features TGT and ANV. It will then export the report to the path ./output/report.html. More details on what reports can be created can be found in the YAML Configuration Guidelines secion.

You can run the program by running this command within the installation directory:

evalairr -i ./yaml_files/quickstart.yaml

The report will be generated in the specified output path in the configuration file or, if a specific path is not provided, in <CURRENT_DIRECTORY>/output/report.html. The report is exported in the HTML format.

YAML Configuration Guidelines

The configuration YAML file consists of 3 main sections: datasets, reports and output.

Datasets

In the datasets section, you have to provide paths to a real and a simulated datasets that you are comparing. This can be done by specifying the file path of each file in the path variable under the sections real and sim respectively. Here is an example of how a configured datasets section looks like:

datasets:
  real:
    path: ./data/encoded_real_1000_200.csv
  sim:
    path: ./data/encoded_sim_1000_200.csv

Reports

In the reports section, you can provide the list of report types you want to create and their parameters. There are three types of report groups depending on the different parameters: feature_based, observation_based and generic. Here is the list of reports you can create that compare the features of the real dataset with the simulated dataset:

Feature-based reports

• ks - Kolmogorov–Smirnov statistic. Parameters: list of features you are creating the report for.
• distr_histogram - feature distribution histogram. Parameters: list of features you are creating the report for.
• distr_boxplot - feature distribution boxplot. Parameters: list of features you are creating the report for.
• distr_violinplot - feature distribution violin plot. Parameters: list of features you are creating the report for.
• distr_densityplot - feature distribution density plot. Parameters: list of features you are creating the report for.
• distance - Euclidean distance between the real and simulated feature. Parameters: list of features you are creating the report for.
• statistics - statistical indicators (average, median, standard deviation and variance) of a feature in both real and simulated datasets. Parameters: list of features you are creating the report for.

Observation-based reports

• observation_distr_histogram - observation distribution histogram. Parameters: list of observations you are creating the report for.
• observation_distr_boxplot - observation distribution boxplot. Parameters: list of observations you are creating the report for.
• observation_distr_violinplot - observation distribution violin plot. Parameters: list of observations you are creating the report for.
• observation_distr_densityplot - observation distribution density plot. Parameters: list of observations you are creating the report for. The observation index 'all' can be used to report on all observations in one plot.
• observation_distance - Euclidean distance between the real and simulated observation. Parameters: list of observations you are creating the report for.
• observation_statistics - statistical indicators (average, median, standard deviation and variance) of an observation in both real and simulated datasets. Parameters: list of observations you are creating the report for.

General reports

• copula_2d - a 2D scatter plot that displays two features in a Gausian Multivariate copula space. Parameters: a report section of any name, under which the compared features are specified.
• copula_3d - a 3D scatter plot that displays three features in a Gausian Multivariate copula space. Parameters: a report section of any name, under which the compared features are specified.
• feature_average_vs_variance - a scatter plot that displays the average value of every feature on one axis and the variance of every feature on the other axis.
• observation_average_vs_variance - a scatter plot that displays the average value of every observation on one axis and the variance of every observation on the other axis.
• corr - correlation matrix heatmaps of the real and simulated datasets. Parameters: percent_features - an optional parameter for dimensionality reduction using PCA. A float value corresponding with the ratio of feature reduction (e.g. percent_features equal to 0.5 would reduce the feature count by half).
• pca_2d - two scatter plots with both datasets reduced to two dimensions using PCA.

Here is a sample reports section of a configuration file containing all of the reports:

reports:
  feature_based:
    report1:
      features:
        - TGT
        - ANV
      report_types:
        - ks
        - distr_histogram
        - distr_boxplot
        - distr_violinplot
        - distr_densityplot
        - distance
        - statistics
  observation_based:
    report1:
      observations:
        - 0
      report_types:
        - observation_distr_histogram
        - observation_distr_boxplot
        - observation_distr_violinplot
        - observation_distr_densityplot
        - observation_distance
        - observation_statistics
    report2:
      observations:
        - all
      report_types:
        - observation_distr_densityplot
  general:
    copula_2d:
      report1:
        - TGT
        - ANV
    copula_3d:
      report1:
        - TGT
        - ANV
        - CAS
    feature_average_vs_variance:
    observation_average_vs_variance:
    corr:
      percent_features: 0.6
    pca_2d:

Output

An optional section where you can specify the file path of the generated report. The default path of the generated report is <INSTALL_DIRECTORY>/output/report.html. The report is exported in the HTML format.

An example output section:

output:
  path: './output/report.html'