mixing state calculator

This script is used for calculating mixing state index

Step 0: click the link here to launch a jupyter notebook

Step 1: upload your own csv file (each row is a particle, each column is the mass of a species)

|upload\_csv|

Step 2: edit the file_name and group_list below

Below is an exmaple with three surrogate species

The definition of surrogate species is here (Figure 2)

- surrogate species 1: “BC” and “POM”

- surrogate species 2: “DUST”

- surrogate species 3: “SS”

Step 3: click Run button on the top of your jupyter notebook

|run\_cell|

Please edit the “file_name” and “group_list”, then run the code below

file_name = "sample_data.csv"
group_list = [["BC","POM"],
              ["DUST"],
              ["SS"]]

# ====== please don't change ======
import numpy as np
import pandas as pd
import pmcpy

# load data
df = pd.read_csv(file_name)
# get matrix for calculation
da = np.concatenate([df[group].values.sum(axis=1).reshape(-1,1) for group in group_list],axis=1)
# calculate mixing state index
D_alpha, D_gamma, chi = pmcpy.get_chi(da)
print("mixing state index:", chi)
print("average particle (alpha) species diversity:", D_alpha)
print("bulk population (gamma) species diversity:", D_gamma)

mixing state index: 0.9408323695414793
average particle (alpha) species diversity: 2.838147712915256
bulk population (gamma) species diversity: 2.9537462489849164