dailylog 5-02-20

GEORGIA GIF SCRIPT

convert -delay 30 georgia_v7*.png -delay 300 georgia_v72020-04-28.png -loop 0 georgia7.gif

NOTEBOOK: COVID-19/Untitled

import pandas as pd
import glob
import os


path = 'csse_covid_19_data/csse_covid_19_daily_reports'                   # use your path
all_files = glob.glob(os.path.join(path, "*.csv"))     # advisable to use os.path.join as this makes concatenation OS independent

df_from_each_file = (pd.read_csv(f) for f in all_files)
concatenated_df   = pd.concat(df_from_each_file, ignore_index=True)

NOTEBOOK: COVID-19/GET_CALIFORNIA_COUNTIES

import pandas as pd
import numpy as np

from urllib.request import urlopen
import json

import plotly.graph_objects as go
import plotly.express as px

with urlopen('https://raw.githubusercontent.com/plotly/datasets/master/geojson-counties-fips.json') as response:
    counties = json.load(response)
df = pd.read_csv("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-counties.csv",
                   dtype={"fips": str})
df_state = pd.read_csv("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv",
                   dtype={"fips": str})

ca = df[df['state']=='California']

def make_plot_by_dates(date):
    fig = px.choropleth(ca[ca['date']==date], geojson=counties, locations='fips', color='cases',
                               color_continuous_scale="Viridis",
                               range_color=(0, 500),
                               scope="usa",

                               labels={'2020-04-25':'infection rate'}
                              )
    fig.update_geos(fitbounds="locations", visible=False)
    fig.update_layout(margin={"r":0,"t":0,"l":0,"b":0}, title="hello")
    fig.update_layout(
        title={
            'text': date,
            'y':0.9,
            'x':0.5,
            'xanchor': 'center',
            'yanchor': 'top'})
    fig.show()

dates = sorted(set(df.date))

for date in dates:
    make_plot_by_dates(date)

UNTESTED WITH CA

def make_plot(date):
    print(date)
#     date = df.columns[0]
    fig = px.choropleth(ca[ca['date'] == date], geojson=counties, locations='fips', color='cases',
                               color_continuous_scale="Viridis",
                               range_color=(0, 1000),
                               scope="usa",

                               labels={'2020-04-25':'infected'}
                              )
    fig.update_geos(fitbounds="locations", visible=False)
    fig.update_layout(margin={"r":0,"t":0,"l":0,"b":0})
    fig.update_layout(
        title={
            'text': date,
            'y':0.9,
            'x':0.5,
            'xanchor': 'center',
            'yanchor': 'top'},
    coloraxis_colorbar=dict(
    title="Number of infections",
            titleside="top",
        tickmode="array",
        tickvals=[0, 100, 500, 1000],
        ticktext=["0", "100", "500", ">1000"],
        ticks="outside"
    )
    )
    filename = 'california_' + date + '.png'
    fig.write_image(filename)
    fig.show()

COLAB FILE