cv19gm.data package

Submodules

cv19gm.data.cv19data module

class cv19gm.data.cv19data.ImportData(tstate=None, initdate=None, enddate=datetime.datetime(2023, 5, 16, 18, 55, 10, 408007), user=None, password=None, localdata=None)

Bases: object

DLab Import Data Library input:

• tstate: [string or string list] CUT por comuna o región

• initdate: [datetime object] Initial date

output:

• ImportData Object.

Usage Example: a = ImportData(tstate=’13’, initdate=datetime(2020,5,15)) a.importdata()

aux = requests.get(’https://api.cv19gm.org/getComunas’, auth=HTTPBasicAuth(‘afosr’, ‘5pI50sOjPTDlpH’)) data = aux.json() # Para usarlo como dataframe de pandas import pandas as pd Data = pd.DataFrame(data)

# For debugging in terminal:

import json import requests from requests.auth import HTTPBasicAuth import pandas as pd from datetime import datetime from datetime import timedelta import numpy as np from os import path from importdata import ImportData

state = ‘13’ initdate = datetime(2020,5,15)

data = ImportData(state,initdate, user, password)

Todo: Add enddate Todo: Opción de guardar data en un archivo csv Todo: Opción de cargar data desde un archivo csv

add_data(data, dates=None, days=None, initdate=None)

imp_adj_matrix_national(tstate='', endpoint='http://192.168.2.223:5006/getNationalAdjacencyMatrix', N=1)

Import adjacency data N is the adjacency order, with 0 meaning the immediate neighbors, 1 the neighbor’s neighbors, and so on. Input:

• tstate [string or list of strings]

• N: Neighors Order

imp_adj_matrix_regional(tstate='', endpoint='http://192.168.2.223:5006/getRegionalAdjacencyMatrix', N=1)

Import adjacency data N is the adjacency order, with 0 meaning the immediate neighbors, 1 the neighbor’s neighbors, and so on.

imp_deaths_accumulated(tstate='', initdate=None, endpoint='getMinsalDeathsByState?state=', user=None, password=None)

Import Acumulated Deaths - Regional input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• Br: Real acumulated deaths

• Br_tr: days from simulation first day

• Br_dates: data dates

Usage:

Br,Br_tr,Br_dates = importAcumulatedDeaths(self=None,tstate = ‘13’,initdate = datetime(2020,5,15))

imp_deaths_deis(tstate='', initdate=None, endpointreg='getDeathsByState?state=', endpointcom='getDeathsByComuna?comuna=', user=None, password=None, name=['D_confirmed', 'D_suspected', 'D_ac_confirmed', 'D_ac_suspected'])

Import Accumulated Deaths input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• Br: Real accumulated deaths

• Br_tr: days from simulation first day

• Br_dates: data dates

Usage:

Br,Br_tr,Br_dates = importAccumulatedDeaths(self=None,tstate = ‘13’,initdate = datetime(2020,5,15))

imp_deaths_deis_mcyt(tstate='', initdate=None, endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto50/DefuncionesDEIS_confirmadosPorComuna.csv', user=None, password=None, name=['D_confirmed', 'D_suspected', 'D_ac_confirmed', 'D_ac_suspected'])

Import Accumulated Deaths input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• Br: Real accumulated deaths

• Br_tr: days from simulation first day

• Br_dates: data dates

Usage:

Br,Br_tr,Br_dates = importAccumulatedDeaths(self=None,tstate = ‘13’,initdate = datetime(2020,5,15))

imp_deaths_excess(path='/home/samuel/Documents/Dlab/data/Excess_dead_daily.csv')

imp_hosp_icu(tstate='', initdate=None, endpoint='getRegionalIcuBedOccupation', user=None, password=None, name=['UCI_capacity', 'UCI_use_covid', 'UCI_use_noncovid'])

Import ICU Bed Occupation data per region. Currently it just supports states, but soon I’ll add Health Services as the minimum territorial data. input:

• tstate: región

• initdate: Fecha de inicio

• endpoint: Data endpoint

output:

• sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot,

(data frame, fechas, dias desde inicio sim, Hospitalizados, capacidad hospitalizados, ventilados, capacidad ventilados)

Normal Usage:

sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot = importSOCHIMI(tstate = ‘13’, initdate = datetime(2020,5,15))

imp_hosp_icu_mcyt(tstate='', initdate=None, endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto58/Camas_UCI_diarias.csv', user=None, password=None, name=['UCI_capacity', 'UCI_use_covid', 'UCI_use_noncovid'])

Import ICU Bed Occupation data per region. Currently it just supports states, but soon I’ll add Health Services as the minimum territorial data. input:

• tstate: región

• initdate: Fecha de inicio

• endpoint: Data endpoint

output:

• sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot,

(data frame, fechas, dias desde inicio sim, Hospitalizados, capacidad hospitalizados, ventilados, capacidad ventilados)

Normal Usage:

sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot = importSOCHIMI(tstate = ‘13’, initdate = datetime(2020,5,15))

imp_hosp_vmibeds(tstate='', initdate=None, endpoint='getRegionalIcuBedOccupation', user=None, password=None, name=['UCI_capacity', 'UCI_use_covid', 'UCI_use_noncovid'])

Import ICU Bed Occupation data per region. Currently it just supports states, but soon I’ll add Health Services as the minimum territorial data. input:

• tstate: región

• initdate: Fecha de inicio

• endpoint: Data endpoint

output:

• sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot,

(data frame, fechas, dias desde inicio sim, Hospitalizados, capacidad hospitalizados, ventilados, capacidad ventilados)

Normal Usage:

sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot = importSOCHIMI(tstate = ‘13’, initdate = datetime(2020,5,15))

imp_hospitalized_deaths(tstate='', initdate=None, endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto57/fallecidos_hospitalizados.csv')

Import Accumulated Deaths input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• Dr_hosp: Hospitalized deaths

• Dr_Nonhosp: Non Hospitalized deaths

• Br_hosp: Hospitalized Accumulated deaths

• Br_Nonhosp: Non Hospitalized Accumulated deaths

• Br_hosp_tr: Days since initdate

• Dr_hosp_dates: Dates

Usage:

Dr_hosp, Dr_Nonhosp,Br_hosp, Br_Nonhosp, hosp_tr, hosp_dates =importAccumulatedDeathsHospitalized(tstate = ‘13’,initdate = datetime(2020,5,15))

imp_infected_accumulated(tstate='', initdate=None, endpoint='getTotalCasesAllComunas', user=None, password=None, name='I_ac')

Import acumulated infected This Function imports the selected area accumulated infected from CyV Endpoint input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (opcional):

output:

• I_ac_r: Real Acumulated infected

• I_ac_r_tr: days from simulation first day

• I_ac_r_dates: data dates

Variables when used as Object:

self.I_ac_r self.I_ac_r_tr self.I_ac_r_dates

Usage as function:

I_ac_r, I_ac_r_tr,I_ac_r_dates= importAccumulatedInfected(tstate = ‘13101’,initdate=datetime(2020,5,15))

imp_infected_accumulated_mcyt(tstate='', initdate=None, endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto1/Covid-19.csv', name='I_ac')

Import acumulated infected input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (opcional):

output:

• I_ac_r: Real Acumulated infected

• I_ac_r_tr: days from simulation first day

• I_ac_r_dates: data dates

imp_infected_active(tstate='', initdate=None, endpoint='getActiveCasesAllComunas', user=None, password=None, name='I')

Import Active infected This function imports the active infected calculated as the infected that are within their 14 days since exposure.

input:

• tstate: [string or string list] CUT por comuna o región

• endpoint (opcional):

output:

• Ir: list of Active infected

• tr: days from simulation beginning

• Ir_dates: dates [datetime object]

Variables when used as Object:

self.Ir self.tr self.Ir_dates

Usage as function example:

Ir,tr,Ir_dates = importActiveInfected(tstate = ‘13101’,initdate=datetime(2020,5,15))

imp_infected_active_mcyt(tstate='', initdate=None, endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto19/CasosActivosPorComuna.csv', name='I')

Import Active infected Minciencia input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• I_minciencia_r: Real acumulated deaths

• I_minciencia_r_tr: days from simulation first day

• I_minciencia_r_dates: data dates

imp_infected_daily(tstate='', initdate=None, endpoint='getTotalCasesAllComunas', user=None, password=None, name='I_d')

Import daily infected input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• I_d_r: Real Daily infected

• I_d_r_tr: days from simulation first day

• I_d_r_dates: data dates

usage

I_d_r, I_d_r_tr, I_d_r_dates = importDailyInfected(tstate = ‘13101’,initdate = datetime(2020,5,15))

imp_infected_daily_mcyt(tstate='', initdate=None, endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto1/Covid-19.csv', name='I_d')

Import daily infected input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• I_d_r: Real Daily infected

• I_d_r_tr: days from simulation first day

• I_d_r_dates: data dates

usage

I_d_r, I_d_r_tr, I_d_r_dates = importDailyInfected(tstate = ‘13101’,initdate = datetime(2020,5,15))

imp_infected_daily_mcyt_backprop(tstate='', initdate=None, endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto1/Covid-19.csv', name='I_d')

Import daily infected smoothed with Backpropagation This function smoothes the daily infected thata and distributes homogeneously the 30k excess cases added in ~2020-6-16 input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• I_d_r: Real Daily infected

• I_d_r_tr: days from simulation first day

• I_d_r_dates: data dates

imp_infected_daily_national(tstate='', initdate=None, endpoint='getNationalNewCases', user=None, password=None, name='I_d')

Import daily infected input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• I_d_r: Real Daily infected

• I_d_r_tr: days from simulation first day

• I_d_r_dates: data dates

usage

I_d_r, I_d_r_tr, I_d_r_dates = importDailyInfected(tstate = ‘13101’,initdate = datetime(2020,5,15))

imp_lockdowns(tstate='', endpoint='', N=1)

Import Lockdowns data So far from local data

imp_pcr_population(endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto7/PCR.csv')

imp_population(endpoint='', tstate='', user=None, password=None)

Import PopulationendpointComunas This Function imports the selected area population.

input:

• tstate: [string or string list] CUT por comuna o región

• endpoint [string](opcional)

output:

• population [int]

object variables:

self.population self.population_male self.population_female

Example usage as function: population = importPopulation(tstate = ‘13101’,initdate=datetime(2020,5,15))

imp_population_mcyt(endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto1/Covid-19.csv', tstate='')

Import Population This Function imports the selected area population from the Minciencia Github Repository

input:

• tstate: [string or string list] CUT por comuna o región

• endpoint [string](opcional)

output:

• population [int]

Variables when used as Object:

self.population

Usage as function: population = importPopulationMinCiencia(tstate = ‘13101’,initdate=datetime(2020,5,15))

imp_reproduction_number(tstate='', initdate=None, endpointcounty='http://192.168.2.223:5006/getEffectiveReproductionAllComunas', endpointstates='http://192.168.2.223:5006/getEffectiveReproductionAllStates', user=None, password=None)

Import Effective Reproduction Number input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• Br: Real accumulated deaths

• Br_tr: days from simulation first day

• Br_dates: data dates

Usage:

Br,Br_tr,Br_dates = importAccumulatedDeaths(self=None,tstate = ‘13’,initdate = datetime(2020,5,15))

imp_sochimi(tstate='', initdate=None, endpoint='getBedsAndVentilationByState?state=', user=None, password=None)

Import SOCHIMI data per state. Currently it just supports states, but soon I’ll add Health Services as the minimum territorial data. input:

• tstate: región

• initdate: Fecha de inicio

• endpoint: Data endpoint

output:

• sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot,

(data frame, fechas, dias desde inicio sim, Hospitalizados, capacidad hospitalizados, ventilados, capacidad ventilados)

Normal Usage:

sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot = importSOCHIMI(tstate = ‘13’, initdate = datetime(2020,5,15))

imp_sochimi_mcyt(tstate='', initdate=None, endpoint='https://raw.githubusercontent.com/MinCiencia/Datos-COVID19/master/output/producto48/SOCHIMI.csv')

Import SOCHIMI data per state. Currently it just supports states, but soon I’ll add Health Services as the minimum territorial data. input:

• tstate: región

• initdate: Fecha de inicio

• endpoint: Data endpoint

output:

• sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot,

(data frame, fechas, dias desde inicio sim, Hospitalizados, capacidad hospitalizados, ventilados, capacidad ventilados)

Normal Usage:

sochimi, sochimi_dates, sochimi_tr, Hr, Hr_tot, Vr, Vr_tot = importSOCHIMI(tstate = ‘13’, initdate = datetime(2020,5,15))

imp_vacc_infected_mcyt(tstate='', initdate=None, endpoint='https://github.com/MinCiencia/Datos-COVID19/raw/master/output/producto90/incidencia_en_vacunados.csv', user=None, password=None)

Product 90 has data of:

Import Vaccines input:

• tstate: [string or string list] CUT por comuna o región

• initdate: datetime object with the initial date

• endpoint (optional):

output:

• V_1st: First Dose (2 doses vaccine)

• V_complete: complete (1 or 2 doses vaccine)

• V_boost: Boost Dose

Usage:

import_data()

import_data_mcyt()

import_data_seir()

load(filename)

plot(y, x='dates', label='default', color=None, thickness=None, plottype='line', ylabel='', xlabel='')

save(filename)

cv19gm.data.cv19data.dataretriever(user=None, password=None, json=None)

cv19gm.data.cv19data.dfappend(df, values, days, dataname)

cv19gm.data.cv19data.help()

cv19gm.data.cv19data_national module

Module contents