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visualize_time_simu.py
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visualize_time_simu.py
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# -*- coding: utf-8 -*-
"""
Created on Mon Jun 29 23:15:47 2020
@author: antje
"""
import time_simu
import numpy as np
import pylab as plt
import read_temperature as rt
import Model_Szenario as MS
#==============================================================================
# Provide a weather plot for the period specified in "Model_Szenario.py"
#==============================================================================
years = MS.years
date = MS.startdate
def makeList(w):
TX=[]
T0=0
for i in range (365*years):
rawData=(w.next())
T1 = rawData *0.1 + T0*0.9
T0 = T1
TX.append(T1)
return(TX)
TX_r1 = makeList(rt.Weather(region = rt.r1, date = date))[0:365*years+1]
TX_r2 = makeList(rt.Weather(region = rt.r2, date = date))[0:365*years+1]
TX_r3 = makeList(rt.Weather(region = rt.r3, date = date))[0:365*years+1]
fig, (ax1, ax2, ax3) = plt.subplots(3,sharex=True,
sharey=True,
figsize=(12,6),
dpi=300)
ax1.plot(TX_r1, label="Region 1",color="black")
ax1.minorticks_on()
ax1.grid(b=True, which='minor', color='0.9', linestyle='--')
ax1.grid(b=True, which='major', color='0.7', linestyle='-')
ax1.tick_params(axis='y', which='major', labelsize=12)
ax1.legend()
ax2.plot(TX_r2, label="Region 2",color="black")
ax2.minorticks_on()
ax2.grid(b=True, which='minor', color='0.9', linestyle='--')
ax2.grid(b=True, which='major', color='0.7', linestyle='-')
ax2.tick_params(axis='y', which='major', labelsize=12)
ax2.legend()
ax3.plot(TX_r3, label="Region 3",color="black")
ax3.minorticks_on()
ax3.grid(b=True, which='minor', color='0.9', linestyle='--')
ax3.grid(b=True, which='major', color='0.7', linestyle='-')
ax3.tick_params(axis='y', which='major', labelsize=12)
ax3.legend()
Pos=(np.arange(0,365*(years+1),365))
dates=['01/01/2018', '01/01/2019', '01/01/2020', '01/01/2021']
plt.xticks(Pos, dates, size="large")
plt.tight_layout()
plt.show()
#==============================================================================
# Show plots for the temperature and season dependant parameters
#==============================================================================
def show_tests():
lat=50.6
sir=time_simu.SIR(lat)
months=["1\n(Jan)","60\n(Mar)","121\n(May)","182\n(July)","244\n(Sept)",
"305\n(Nov)","366\n(Jan)"]
dates=[1,60,121,182,244,305,366]
"""
biting_rate, bL und bM sowie mL and mM
"""
T=np.linspace(-5.0,45.0,1000)
biting_rate=sir.biting_rate(T)
bL=sir.bL(T)
bM=sir.bM(T)
mL=[]
mM=[]
for TX in T:
mL.append(sir.mL(TX))
mM.append(sir.mM(TX))
plt.figure(figsize=(12,4),dpi=300)
plt.subplot(121)
plt.plot(T,biting_rate,linestyle='dotted',color="black",
label="biting rate")
plt.plot(T,bL,linestyle='dashed',color="black",
label="birth rate of larvae")
plt.plot(T,bM,linestyle='solid',color="black",
label="birth rate of imagos")
plt.grid(linestyle="dotted",c="0.8")
plt.legend()
plt.xlabel('Temperature (°C)')
plt.ylabel('Daily rate')
plt.title('a)' , loc='left',fontweight='bold')
plt.subplot(122)
plt.plot(T,mM, linestyle='solid', color="black", label="larvae")
plt.plot(T,mL, linestyle='dashed', color="black", label="imagos")
plt.grid(linestyle="dotted",c="0.8")
plt.legend()
plt.xlabel('Temperature (°C)')
plt.ylabel('Daily mortality rate')
plt.title('b)' , loc='left',fontweight='bold')
plt.tight_layout(w_pad=3)
#plt.savefig('PopulationControl_new.pdf',bbox_inches='tight')
plt.show()
"""
gammaM and EIP
"""
gammaM=[]
EIP=[]
for TX in T:
gammaM.append(sir.gammaM(TX))
for TX in T:
if(sir.gammaM(TX)<=0):
EIP.append(170)
else:
EIP.append(1/sir.gammaM(TX))
plt.figure(figsize=(12,4),dpi=300)
plt.subplot(122)
plt.plot(T,gammaM, color="black")
plt.grid(linestyle="dotted",c="0.8")
plt.xlim([12,35])
plt.ylim([0.0,0.2])
plt.xlabel('Temperature (°C)')
plt.ylabel('$\gamma_{M}$',labelpad=10)
plt.title('b)' , loc='left',fontweight='bold')
plt.subplot(121)
plt.plot(T,EIP, color="black")
plt.grid(linestyle="dotted",c="0.8")
plt.ylim([0,100])
plt.xlim([12,35])
plt.xlabel('Temperature (°C)')
plt.ylabel('EIP in days',labelpad=10)
plt.title('a)' , loc='left',fontweight='bold')
plt.tight_layout(w_pad=3)
#plt.savefig('gammaM_EIP.pdf',bbox_inches='tight')
plt.show()
"""
deltaM
"""
t=np.linspace(1,365,365)
deltaM=[]
for tx in t:
deltaM.append(sir.deltaM(tx))
plt.figure(dpi=300)
plt.plot(t,deltaM, color="black")
plt.grid(linestyle="dotted",c="0.8")
plt.xlabel('time in days')
plt.xticks(dates,months,rotation = 45)
plt.ylabel('deltaM')
plt.show()
"""
k(T)*p and transmission rate (betaB) from bird to mosquito
"""
betaB_j = sir.biting_rate(T)*0.17*0.165*0.75
kp_j = sir.biting_rate(T)*0.17
betaB_c1 = sir.biting_rate(T)*0.06 *0.33 *0.75
betaB_c2 = sir.biting_rate(T)*0.06 *0.66 *0.75
betaB_c3 = sir.biting_rate(T)*0.06 *0.96 *0.75
kp_c = sir.biting_rate(T)*0.06
plt.figure(figsize=(12,4),dpi=300)
plt.subplot(121)
plt.plot(T,kp_j,color="black",linestyle ="--",
label="$Ae.$ $j.$ $japonicus$")
plt.plot(T,kp_c,color="black",linestyle ="-",
label="$Culex$ $agg.$")
plt.grid(linestyle="dotted",c="0.8")
plt.legend()
plt.xlabel('Temperature (°C)')
plt.ylabel('$k(T)p_{B}$',labelpad=10)
plt.title('a)' , loc='left',fontweight='bold')
plt.subplot(122)
plt.plot(T,betaB_j, color="black",linestyle ="--",
label="$Ae.$ $j.$ $japonicus$, $P_{J} = 0.165$")
plt.plot(T,betaB_c1,color="0.75",linestyle ="-",
label="$Culex$ $agg.$, $P$ = 0.33")
plt.plot(T,betaB_c2,color="0.5 ",linestyle ="-",
label="$Culex$ $agg.$, $P$ = 0.66")
plt.plot(T,betaB_c3,color="0.0",linestyle ="-",
label="$Culex$ $agg.$, $P$ = 0.96")
plt.grid(linestyle="dotted",c="0.8")
plt.legend()
plt.xlabel('Temperature (°C)')
plt.ylabel(r'$\beta_{B}$',labelpad=10)
plt.title('b)' , loc='left',fontweight='bold')
plt.tight_layout(w_pad=3)
#plt.savefig('betaB_kp.pdf',bbox_inches='tight')
plt.show()
"""
Bird birth as function of the year
"""
t=np.linspace(1,365,365)
bB=[]
Pre_bB=[]
for tx in t:
bB.append(sir.bB(tx))
Pre_bB.append(sir.bB(tx)/0.614)
X = [125, 135, 145, 156, 166, 176, 186, 196, 206]
Y = np.array([1.52, 15.27, 33.27, 25.27, 10.27, 5.77, 4.27, 2.77, 1.60])
plt.figure(figsize=(6,4),dpi=300)
plt.bar(X, Y/1000, width=11,color="0.75", label="observations")
plt.plot(t, Pre_bB, color="0.5", label = "fit")
plt.plot(t, bB, color="black", label = "fit * 0.614")
plt.grid(linestyle="dotted",c="0.8")
plt.legend()
plt.xticks(dates,months,rotation=0)
plt.ylabel('$b_{B}$')
plt.subplots_adjust(bottom=0.15)
plt.subplots_adjust(left=0.15)
#plt.savefig('MagpieBirth_New.pdf',bbox_inches='tight')
plt.show()
"""
Daylength
"""
daylength=[]
for tx in t:
daylength.append(sir.daylength(tx))
plt.figure(figsize=(6,4),dpi=300)
plt.plot(t,daylength, color="black")
plt.grid(linestyle="dotted",c="0.8")
plt.xticks(dates,months,rotation=0)
plt.ylabel('D',labelpad=10)
plt.subplots_adjust(bottom=0.15)
#plt.savefig('Daylength.pdf',bbox_inches='tight')
plt.show()
return sir
sir=show_tests()