Hello i'm looking for the computer code of SIR for python in order to do some experiments. Could you please send me your code ( program)? It will be really nice.
Hi! I'm afraid I don't have the code anymore, but you can easily copy it from the video which can't take more than 1-2 minutes. I hope you found this tutorial helpful.
sorry i get an error, line 29, in solution = scipy.integrate.odeint(modelo_sir, [S0, I0, R0], t, args=(beta, gamma)) File "C:\Users\HP\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\integrate\odepack.py", line 233, in odeint int(bool(tfirst))) RuntimeError: The size of the array returned by func (2) does not match the size of y0 (3).
Hi! I'm afraid I can't figure out the problem from the error message. Can you please check again that your code is the same as the code in the video? If it is the same, can you post your code here? I will have time to check it during the evening (EU time).
For the people interested in source code, here there is a implementation of the basic SIR model in Python using SciPy (NumPy and other packages): scipython.com/book/chapter-8-scipy/additional-examples/the-sir-epidemic-model/ . Here another one, from the epirecipes project: epirecip.es/epicookbook/chapters/kr08/2_1/python_original . Searching "sir model python" on the web, you can find many others examples.
Hello, in your publication you say that gamma represents the inverse of the average number of days to heal. In this case, if I set beta to zero, there will be no more new infected people and the number of infected people will have to go to zero after ten days plus at least a certain interval since it's an average. I've done the test, the number of infected people goes to zero around the fiftieth day. Can you please explain to me what is wrong with my thinking?
@@marbellydavila3065 import numpy as np from scipy.integrate import odeint import matplotlib.pyplot as plt # Total population, N. N = 1000 # Initial number of infected and recovered individuals, I0 and R0. I0, R0 = 1, 0 # Everyone else, S0, is susceptible to infection initially. S0 = N - I0 - R0 # Contact rate, beta, and mean recovery rate, gamma, (in 1/days). beta, gamma = 0.2, 1./10 # A grid of time points (in days) t = np.linspace(0, 150, 150) # The SIR model differential equations. def deriv(y, t, N, beta, gamma): S, I, R = y dSdt = -beta * S * I / N dIdt = beta * S * I / N - gamma * I dRdt = gamma * I return dSdt, dIdt, dRdt # Initial conditions vector y0 = S0, I0, R0 # Integrate the SIR equations over the time grid, t. ret = odeint(deriv, y0, t, args=(N, beta, gamma)) S, I, R = ret.T # Plot the data on three separate curves for S(t), I(t) and R(t) fig = plt.figure(facecolor='w') ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True) ax.plot(t, S/1000, 'b', alpha=0.5, lw=2, label='Susceptible') ax.plot(t, I/1000, 'r', alpha=0.5, lw=2, label='Infected') ax.plot(t, R/1000, 'g', alpha=0.5, lw=2, label='Recovered with immunity') ax.set_xlabel('Time /days') ax.set_ylabel('Number (1000s)') ax.set_ylim(0,1.2) ax.yaxis.set_tick_params(length=0) ax.xaxis.set_tick_params(length=0) ax.grid(b=True, which='major', c='w', lw=2, ls='-') legend = ax.legend() legend.get_frame().set_alpha(0.5) for spine in ('top', 'right', 'bottom', 'left'): ax.spines[spine].set_visible(False) plt.show()
@@kaoutarbentalha7620 maybe i'm missing something (you can tell me). (1) you have csv with infection counts. (2) you have SIR model, where I(t) = exp(aS-b)*t. (3) you must FIT your csv infection count data to the exponential: (4) take the log of Infection count and (5) run a linear regression vs time. (6) this will give you (aS-b) coefficient in toto, and (7) then use eqn for R(t) = b*exp(as-b)*t and deduce the "b". (8) then you can back out the "a" from earlier, now that you know "b"; thusly you have fitted the entire SIR model...no?
import numpy as np
import scipy.integrate
import matplotlib.pyplot as plt
def SIRD_model(y, t, beta, gamma, delta): #adding death separately from recovery
S, I, R, D = y
dS = -beta*S*I
dI = beta*S*I - gamma*I - delta*I
dR = gamma*I
dD = delta*I
return ([dS, dI, dR, dD])
t = np.linspace(0, 100,1000)
S0 = 0.9
I0 = 0.1
R0 = 0.0
D0 = 0.0
beta = 0.45
gamma = 0.1
delta = 0.15
Ro = beta/(delta+gamma)
print('R0 =',Ro)
solution = scipy.integrate.odeint(SIRD_model, [S0, I0, R0, D0], t, args=(beta, gamma, delta))
plt.figure(figsize=[6,4])
plt.plot(t, solution[:, 0], label="S(t)")
plt.plot(t, solution[:, 1], label="I(t)")
plt.plot(t, solution[:, 2], label="R(t)")
plt.plot(t, solution[:, 3], label="D(t)")
plt.grid()
plt.legend()
plt.xlabel("Time")
plt.ylabel("Proportions")
plt.title("SIRD model")
plt.show()
ah you got me. its not linespace its linspace.
Thank you, I have this due in 18 minutes
Beautiful
Pls i do not understand the S,I,R = y. what is 'y'? ------ SIR_model function
Is the time measured in days?
How can I model the exact same but instead of graphs to me like point ?
And How can I add E=exposed into this code ?
Hello i'm looking for the computer code of SIR for python in order to do some experiments. Could you please send me your code ( program)? It will be really nice.
Hi! I'm afraid I don't have the code anymore, but you can easily copy it from the video which can't take more than 1-2 minutes. I hope you found this tutorial helpful.
sorry i get an error, line 29, in
solution = scipy.integrate.odeint(modelo_sir, [S0, I0, R0], t, args=(beta, gamma))
File "C:\Users\HP\AppData\Local\Programs\Python\Python36\lib\site-packages\scipy\integrate\odepack.py", line 233, in odeint
int(bool(tfirst)))
RuntimeError: The size of the array returned by func (2) does not match the size of y0 (3).
Hi! I'm afraid I can't figure out the problem from the error message. Can you please check again that your code is the same as the code in the video? If it is the same, can you post your code here? I will have time to check it during the evening (EU time).
import scipy.integrate
import numpy
import matplotlib.pyplot as plt
def modelo_sir(y, t, beta, gamma):
S, I, R = y
dS_dt = -beta*S*I
dI_dt = beta*S*I - gamma*I
dR_dt = gamma*I
return([dS_dt, dI_dt,])
# Condiciones iniciales
S0 = 0.9
I0 = 0.1
R0 = 0.0
beta = 0.3
gamma = 0.1
# Vector tiempo
t = numpy.linspace(0, 100, 1000)
# Resultado
solucion = scipy.integrate.odeint(modelo_sir, [S0, I0, R0], t, args=(beta, gamma))
solucion = numpy.array(solucion)
# Resultado en grafica
plt.figure(figsize=[6, 4])
plt.plot(t, solucion[:, 0], label="S(t)")
plt.plot(t, solucion[:, 1], label="I(t)")
plt.plot(t, solucion[:, 2], label="R(t)")
plt.grid()
plt.legend()
plt.xlabel("Tiempo")
plt.ylabel("Proporciones")
plt.title("Modelo SIR (Epidemia)")
plt.show()
I already solved the problem, thanks, like
For the people interested in source code, here there is a implementation of the basic SIR model in Python using SciPy (NumPy and other packages): scipython.com/book/chapter-8-scipy/additional-examples/the-sir-epidemic-model/ . Here another one, from the epirecipes project: epirecip.es/epicookbook/chapters/kr08/2_1/python_original . Searching "sir model python" on the web, you can find many others examples.
Hello, in your publication you say that gamma represents the inverse of the average number of days to heal. In this case, if I set beta to zero, there will be no more new infected people and the number of infected people will have to go to zero after ten days plus at least a certain interval since it's an average. I've done the test, the number of infected people goes to zero around the fiftieth day. Can you please explain to me what is wrong with my thinking?
I tried to run the code you shared above and I am getting errors when running the last part "Plotting the data" . :-(
Can you share your code?
@@marbellydavila3065
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plt
# Total population, N.
N = 1000
# Initial number of infected and recovered individuals, I0 and R0.
I0, R0 = 1, 0
# Everyone else, S0, is susceptible to infection initially.
S0 = N - I0 - R0
# Contact rate, beta, and mean recovery rate, gamma, (in 1/days).
beta, gamma = 0.2, 1./10
# A grid of time points (in days)
t = np.linspace(0, 150, 150)
# The SIR model differential equations.
def deriv(y, t, N, beta, gamma):
S, I, R = y
dSdt = -beta * S * I / N
dIdt = beta * S * I / N - gamma * I
dRdt = gamma * I
return dSdt, dIdt, dRdt
# Initial conditions vector
y0 = S0, I0, R0
# Integrate the SIR equations over the time grid, t.
ret = odeint(deriv, y0, t, args=(N, beta, gamma))
S, I, R = ret.T
# Plot the data on three separate curves for S(t), I(t) and R(t)
fig = plt.figure(facecolor='w')
ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True)
ax.plot(t, S/1000, 'b', alpha=0.5, lw=2, label='Susceptible')
ax.plot(t, I/1000, 'r', alpha=0.5, lw=2, label='Infected')
ax.plot(t, R/1000, 'g', alpha=0.5, lw=2, label='Recovered with immunity')
ax.set_xlabel('Time /days')
ax.set_ylabel('Number (1000s)')
ax.set_ylim(0,1.2)
ax.yaxis.set_tick_params(length=0)
ax.xaxis.set_tick_params(length=0)
ax.grid(b=True, which='major', c='w', lw=2, ls='-')
legend = ax.legend()
legend.get_frame().set_alpha(0.5)
for spine in ('top', 'right', 'bottom', 'left'):
ax.spines[spine].set_visible(False)
plt.show()
ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True)
what is S0
what is the y in S,I,R=y
wondering the same thing
Thank You Somuch
Thank you so much...
Make a vedio for bifurcation diagram
how can we apply that model on a dataset(csv file format)?
Would you like to calibrate the model to an existing dataset?
@@computationalscientist6368 that is exactly what i am looking for, can you make a video to fit data on this ODE system? Please
Apply regression
@@klam77 i mean to determine those.coefficient from our dataset?
@@kaoutarbentalha7620 maybe i'm missing something (you can tell me). (1) you have csv with infection counts. (2) you have SIR model, where I(t) = exp(aS-b)*t. (3) you must FIT your csv infection count data to the exponential: (4) take the log of Infection count and (5) run a linear regression vs time. (6) this will give you (aS-b) coefficient in toto, and (7) then use eqn for R(t) = b*exp(as-b)*t and deduce the "b". (8) then you can back out the "a" from earlier, now that you know "b";
thusly you have fitted the entire SIR model...no?
Why R0 is 0 if in the SIR model R0 is beta/gamma?
Initial Removed value
Yes, unfortunate notation but initial removed R(0) vs basic reproduction R_0 are two very different things..
is there a way to change the step size of t in this model?
linspace: 3rd argument controls how many total time steps to take
¡No sirve!