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I am extremely new to any coding and am having a lot of python issues (python 3). I am trying to recreate figures in a scientific paper relating to HIV. They have used a computer simulation of there model which I have to recreate. I keep changing aspects and keep getting different error messages - the current one is TypeError: odeint() missing 1 required positional argument: 't'

Here is the code I am using,based off of a previous assignment I did.

#Import necessary programmes
import numpy as np
from scipy.integrate import odeint as od 
import matplotlib.pyplot as plt
#define equation for uninfected vs free virus
def free_virus(x,y,v,vm):
    x=x=l-(d*x)-(b*x*v)-(bm*x*vm) 
    v=(k*y)-(u*v)
    return np.array(x,v)
l=10
d=0.01
a=0.5
u=3
b=0.01
bm=0.005
e=0.0001
k=km=10
init= [0,0]
t= np.arange(0,40,5)
figure_1=od(free_virus,t,args=(0,40))
plt.plot(figure_1,t)

x and v are equations given in the scientific paper which I need to graph against one anotherodeint code:

The variables were given in the paper I'm sorry if this seems really basic but would really appreciate any help. This has been edited to add in my code.

Eilish McBurnie
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1 Answers1

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You do not use it correctly. Your ode function MUST be of the form f(x,t,params), where x can be a vector (2-dimensional in your case: for x and v as a variables dependent on time).

Try to rewrite your code in the following way:

#Import necessary programmes
import numpy as np
from scipy.integrate import odeint as od 
import matplotlib.pyplot as plt
#define equation for uninfected vs free virus
def free_virus(X,t,params):
    x = your eq dependent on X, t and params
    v = your second eq
    return np.array(x,v)
paramsDict = {'l':10, 'd':0.01 .... and so on}
init= [0,0]
t= np.arange(0,40,5)
figure_1=od(free_virus,t,args=paramsDict)
plt.plot(figure_1,t)

For equation parameters it is good to use python dictionary.

pptaszni
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