Python 改进SIR模型的可视化
我试图修改eon包中的SIR模型,并对其进行了一些更改。它有一个新的疫苗接种参数,附加了新的参数beta、omega和Vl,我的代码是-Python 改进SIR模型的可视化,python,numpy,networkx,eon,Python,Numpy,Networkx,Eon,我试图修改eon包中的SIR模型,并对其进行了一些更改。它有一个新的疫苗接种参数,附加了新的参数beta、omega和Vl,我的代码是- def test_transmission(u, v, p): return random.random()<p def discrete_SIR(G, initial_infecteds,beta, w,Vl,return_full_data=True): if G.has_node(initia
def test_transmission(u, v, p):
return random.random()<p
def discrete_SIR(G,
initial_infecteds,beta,
w,Vl,return_full_data=True):
if G.has_node(initial_infecteds):
initial_infecteds=[initial_infecteds]
if return_full_data:
node_history = defaultdict(lambda : ([tmin], ['S']))
transmissions = []
for node in initial_infecteds:
node_history[node] = ([tmin], ['I'])
transmissions.append((tmin-1, None, node))
node_history = defaultdict(lambda : ([tmin], ['S']))
# transmissions = []
for node in initial_infecteds:
node_history[node] = ([tmin], ['I'])
#transmissions.append((tmin-1, None, node))
N=G.order()
t = [tmin]
S = [N-len(initial_infecteds)]
I = [len(initial_infecteds)]
R = [0]
V = [0]
susceptible = defaultdict(lambda: True)
#above line is equivalent to u.susceptible=True for all nodes.
for u in initial_infecteds:
susceptible[u] = False
infecteds = set(initial_infecteds)
while infecteds and t[-1]<tmax :
new_infecteds = set()
vaccinated= set()
infector = {} #used for returning full data. a waste of time otherwise
for u in infecteds:
# print('u-->' +str(u))
for v in G.neighbors(u):
# print('v --> '+ str(v))
##vaccination
if len(vaccinated)+V[-1]< (Vl*N) : #check if vaccination over or not
#print(len(vaccinated),Vl*N)
#print("HI")
if susceptible[v] and test_transmission(u, v, w):
vaccinated.add(v)
susceptible[v] = False
# print('transmitting vaccination')
elif susceptible[v] and test_transmission(u,v,beta):
new_infecteds.add(v)
susceptible[v]=False
infector[v] = [u]
# print('transmitting infection')
else:
# print("BYE")
if susceptible[v] and test_transmission(u, v,beta):
new_infecteds.add(v)
susceptible[v] = False
infector[v] = [u]
#infector[v] = [u]
if return_full_data:
for v in infector.keys():
transmissions.append((t[-1], random.choice(infector[v]), v))
next_time = t[-1]+1
if next_time <= tmax:
for u in infecteds:
node_history[u][0].append(next_time)
node_history[u][1].append('R')
for v in new_infecteds:
node_history[v][0].append(next_time)
node_history[v][1].append('I')
infecteds = new_infecteds
R.append(R[-1]+I[-1])
V.append(len(vaccinated)+V[-1])
I.append(len(infecteds))
S.append(N-V[-1]-I[-1]-R[-1])
#S.append(S[-1]-V[-1]-I[-1])
t.append(t[-1]+1)
print(str(R[-1])+','+str(V[-1])+','+str(I[-1])+','+str(S[-1]))
if not return_full_data:
return scipy.array(t), scipy.array(S), scipy.array(I), \
scipy.array(R)
else:
return EoN.Simulation_Investigation(G, node_history, transmissions)
我需要在代码中做哪些更改才能使显示功能正常工作,还是还需要对显示功能进行更改?以下是我现在得到的输出: 您必须安装github页面上提供的EoN版本
1.0.8rc3
或更高版本(请参阅)。目前,pip
无法安装它。我想确保我没有损坏任何东西,然后将其设置为默认安装程序pip
这是基于你的代码。你应该仔细看看我所做的改变。它也值得一看(包括一个SIRV模型,其中疫苗接种规则与您现有的不同)
从集合导入defaultdict
导入EoN
将networkx导入为nx
随机输入
将matplotlib.pyplot作为plt导入
def测试_变速箱(u、v、p):
return random.random()目前,您需要修改代码和display函数。我希望很快做修改,这样你就可以不用做重大的改变。我稍后会尝试给出一个答案(目前没有时间)给出更多细节。@Joel我对代码做了一些更改,看起来模拟是正确的,但当然它只显示SIR图而不是SIRV。我会发布我的更改,如果您能告诉我要对显示函数进行哪些更改,以包括将要使用的V参数helpful@Joel你有时间调查吗?。你也可以告诉我需要做什么。我很乐意为EON做贡献。嘿-对不起,我没有机会做。需要做的第一个更改是,当一个节点变成'V'
时,您需要更新该节点的节点历史记录。第二个变化是,类模拟调查(G、节点\u历史、传输)
的\uuu初始化\uuuuuuuu
代码需要修改,以处理节点是否为'V'
,处理方式与处理S、I和R的方式相同。最后需要修改\uplot\ucode>方法。我希望将我编写的代码变得更加通用,这样人们可以在任何新状态下执行此操作,但我暂时没有时间。@Joel将尝试执行此操作,并将其发布到此处或github,供您查看。
m=5
G=nx.grid_2d_graph(m,m,periodic=True)
initial_infections = [(u,v) for (u,v) in G if u==int(m/2) and v==int(m/2)]
sim = EoN.basic_discrete_SIR(G,0.5,initial_infecteds = initial_infections,
return_full_data=True, tmax = 25)
pos = {node:node for node in G}
sim.set_pos(pos)
sim.display(0, node_size = 40) #display time 6
plt.show()
plt.savefig('SIR_2dgrid.png')
from collections import defaultdict
import EoN
import networkx as nx
import random
import matplotlib.pyplot as plt
def test_transmission(u, v, p):
return random.random()<p
def discrete_SIRV(G, initial_infecteds,beta,
w,Vl,tmin=0,tmax=float('Inf'), return_full_data=True):
if G.has_node(initial_infecteds):
initial_infecteds=[initial_infecteds]
if return_full_data:
node_history = defaultdict(lambda : ([tmin], ['S']))
transmissions = []
for node in initial_infecteds:
node_history[node] = ([tmin], ['I'])
transmissions.append((tmin-1, None, node))
'''
node_history = defaultdict(lambda : ([tmin], ['S']))
# transmissions = []
for node in initial_infecteds:
node_history[node] = ([tmin], ['I'])
#transmissions.append((tmin-1, None, node))
'''
N=G.order()
t = [tmin]
S = [N-len(initial_infecteds)]
I = [len(initial_infecteds)]
R = [0]
V = [0]
susceptible = defaultdict(lambda: True)
#above line is equivalent to u.susceptible=True for all nodes.
for u in initial_infecteds:
susceptible[u] = False
infecteds = set(initial_infecteds)
while infecteds and t[-1]<tmax :
new_infecteds = set()
vaccinated= set()
infector = {} #used for returning full data. a waste of time otherwise
for u in infecteds:
# print('u-->' +str(u))
for v in G.neighbors(u):
# print('v --> '+ str(v))
##vaccination
if len(vaccinated)+V[-1]< (Vl*N) : #check if vaccination over or not
#print(len(vaccinated),Vl*N)
#print("HI")
if susceptible[v] and test_transmission(u, v, w):
vaccinated.add(v)
susceptible[v] = False
'''It's probably better to define a `new_vaccinated`
set and then do the `return_full_data` stuff later
where all the others are done.'''
if return_full_data:
node_history[v][0].append(t[-1]+1)
node_history[v][1].append('V')
# print('transmitting vaccination')
elif susceptible[v] and test_transmission(u,v,beta):
new_infecteds.add(v)
susceptible[v]=False
infector[v] = [u]
# print('transmitting infection')
else:
# print("BYE")
if susceptible[v] and test_transmission(u, v,beta):
new_infecteds.add(v)
susceptible[v] = False
infector[v] = [u]
#infector[v] = [u]
if return_full_data:
for v in infector.keys():
'''This random choice is no longer needed as you've taken out
the possibility of multiple nodes transmitting to `v` in a given
time step. Now only the first one encountered does it.'''
transmissions.append((t[-1], random.choice(infector[v]), v))
next_time = t[-1]+1
if next_time <= tmax:
for u in infecteds:
node_history[u][0].append(next_time)
node_history[u][1].append('R')
for v in new_infecteds:
node_history[v][0].append(next_time)
node_history[v][1].append('I')
infecteds = new_infecteds
R.append(R[-1]+I[-1])
V.append(len(vaccinated)+V[-1])
I.append(len(infecteds))
S.append(N-V[-1]-I[-1]-R[-1])
#S.append(S[-1]-V[-1]-I[-1])
t.append(t[-1]+1)
print(str(R[-1])+','+str(V[-1])+','+str(I[-1])+','+str(S[-1]))
if not return_full_data:
return scipy.array(t), scipy.array(S), scipy.array(I), \
scipy.array(R)
else:
return EoN.Simulation_Investigation(G, node_history, transmissions, possible_statuses=['S', 'I', 'R', 'V'])
print(EoN.__version__)
print("line above needs to be 1.0.8rc3 or greater or it will not work\n\n")
m=20
G=nx.grid_2d_graph(m,m,periodic=True)
initial_infections = [(u,v) for (u,v) in G if u==int(m/2) and v==int(m/2)]
beta=0.8
Vl=0.3
w=0.1
sim = discrete_SIRV(G, initial_infections, beta, w, Vl, return_full_data=True)
pos = {node:node for node in G}
sim.set_pos(pos)
sim.sim_update_colordict({'S': '#009a80','I':'#ff2000', 'R':'gray','V': '#5AB3E6'})
sim.display(6, node_size = 40) #display time 6
plt.savefig('SIRV_2dgrid.png')