guinness submission

README.md

@@ -1 +1,15 @@
-# Intro_Biocom_ND_319_Tutorial10
+# Intro_Biocom_ND_319_Tutorial10
+
+QUESTION 2 COMMENTARY
+
+Unsurprisingly, as R0 increases (in our scenario, ranging from 0.5 to 10), the maximum daily prevalence and incidence rise along with it, and in the highest scenario, our disease affected nearly 100% of the population. 
+
+The math for this mechanism is relatively simple: 
+
+The disease is transmitted at some rate beta which forces people from susceptible into affected by the interaction of their quantities. (i.e. I increases with beta*I*S and S DECREASES in tandem). 
+
+Additionally, people are removed from the infected pool at some rate gamma (either by recovery or death). Thus, I = beta*I*S - gamma*I. 
+
+
+
+

Tut10.py

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+# Question 1 #
+
+# Loading Packages
+import pandas
+import scipy
+import scipy.integrate as spint
+from plotnine import *
+
+# Simulating Equation
+def ddSim(y, t0, r, K):
+    N=y[0]
+    dNdt=r*(1-N/K)*N
+    return [dNdt]
+
+# Setting up parameters for each r condition
+rlist = [-0.1,0.1,0.4,0.8,1]
+# N0 and time range
+N0 = 10
+K = 100
+times = range(0,50)
+# creating a dataframe to store model outputs with a column for each r value
+store_rs=pandas.DataFrame({"time":times, "r1":0, "r2":0, "r3":0, "r4":0, "r5":0})
+
+# setting up the model
+for i in range(0,len(rlist)):
+    pars=(rlist[i],K)
+    sim = spint.odeint(func=ddSim, y0=N0, t=times, args=pars)
+    store_rs.iloc[:,i]=sim[:,0]
+
+cols = ["black", "red", "blue", "green", "orange"]
+#Simulating plot
+p = ggplot(store_rs, aes(x='time', y='r1')) + geom_line()  #r1
+p = p + geom_line(aes(x='time', y='r2'), colour = "red") #r2
+p = p + geom_line(aes(x='time', y='r3'), colour = "blue") #r3
+p = p + geom_line(aes(x='time', y='r4'), colour = "green") #r4
+p = p + geom_line(aes(x='time', y='r5'), colour = "orange") #r5
+print p 
+
+# Varying Ks
+Klist = [10,50,100]
+r = 0.2
+N0 =1
+store_Ks=pandas.DataFrame({"time":times, "K1":0, "K2":0, "K3":0})
+
+for i in range(0,len(Klist)):
+    pars=(r,Klist[i])
+    sim = spint.odeint(func=ddSim, y0=N0, t=times, args=pars)
+    store_Ks.iloc[:,i]=sim[:,0]
+
+p2 = ggplot(store_Ks, aes(x='time', y='K3')) + geom_line()
+p2 = p2 + geom_line(aes(x='time',y='K2'), colour = "blue")
+p2 = p2 + geom_line(aes(x='time', y='K1'), colour = "red")
+print p2
+
+#Varying Ns
+Nlist=[1,50,100]
+r=0.1
+K=50
+store_Ns=pandas.DataFrame({"time":times, "N0_1":0, "N0_2":0, "N0_3":0})
+
+for i in range(0,len(Nlist)):
+    pars=(r,K)
+    sim = spint.odeint(func=ddSim, y0=Nlist[i], t=times, args=pars)
+    store_Ns.iloc[:,i]=sim[:,0]
+
+p3 = ggplot(store_Ns, aes(x='time',y='N0_3')) + geom_line()
+p3 = p3 + geom_line(aes(x='time',y='N0_2'), colour = "green")
+p3 = p3 + geom_line(aes(x='time',y='N0_1'), colour = 'yellow')
+print p3
+
+# Question 2 #
+
+# Multifaceted equation
+def SIR(y,t0,beta,gamma):
+    S = y[0]
+    I = y[1]
+    R = y[2]
+
+    dSdt = -beta*I*S
+    dIdt = beta*I*S - gamma*I
+    dRdt = gamma*I
+    return [dSdt, dIdt, dRdt]
+
+betalist = [0.0005, 0.005, 0.0001, 0.00005,0.0001,0.0002,0.0001]
+gammalist = [0.05,0.5,0.1,0.1,0.05,0.05,0.06]
+#inital values for S, I, R
+SIRvalues = [999,1,0]
+times = range(0,500)
+
+#creating a dataframe to store outputs for 7 scenarios
+SIRframe = pandas.DataFrame({"beta":betalist, "gamma":gammalist, "MDI":0, "MDP":0, "percent_affected":0, "R0":0})
+
+#calculating the R0 
+SIRframe.R0 = (SIRframe.beta * 1000)/SIRframe.gamma
+
+inc = range(0,500) #initializing incidence parameter
+prev = range(0,500) #initilaizing prevalence parameter 
+
+for i in range(0,7):
+    pars = (betalist[i],gammalist[i])
+    sim = spint.odeint(func=SIR, y0=SIRvalues, t=times, args=pars) #simulate model for each beta,gamma pair
+    for j in range(500):
+        inc[j] = sim[j,1] - sim[j-1,1] #calculate incidence for all time points
+        SIRframe.iloc[i,0] = max(inc) #select maximum incidence 
+        prev[j] = sim[j,1] / (sim[j,0] + sim[j,1] + sim[j,2]) #calculate prevalence for all time points
+        SIRframe.iloc[i,1] = max(prev) #select maximum prevalence
+        SIRframe.iloc[i,5] = (sim[499,1] + sim[499,2]) / (sim[499,0] + sim[499,1] + sim[499,2]) #calculate final percent affected
+
+
+print SIRframe
+