Objective: Estimating reproduction number (R0) using contact rate, transmission probability, infectious period

Remove all objects from workspace.

remove (list = objects () )

Load add-on packages - R0 - contains different methods to estimate reproduction number.

library (R0)
## Loading required package: MASS

Question 1: Estimation of reproductive number (R0) using contact rate, transmission probability, and infectious period

#Question 1a
contact_rate = 10
transmission_probability = 0.06
infectious_period = 4
R0 = contact_rate * transmission_probability * infectious_period
c ("R0 = ", R0)
## [1] "R0 = " "2.4"
#Question 1b
contact_rate = 8
transmission_probability = 0.15
infectious_period = 6
R0 = contact_rate * transmission_probability * infectious_period
c ("R0 = ", R0)
## [1] "R0 = " "7.2"

Question 2: Estimation of reproductive number (R0) using attack rate

#Attack rate = 30%
attack_rate = 0.3
est.R0.AR (AR = attack_rate)
## Reproduction number estimate using  Attack Rate  method.
## R :  1.188916
#Attack rate = 40%
attack_rate = 0.4
est.R0.AR (AR = attack_rate)
## Reproduction number estimate using  Attack Rate  method.
## R :  1.277064
#Attack rate = 55%
attack_rate = 0.55
est.R0.AR (AR = attack_rate)
## Reproduction number estimate using  Attack Rate  method.
## R :  1.451832
#Attack rate = 80%
attack_rate = 0.8
est.R0.AR (AR = attack_rate)
## Reproduction number estimate using  Attack Rate  method.
## R :  2.011797

Question 3: Estimation of reproductive number (R0) using average age of infection and life expectancy

#Question 3a
average_age = 10
life_expectancy = 65
R0 = life_expectancy / average_age
c ("R0 = ", R0)
## [1] "R0 = " "6.5"
#Question 3b
average_age = 5
life_expectancy = 70
R0 = life_expectancy / average_age
c ("R0 = ", R0)
## [1] "R0 = " "14"

Objective: To estimate the reproduction number (R0) using different methods

Remove all objects from workspace.

remove (list = objects () )

Load add-on packages - R0 - contains different methods to estimate reproduction number.

library (R0)

Method 1: Contact Rate, transmission probability, infectious period

Estimate R0 using contact rate, transmission probability, and infectious period

contact_rate = 5
transmission_probability = 0.15
infectious_period = 6
R0 = contact_rate * transmission_probability * infectious_period
c ("R0 = ", R0)
## [1] "R0 = " "4.5"

Method 2: Attack Rate

Estimate R0 using attack rate.

attack_rate = 0.6
R0 = (- log (1 - attack_rate)) / attack_rate
c ("R0 = ", R0)
## [1] "R0 = "            "1.52715121979026"

Estimate R0 using attack rate.

attack_rate = 0.6
est.R0.AR (AR = attack_rate)
## Reproduction number estimate using  Attack Rate  method.
## R :  1.527151

Method 3: Average Age of infection (and life expectancy)

Average age of infection for chicken pox was 6.7 in Maryland during 1913-1917, and life expectancy was 60 years.

average_age = 6.7
life_expectancy = 60
R0 = life_expectancy / average_age
c ("R0 = ", R0)
## [1] "R0 = "            "8.95522388059701"

Method 4: Exponential Growth Rate

Estimate R0 using exponential growth rate for the 1918 influenza pandemic in Germany, using the data from the paper by Nishiura for key transmission parameters of an institutional outbreak during the 1918 influenza pandemic in Germany.

data (Germany.1918)

#plot epidemic
plot (Germany.1918, xlab = "Time")

#plot log of epidemic curve
plot (log (Germany.1918), xlab='Time')

#generation time distribution
mGT = generation.time ("gamma", c(3, 1.5))

#estimate R0 using exponential growth method using start date of first day and end date of 30 days.
#Question 4
est.R0.EG (Germany.1918, mGT, begin=1, end=30)
## Waiting for profiling to be done...
## Reproduction number estimate using  Exponential Growth  method.
## R :  1.43944[ 1.416545 , 1.462916 ]

Method 5: Maximum Likelihood

#estimate R0 using maximum likelihood method
#Question 5
mGT = generation.time("gamma", c(2.45, 1.38))
est.R0.ML (Germany.1918, mGT)
## Reproduction number estimate using  Maximum Likelihood  method.
## R :  1.205348[ 1.152364 , 1.259946 ]