exponential_growth {swash} | R Documentation |
Exponential Growth Model for Epidemic Data
Description
Estimation of exponential growth models from daily infections data
Usage
exponential_growth(
y,
t,
GI = 4
)
Arguments
y |
|
t |
|
GI |
Generation interval for computing |
Details
This function allows the estimation of an exponential growth model. The user must specify the dependent variable (daily infections) and the time variable (time counter or date values). The estimation is performed using a linearized model as an OLS estimator. The results are the exponential growth rate r
, basic reproduction number R_0
, and the doubling rate.
Value
list
with four entries:
exp_gr: |
|
R0: |
|
doubling: |
|
model_data: |
|
Author(s)
Thomas Wieland
References
Bonifazi G et al. (2021) A simplified estimate of the effective reproduction number Rt using its relation with the doubling time and application to Italian COVID-19 data. The European Physical Journal Plus 136, 386. doi:10.1140/epjp/s13360-021-01339-6
Chowell G, Viboud C, Hyman JM, Simonsen L (2015) The Western Africa ebola virus disease epidemic exhibits both global exponential and local polynomial growth rates. PLOS Currents Outbreaks, ecurrents.outbreaks.8b55f4bad99ac5c5db3663e916803261. doi:10.1371/currents.outbreaks.8b55f4bad99ac5c5db3663e916803261
Pell B, Kuang Y, Viboud C, Chowell G (2018) Using phenomenological models for forecasting the 2015 ebola challenge. Epidemics 22, 62–70. doi:10.1016/j.epidem.2016.11.002
Wieland T (2020) A phenomenological approach to assessing the effectiveness of COVID-19 related nonpharmaceutical interventions in Germany. Safety Science 131, 104924. doi:10.1016/j.ssci.2020.104924
See Also
growth_initial, logistic_growth
Examples
data(COVID19Cases_geoRegion)
# Get SWISS COVID19 cases at NUTS 3 level
COVID19Cases_ZH <-
COVID19Cases_geoRegion[(COVID19Cases_geoRegion$geoRegion == "ZH")
& (COVID19Cases_geoRegion$sumTotal > 0),]
# COVID cases for Zurich
expgrowth_BS <- exponential_growth (
y = COVID19Cases_ZH$sumTotal[1:28],
t = COVID19Cases_ZH$datum[1:28]
)
# Exponential growth model for the first 4 weeks
expgrowth_BS$doubling
# Doubling rate