Read case data
Clean and validate
Figure 1
Example of data cleaning report generated by
{cleanepi}
Aggregate and visulaize
Figure 1
Figure 2
Simple analysis
Figure 1
Figure 2
Figure 3
Figure 4
Access epidemiological delay distributions
Figure 1
Definition of key time periods. From Xiang
et al, 2021
Figure 2
Video from the MRC Centre for Global Infectious
Disease Analysis, Ep 76. Science In Context - Epi Parameter Review Group
with Dr Anne Cori (27-07-2023) at https://youtu.be/VvpYHhFDIjI?si=XiUyjmSV1gKNdrrL
Figure 3
A schematic of the relationship of different
time periods of transmission between an infector and an infectee in a
transmission pair. Exposure window is defined as the time interval
having viral exposure, and transmission window is defined as the time
interval for onward transmission with respect to the infection time (Chung
Lau et al., 2021).
Figure 4
Serial intervals of possible case pairs in (a)
COVID-19 and (b) MERS-CoV. Pairs represent a presumed infector and their
presumed infectee plotted by date of symptom onset (Althobaity
et al., 2022).
Figure 5
Fitted serial interval distribution for (a)
COVID-19 and (b) MERS-CoV based on reported transmission pairs in Saudi
Arabia. We fitted three commonly used distributions, Lognormal, Gamma,
and Weibull distributions, respectively (Althobaity
et al., 2022).
Figure 6
Serial interval of novel coronavirus (COVID-19)
infections overlaid with a published distribution of SARS. (Nishiura
et al., 2020)
Figure 7
Quantifying transmission
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Use delay distributions in analysis
Figure 1
The four probability functions for the normal
distribution (Jack
Weiss, 2012)
Figure 2
Figure 3
Figure 4
Timeline for chain of disease reporting,
the Netherlands. Lab, laboratory; PHA, public health authority.
From Marinović
et al., 2015
Figure 5
\(R_{t}\) is a measure of transmission at
time \(t\). Observations after
time \(t\) must be adjusted. ICU,
intensive care unit. From Gostic
et al., 2020
Figure 6
Figure 7
Figure 8
