Instructor Notes
Instructor notes
Access epidemiological delay distributions
Instructor Note
The objective of the assessment above is to assess the interpretation of a larger or shorter generation time.
Instructor Note
An interesting element is the method_assess nested
entry, which refers to the methods used by the study authors to assess
for bias while estimating the serial interval distribution.
R
covid_serialint$method_assess
OUTPUT
$censored
[1] TRUE
$right_truncated
[1] TRUE
$phase_bias_adjusted
[1] FALSEWe will explore these concepts following episodes!
Instructor Note
In the context of user interfaces and graphical user interfaces (GUIs), like the Distribution Zoo shiny app, a slider is a graphical control element that allows users to adjust a value by moving a handle along a track or bar. Conceptually, it provides a way to select a numeric value within a specified range by visually sliding or dragging a pointer (the handle) along a continuous axis.
Quantifying transmission
Instructor Note
This tutorial illustrates the usage of epinow() to
estimate the time-varying reproduction number and infection times.
Learners should understand the necessary inputs to the model and the
limitations of the model output.
Instructor Note
Refer to the prior probability distribution and the posterior probability distribution.
In the “Expected change in daily cases”
callout, by “the posterior probability that \(R_t < 1\)”, we refer specifically to the
area
under the posterior probability distribution curve.
Use delay distributions in analysis
Instructor Note
Access to the reference documentation (Help files) for these
functions is accessible with the three double-colon notation:
epiparameter:::
?epiparameter:::density.epidist()?epiparameter:::cdf.epidist()?epiparameter:::quantile.epidist()?epiparameter:::generate.epidist()
Create a short-term forecast
Estimation of outbreak severity
Instructor Note
The periods are relevant: Period 1 – 15 days where CFR is zero to indicate this is due to no reported deaths; Period from Mar 15 – Apr 26 where CFR appears to be rising; Period Apr 30 – May 30 where the CFR estimate stabilises.
Instructor Note
We can showcase this last bias using the concept
described in this {cfr} vignette.