Epidemic curve, EDR and effective reproduction number plots

Epidemic curve, EDR and effective reproduction number plots

Reads a comma separated value (*.csv) file providing details of the timing of events (one row for each event). Returns: (1) a frequency histogram of the number of events as a function of calendar time; (2) a plot of the estimated dissemination ratio as a function of calendar time on the log2 scale; and (3) a plot of the effective effective reproduction number (the number of secondary infections generated per case) as a function of calendar time, again on the log2 scale. The input *.csv file should consist of two named columns: oid (object identifier, numeric) and event date (date of event, DD/MM/YYYY). Additional columns can be included but these will be ignored. Typical input data would be as follows:


            oid
            edate

1, 8/11/1967
2, 8/11/1967
3, 1/11/1967
4, 11/11/1967

Upload *.csv file:

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EPIDEMIC CURVE

Number of days between x-axis ticks:

Maximum value for y-axis:

Superimpose line to indicate growth phase of epidemic?

Start of growth phase of epidemic:

End of growth phase of epidemic:

ESTIMATED DISEMINATION RATIO (EDR) An EDR plot will only be drawn if there are more than 14 days of data.

Span for EDR (days):

Span for loess smooth:

Include 95% confidence interval for EDR

EFFECTIVE REPRODUCTION NUMBERS
For the disease of interest, what is the:

Mean serial interval (days)?

Standard deviation of the serial interval (days)?

Infectious duration (days)?

EXAMPLE DATA
Click on the button below to download correctly formatted data from the 2001 outbreak of foot and mouth disease in Cumbria, United Kingdom: Example data

References:

Cori A (2021) EpiEstim: A package to estimate time varying reproduction numbers from epidemic curves . R package version 2.2-4.

Perez-Reche FJ, Taylor N, McGuigan C, Conaglen P, Forbes K, Strachan N, Honhold N (2021) Estimated Dissemination Ratio --- A practical alternative to the reproduction number for infectious diseases. Frontiers in Public Health 9. DOI: 10.3389/fpubh.2021.675065.

Stevenson M, Sergeant E, Nunes T, Heuer C, Marshall J, Sanchez J, Thornton R, Reiczigel J, Robison-Cox J, Sebastiani P, Solymos P, Yoshida K, Jones G, Pirikahu S, Firestone S, Kyle R, Popp J, Jay M, Reynard C, Cheung A, Singanallur N, Szabo A and Rabiee A (2024) epiR: Tools for the Analysis of Epidemiological Data . R package version 2.0.70.

Veterinary Epidemiology @ Melbourne: https://mvs.unimelb.edu.au/ve@m