London_smallpox

Data and R scripts associated with

"Patterns of smallpox mortality in London, England, over three centuries"
by Olga Krylova and David J. D. Earn.
PLoS Biology, 2020

DOI of the manuscript

10.1371/journal.pbio.3000506

Article Title

Patterns of smallpox mortality in London, England, over three centuries.

Contents

Data/London_smallpox.csv

The original digitized weekly reported smallpox deaths (column smpx), birth (column births) and all-cause mortality (column acm) records for London throughout the period 1661-1934. We also included various transformations of this data such as trends, normalizations, etc., that were used for the main analysis.

Data/LondonPopulation1550_1931annual.csv

Estimated annual population of London for 1550-1931.

Data/peaks_by_eye.csv

Epidemic peaks, i.e., the highest value of normalized smallpox mortality during the epidemic year, which were identified by visual inspection.

Data/Wavelet_peaks.csv

The primary spectral peaks, as estimated in this paper (based on a wavelet analysis of weekly data)

Data/Spectral_peaks_Cliff.csv

The primary spectral peaks, as estimated in previous work by Cliff and co-workers in "Infectious diseases: Emergence and re-emergence: a geographical analysis." Oxford University Press (2009).

Data/Spectral_peaks_Duncan.csv

The primary spectral peaks, as estimated in previous work by Duncan and co-workers in "Oscillatory dynamics of smallpox and the impact of vaccination." Journal of Theoretical Biology 183(4):447-454 (1996).

Data/annual_data.csv

Annual smallpox deaths, all-cause mortality, and births based on the data presented in this paper (Data/London_smallpox.csv, variable smpx).

Data/Creighton_annual_smallpox.csv

Annual smallpox deaths and all-couse mortality from Creighton (1894).

Data/WaveletDiagram folder

The data files that are used to plot the wavelet spectrum.

R_code folder

R scripts that create all the figures in the text of the manuscript. The R code uses data in the Data folder as input, and outputs Figures and Tables into the Figures_and_Tables folder.

Figures_and_Tables folder

Output that is produced by running R scripts in the R_code folder, i.e. all figures and tables provided in the paper.