nrevss.R: script for reading and producing figures from the coronavirus incidene data
NationalCoV.csv: Dataset containing percent positive coronavirus by virus type from the CDC, 2 July 2016 -- 18 Jan 2020. These are stitched together from web archive snapshots of CDC data files accessed on 30 June 2018, 19 June 2019, and 26 June 2020.
ntests.csv: Number of tests performed weekly between 1 July 2014 and 27 June 2017 to detect any of the four coronaviruses reported to NREVSS, scraped from Figure 1A by Killerby et al. (2018) using PlotDigitizer.
ILINet.csv: Weekly ILI data from the CDC. Accessed through FluView Interactive.
NREVSSClinicalFlu.csv: Lab-confirmed influenza dataset from the CDC capturing clinical samples as reported to the NREVSS dataset. Accessed through FluView Interactive.
NREVSSPublicHealthFlu.csv: Lab-confirmed influenza dataset from the CDC capturing public health samples as reported to the NREVSS dataset. Accessed through FluView Interactive.
YearWeekConversion.csv: A useful data frame for converting between the CDC's Year/Week numbering system to a date. Note that the dates fall on Saturdays, following the CoV data, whereas flu data are normally tagged on Sundays. Add 1 to each date to get to the corresponding Sunday.
natcov.pdf: Depicts weekly percent positive by coronavirus from the NationalCoV.csv dataset.
testsperweek.pdf Reproduces Figure 1A from Killerby et al. (2018), giving weekly number of coronavirus tests in the US between 1 July 2014 and 27 June 2017.
natcov_ili.pdf: Same as natcov.pdf with percent ILI overlaid.
natcov_nrevssclinflu.pdf: Same as natcov.pdf with percent positive clinical influenza overlaid.
natcov_nrevssphflu.pdf: Same as natcov.pdf with percent positive public health influenza overlaid.