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Introduction to Rnaught

+ + + Source: vignettes/Rnaught.Rmd +
Rnaught.Rmd
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The goal of Rnaught is to provide a collection of methods for +estimating the basic +reproduction number +(R0R_0) +of infectious diseases.

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Estimators +

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The following estimators are currently available:

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  • +id(): Incidence Decay (ID)
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  • +idea(): Incidence Decay and Exponential Adjustment +(IDEA)
    • +
  • +seq_bayes(): Sequential Bayes (seqB)
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  • +wp(): White and Pagano (WP)
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Every estimator employs its own model, has its own set of parameters, +and is better suited to particular scenarios. You should consult each +method’s documentation for technical details. Below is a short example +computing estimates for a given set of case counts.

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+library(Rnaught)
+
+# Weekly case counts.
+cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4)
+
+# Compute estimates of R0, assuming a serial interval of five days.
+mu <- 5 / 7
+
+id(cases, mu)
+#> [1] 1.245734
+idea(cases, mu)
+#> [1] 1.419546
+seq_bayes(cases, mu)
+#> [1] 1.026563
+wp(cases, mu)
+#> [1] 1.107862
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+

Web Application +

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This serves as a graphical interface for the package. An instance is +available at https://immune.math.yorku.ca/Rnaught. It can also be run +locally by invoking the web() function.

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Datasets can be uploaded as a CSV file, or entered manually. The data +is visualized in the application through plots that show the case counts +(either daily or weekly). If multiple datasets are added, the trends +corresponding to these datasets are populated in the same plot. This +plot can be exported as a PNG image. Furthermore, the datasets entered +can be exported as a CSV.

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Two sample datasets are included: weekly Canadian COVID-19 case count +data from March 3rd, 2020 to March 31st, 2020, and weekly Ontario +COVID-19 case count data from March 3rd, 2020 to March 31st, 2020.

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To estimate the basic reproductive number, the user can choose their +preferred estimator, and if applicable, must enter the known serial interval +prior to estimation. If multiple estimates of the basic reproductive +number are calculated, they are all included in a table where each row +represents an estimate. If multiple datasets are being considered, the +basic reproduction number is estimated for all datasets and the columns +of the table correspond to the different datasets. The table also +consists of a column corresponding to the value of the serial interval. +This table can also be exported as a CSV.

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Datasets +

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The package includes two datasets provided by the COVID-19 Canada +Open Data Working Group. These report the national and provincial +case counts of COVID-19 in Canada. For details, see +?COVIDCanada and ?COVIDCanadaPT. They are also +available as CSV +files.

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