One of the key research products of Project AERO is the R package spaero (pronounced “sparrow”) for estimating distributional properties along rolling windows of time series. Such estimates may in some cases provide signals that the system generating the data is approaching a regime shift. Regime shifts are marked changes in the dynamics of a system that may sometimes be modeled as bifurcations of dynamical systems. Examples of such regime shifts in nature include the eutrophication of lakes, changes in climate, and the emergence or eradication of infectious diseases. Because these methods are based on generic properties of dynamical systems, they have the potential to apply to a broad range of models. The spaero package also provides functions to simulate epidemics and support computational experiments designed to evaluate these methods for application to infectious disease systems. The package’s most recently released source code, binaries, and introductory documentation (i.e., vignette) are available at https://cran.r-project.org/web/packages/spaero/.
The tycho2 R package provides a simple wrapper for the Project Tycho 2.0 web API. The tycho2 package facilitates querying the Project Tycho global health database of weekly case reports for 78 notifiable conditions in 50 US states and 1284 US cities between 1888 and 2014, reported by health agencies in the United States, as well as data for dengue-related conditions for 100 countries between 1955 and 2010, obtained from the World Health Organization and national health agencies. The tycho2 package’s most recently released source code and documentation are available at https://github.com/allopole/tycho2.
The development of these software packages was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number U01GM110744. The content is solely the responsibility of the authors and does not necessarily reflect the official views of the National Institutes of Health.