Early warning signals of malaria resurgence in Kericho, Kenya

Campaigns to eliminate infectious diseases could be greatly aided by methods for providing early warning signals of resurgence. Theory predicts that as a disease transmission system undergoes a transition from stability at the disease-free equilibrium to sustained transmission, it will exhibit characteristic behaviours known as critical slowing down, referring to the speed at which fluctuations in the number of cases are dampened, for instance the extinction of a local transmission chain after infection from an imported case. These phenomena include increases in several summary statistics, including lag-1 autocorrelation, variance, and the first difference of variance. Here, we report the first empirical test of this prediction during the resurgence of malaria in Kericho, Kenya. For 10 summary statistics, we measured the approach to criticality in a rolling window to quantify the size of effect and directions. Nine of the statistics increased as predicted and variance, the first differe..., , , # Early warning signals of malaria resurgence in Kericho, Kenya

[https://doi.org/10.5061/dryad.ghx3ffbjx](https://doi.org/10.5061/dryad.ghx3ffbjx)

## Description of the data and file structure

This repository contains data discussed in the manuscript: Harris MJ, Hay SI, Drake JM. Early warning signals of malaria resurgence in Kericho, Kenya. Biol Lett. 2020 Mar;16(3):20190713. doi: 10.1098/rsbl.2019.0713. Epub 2020 Mar 18. PMID: 32183637; PMCID: PMC7115183.

All analyses were conducted in RStudio using R version 3.5.1

### Files and variables

#### File: kericho.csv

**Description:** Monthly malaria incidence in Kericho, Kenya between January 1965 and November 2002.

The remaining files are all Rdata files.

#### File: pvals

**Description:** returns a vector of the p-values corresponding to all ten indicators (calculated based on Kendall's Tau).

#### File: pvals\_rf

**Description:** list of length 96 where the ith entry corresponds to early warning signal testing beginning in Dece...