DOI: 10.5061/dryad.779rd
title: Data from: Modelling vaccination strategies against Rift Valley fever in livestock in Kenya: model code

description: The impacts of vaccination on the transmission of Rift Valley fever virus
 (RVFV) have not been evaluated. We have developed a RVFV transmission
 model comprising two hosts -- cattle as a separate host and sheep and
 goats as one combined host (herein after referred to as sheep) -- and two
 vectors -- Aedes species (spp) and Culex spp -- and used it to predict the
 impacts of: (1) reactive vaccination implemented at various levels of
 coverage at pre-determined time points, (2) targeted vaccination involving
 either of the two host species, and (3) a periodic vaccination implemented
 biannually or annually before an outbreak. Methodology/Principal Findings:
 The model comprises coupled vector and host modules where the dynamics of
 vectors and hosts are described using a system of difference equations.
 Vector populations are structured into egg, larva, pupa and adult stages
 and the latter stage is further categorized into three infection
 categories: susceptible, exposed and infectious mosquitoes. The survival
 rates of the immature stages (egg, larva and pupa) are dependent on
 rainfall densities extracted from the Tropical Rainfall Measuring Mission
 (TRMM) for a Rift Valley fever (RVF) endemic site in Kenya over a period
 of 1827 days. The host populations are structured into four age classes
 comprising young, weaners, yearlings and adults and four infection
 categories including susceptible, exposed, infectious, and immune
 categories. The model reproduces the 2006/2007 RVF outbreak reported in
 empirical surveys in the target area and other seasonal transmission
 events that are perceived to occur during the wet seasons. Mass reactive
 vaccination strategies greatly reduce the potential for a major outbreak.
 The results also suggest that the effectiveness of vaccination can be
 enhanced by increasing the vaccination coverage, targeting vaccination on
 cattle given that this species plays a major role in the transmission of
 the virus, and using both periodic and reactive vaccination strategies.
 Conclusion/Significance: Reactive vaccination can be effective in
 mitigating the impacts of RVF outbreaks but practically, it is not always
 possible to have this measure implemented satisfactorily due to the rapid
 onset and evolution of RVF epidemics. This analysis demonstrates that both
 periodic and reactive vaccination ought to be used strategically to
 effectively control the disease.
description: Gachohi et al RVF Model
 codeThis code, implemented
 in R, is about simulating population dynamics of two species of mosquitoes
 namely Aedes and Culex and two livestock species namely cattle and sheep.
 Hosts are classified into four age groups (young, weaner, yearling and
 adult groups) while vectors are classified into eggs, larvae, pupae and
 adults. Transition rates govern the population dynamics. Further, the code
 simulates transmission dynamics of Rift Valley fever virus between the
 mosquitoes and the livestock. Mosquito growth is regulated by amounts of
 rainfall implicitly through probability functions - suitability function
 for Aedes and logistic distribution function for Culex. The code is used
 to simulate diverse policy-relevant interventions on the effectiveness of
 reactive and periodic Rift Valley fever vaccination
 strategies.Modelling vaccination
 strategies against Rift Valley fever in livestock in Kenya: Precipitation
 dataThis data contains
 precipitation data used to drive mosquito population growth. In the code,
 the rain is sourced as follows: Rain&lt;-read.csv("D:\\RVF R model
 rain\\Rain.csv", header=TRUE) saved in D in a folder RVF R model rain
 under fie name Rain.csv. To import precipitation data, download the data
 from Dryad and save in your PC and import appropriately to run the
 model.Rain.csv