diff --git a/DESCRIPTION b/DESCRIPTION index b7ccbc5..a890b1d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: hrp2malaRia Type: Package Title: pfhrp2 gene deletion malaria modelling -Version: 0.1.2 -Date: 2023-01-20 +Version: 0.1.3 +Date: 2023-01-25 Author: OJ Watson Maintainer: Description: Individual based malaria transmission model. diff --git a/NEWS.md b/NEWS.md index 412d728..8c6bacf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +## hrp2malaRia 0.1.3 + +* Better NMF documentation + ## hrp2malaRia 0.1.2 * Fix to hrp2_Simulation introduced during previous version diff --git a/R/hrp2-simulation.R b/R/hrp2-simulation.R index acdc26f..ea9c4ee 100644 --- a/R/hrp2-simulation.R +++ b/R/hrp2-simulation.R @@ -45,8 +45,9 @@ #' @param microscopy.use Probability of microscopy use. Default = 0, i.e. no microscopy #' @param include.nmf Boolean detailing whether to include nmf section. Default = FALSE #' @param fever.age.breaks Age breaks for fevers -#' @param annual.nmf.per.age.bracket Annual number of non malarial fevers for each age bracket in fever.age.breaks. -#' Default is mean across 5 representative surveys from Burundi 2012, Liberia 2009/2011 and Nigeria 2010/2015 +#' @param annual.nmf.per.age.bracket Annual number of non malarial fevers sufficiently severe to trigger +#' treatment seeking for the fever and receieve assessment. These are reported for each age bracket in fever.age.breaks. +#' Default is based on eLife 2017 Watson et al. #' @param nmf.multiplier Multiplication for annual.nmf.per.age.bracket to introduce sensitivity. Default = 1 #' ## delays and durations #' @param delay.mos Mosquito extrinsic incubation period (days). Default = 10 @@ -1040,8 +1041,9 @@ hrp2_Simulation <- function( # identify any hrp2' only individuals rdt.det.D.or.A.nmf <- rep(1,length(D.or.A.pos.nmf)) + # probability that hrp2' only individual will still be treated, 1 - chance of not being hrp3, microscopied or nonadherence - rdt.det.D.or.A.nmf[which(res$N.Sens[D.or.A.pos.nmf,res$Counter] == 0)] <- ft * (1 - ((1-rdt.det)*(1-rdt.nonadherence)*(1-microscopy.use))) + rdt.det.D.or.A.nmf[which(res$N.Sens[D.or.A.pos.nmf,res$Counter] == 0)] <- (1 - ((1-rdt.det)*(1-rdt.nonadherence)*(1-microscopy.use))) D.or.A.treated.pos.nmf <- D.or.A.pos.nmf[which(rbinom(length(D.or.A.pos.nmf),size = 1,rdt.det.D.or.A.nmf)==1)] res$Status[D.or.A.treated.pos.nmf,res$Counter] <- 5