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Merge pull request #200 from dd-harp/dev
Travel and exposure while traveling
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| #' @title Travel EIR | ||
| #' @description Compute the EIR while traveling | ||
| #' @param t the time | ||
| #' @param pars an **`xds`** object | ||
| #' @param i the host species index | ||
| #' @return the daily travel EIR, a [numeric] vector | ||
| #' @export | ||
| travel_eir <- function(t, pars, i){ | ||
| with(pars$travel_eir[[i]], return(travelEIR*F_season(t)*F_trend(t))) | ||
| } | ||
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| #' @title Setup Travel EIR | ||
| #' @description Set up a function to compute the travel EIR | ||
| #' @param pars a [list] | ||
| #' @param travelEIR the time spent traveling | ||
| #' @param F_season a function describing a seasonal pattern | ||
| #' @param F_trend a function describing a trend | ||
| #' @param i the host species index | ||
| #' @return an **`xds`** object | ||
| #' @export | ||
| setup_travel_eir = function(pars, travelEIR=0, F_season=F_flat, F_trend=F_flat, i=1){ | ||
| trv <- list() | ||
| trv$travelEIR <- travelEIR | ||
| trv$F_season <- F_season | ||
| trv$F_trend <- F_trend | ||
| pars$travel_eir[[i]] <- trv | ||
| return(pars) | ||
| } | ||
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| #' @title A model for the travel FoI | ||
| #' @description Implements [traveling]. The function is | ||
| #' called by [make_TaR] to set the fraction of time spent | ||
| #' traveling | ||
| #' @param t current simulation time | ||
| #' @param pars a [list]# | ||
| #' @param i host species index | ||
| #' @return an **`xds`** object | ||
| #' @export | ||
| traveling <- function(t, pars, i) { | ||
| UseMethod("traveling", pars$travel[[i]]) | ||
| } | ||
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| #' @title A model for the travel FoI | ||
| #' @description Implements [traveling] through a model for the travel FoI | ||
| #' @inheritParams traveling | ||
| #' @return an **`xds`** object | ||
| #' @export | ||
| traveling.static <- function(t, pars, i) { | ||
| return(pars) | ||
| } | ||
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| #' @title A model for the travel FoI | ||
| #' @description Implements [traveling] through a model for the travel FoI | ||
| #' @inheritParams traveling | ||
| #' @return an **`xds`** object | ||
| #' @export | ||
| traveling.setup <- function(t, pars, i) { | ||
| pars$time_traveling[[i]] <- pars$travel[[i]]$traveling_fraction | ||
| pars <- trigger_setup(pars$BFpar) | ||
| return(pars) | ||
| } | ||
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| #' @title A model for the travel FoI | ||
| #' @description Implements [traveling] through a model for the travel FoI | ||
| #' @inheritParams traveling | ||
| #' @return an **`xds`** object | ||
| #' @export | ||
| traveling.dynamic <- function(t, pars, i) { | ||
| with(pars$travel[[i]],{ | ||
| pars$time_traveling[[i]] = traveling*F_season(t)*F_trend(t) | ||
| return(pars) | ||
| }) | ||
| } | ||
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| #' @title A function to set up malaria importation | ||
| #' @description Setup a static model for travel malaria | ||
| #' @param pars a [list] | ||
| #' @param i the host species index | ||
| #' @return a [list] | ||
| #' @export | ||
| setup_no_travel = function(pars, i=1){ | ||
| trv <- list() | ||
| class(trv) <- "static" | ||
| trv$traveling_fraction <- 0 | ||
| pars$travel[[i]] <- trv | ||
| return(pars) | ||
| } | ||
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| #' @title A function to set up malaria importation | ||
| #' @description Setup a static model for travel malaria | ||
| #' @param pars an **`xds`** object | ||
| #' @param traveling_fraction the fraction of time spent traveling | ||
| #' @param i the host species index | ||
| #' @return a [list] | ||
| #' @export | ||
| setup_static_travel = function(pars, traveling_fraction=0, i=1){ | ||
| trv <- list() | ||
| class(trv) <- "setup" | ||
| trv$traveling_fraction <- traveling_fraction | ||
| pars$travel[[i]] <- trv | ||
| return(pars) | ||
| } | ||
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| #' @title A function to set up malaria importation | ||
| #' @description Setup a static model for travel malaria | ||
| #' @param pars a [list] | ||
| #' @param traveling the time spent traveling | ||
| #' @param F_season a function describing a seasonal pattern | ||
| #' @param F_trend a function describing a trend | ||
| #' @param i the host species index | ||
| #' @return a [list] | ||
| #' @export | ||
| setup_dynamic_travel = function(pars, traveling=0, F_season=F_flat, F_trend=F_flat, i=1){ | ||
| trv <- list() | ||
| class(trv) <- "dynamic" | ||
| class(pars$BFpar) <- "dynamic" | ||
| trv$traveling <- traveling | ||
| trv$F_season <- F_season | ||
| trv$F_trend <- F_trend | ||
| pars$travel[[i]] <- trv | ||
| return(pars) | ||
| } |
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