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Merge pull request #156 from dd-harp/dev
Major Update: blood feeding, egg laying, and resource dynamics
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,77 @@ | ||
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| #' @title Update the availability of blood hosts | ||
| #' @description This method dispatches on the type of `pars$BFpar`. | ||
| #' @param t current simulation time | ||
| #' @param y vector of state variables | ||
| #' @param pars an [list] | ||
| #' @return a [list] | ||
| #' @export | ||
| AvailableBlood <- function(t, y, pars) { | ||
| UseMethod("AvailableBlood", pars$BFpar) | ||
| } | ||
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| #' @title Compute availability of local humans for blood feeding | ||
| #' @description Compute the availability for the pathogen's hosts for blood feeding | ||
| #' @param t current simulation time | ||
| #' @param y state vector | ||
| #' @param pars a [list] | ||
| #' @return a [numeric] vector of length `nPatches` | ||
| #' @export | ||
| AvailableBlood.static <- function(t, y, pars){ | ||
| return(pars) | ||
| } | ||
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| #' @title Compute availability of local humans for blood feeding | ||
| #' @description Compute the availability for the pathogen's hosts for blood feeding | ||
| #' @param t current simulation time | ||
| #' @param y state vector | ||
| #' @param pars a [list] | ||
| #' @return a [numeric] vector of length `nPatches` | ||
| #' @export | ||
| AvailableBlood.setup <- function(t, y, pars){ | ||
| for(s in 1:pars$nVectors) | ||
| pars = compute_AvailableHosts(t, y, pars, s) | ||
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| return(pars) | ||
| } | ||
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| #' @title Compute availability of local humans for blood feeding | ||
| #' @description Compute the availability for the pathogen's hosts for blood feeding | ||
| #' @param t current simulation time | ||
| #' @param y state vector | ||
| #' @param pars a [list] | ||
| #' @return a [numeric] vector of length `nPatches` | ||
| #' @export | ||
| AvailableBlood.forced <- function(t, y, pars){ | ||
| for(s in 1:pars$nVectors) | ||
| pars = compute_AvailableHosts(t, y, pars, s) | ||
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| return(pars) | ||
| } | ||
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| #' @title Compute availability blood hosts of the i^th species | ||
| #' @description Compute the availability for the pathogen's hosts for blood feeding | ||
| #' @param t current simulation time | ||
| #' @param y state vector | ||
| #' @param pars a [list] | ||
| #' @param s the vector species index | ||
| #' @return a [numeric] vector of length `nPatches` | ||
| #' @export | ||
| compute_AvailableHosts <- function(t, y, pars, s){ | ||
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| H = F_H(t, y, pars, 1) | ||
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| pars$vars$Wi[[1]][[s]] = as.vector(with(pars$BFpar, TaR[[1]][[s]] %*% (searchWts[[1]][[s]]*H))) | ||
| pars$vars$W[[s]] = pars$vars$Wi[[1]][[s]] | ||
| if(pars$nHosts > 1){ | ||
| for(i in 2:pars$nHosts){ | ||
| H = F_H(t, y, pars, i) | ||
| pars$vars$Wi[[i]][[s]] = as.vector(with(pars$BFpar, TaR[[i]][[s]] %*% (searchWts[[i]][[s]]*H))) | ||
| pars$vars$W[[s]] = pars$vars$W[[s]] + pars$vars$Wi[[i]][[s]] | ||
| } | ||
| } | ||
| pars$vars$W[[s]] = as.vector(pars$vars$W[[s]]) | ||
| pars$vars$B[[s]] = as.vector(with(pars$vars, W[[s]] + Visitors[[s]] + Other[[s]])) | ||
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| return(pars) | ||
| } |
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