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Merge pull request #2 from stewid/SIR
Add 'SIR' compartment model
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| ## SimInf, a framework for stochastic disease spread simulations | ||
| ## Copyright (C) 2015 - 2016 Stefan Widgren | ||
| ## | ||
| ## This program is free software: you can redistribute it and/or modify | ||
| ## it under the terms of the GNU General Public License as published by | ||
| ## the Free Software Foundation, either version 3 of the License, or | ||
| ## (at your option) any later version. | ||
| ## | ||
| ## This program is distributed in the hope that it will be useful, | ||
| ## but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| ## GNU General Public License for more details. | ||
| ## | ||
| ## You should have received a copy of the GNU General Public License | ||
| ## along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
|
|
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| ##' Class \code{"SIR"} | ||
| ##' | ||
| ##' Class to handle the SIR \code{\link{siminf_model}}. | ||
| ##' @include siminf_model.R | ||
| ##' @include AllGenerics.R | ||
| ##' @export | ||
| setClass("SIR", contains = c("siminf_model")) | ||
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| ##' Create a SIR model | ||
| ##' | ||
| ##' Create a SIR model to be used by the simulation framework. | ||
| ##' | ||
| ##' | ||
| ##' The argument \code{u0} must be a \code{data.frame} with one row for | ||
| ##' each node with the following columns: | ||
| ##' \describe{ | ||
| ##' \item{S}{The number of sucsceptible in each node} | ||
| ##' \item{I}{The number of infected in each node} | ||
| ##' \item{R}{The number of recovered in each node} | ||
| ##' } | ||
| ##' | ||
| ##' @param u0 A \code{data.frame} with the initial state in each node, | ||
| ##' see details. | ||
| ##' @param tspan An increasing sequence of points in time where the | ||
| ##' state of the system is to be returned. | ||
| ##' @param events a \code{data.frame} with the scheduled events, see | ||
| ##' \code{\link{siminf_model}}. | ||
| ##' @param beta The transmission rate from susceptible to infected. | ||
| ##' @param gamma The recovery rate from infected to recovered. | ||
| ##' @return \code{SIR} | ||
| ##' @include check_arguments.R | ||
| ##' @export | ||
| SIR <- function(u0, | ||
| tspan, | ||
| events = NULL, | ||
| beta = NULL, | ||
| gamma = NULL) | ||
| { | ||
| compartments <- c("S", "I", "R") | ||
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| ## Check arguments. | ||
|
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| ## Check u0 | ||
| if (!is.data.frame(u0)) | ||
| stop("'u0' must be a data.frame") | ||
| if (!all(compartments %in% names(u0))) | ||
| stop("Missing columns in u0") | ||
| u0 <- u0[, compartments] | ||
|
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| ## Check for non-numeric parameters | ||
| check_gdata_arg(beta, gamma) | ||
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| ## Arguments seems ok...go on | ||
|
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| E <- Matrix(c(1, 1, | ||
| 0, 1, | ||
| 0, 1), | ||
| nrow = 3, | ||
| ncol = 2, | ||
| byrow = TRUE, | ||
| sparse = TRUE) | ||
| E <- as(E, "dgCMatrix") | ||
| colnames(E) <- as.character(1:2) | ||
| rownames(E) <- compartments | ||
|
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| N <- matrix(integer(0), nrow = 0, ncol = 0) | ||
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| G <- Matrix(c(1, 1, | ||
| 1, 1), | ||
| nrow = 2, | ||
| ncol = 2, | ||
| byrow = TRUE, | ||
| sparse = TRUE) | ||
| G <- as(G, "dgCMatrix") | ||
| colnames(G) <- as.character(1:2) | ||
| rownames(G) <- c("S -> I", "I -> R") | ||
|
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| S <- Matrix(c(-1, 0, | ||
| 1, -1, | ||
| 0, 1), | ||
| nrow = 3, | ||
| ncol = 2, | ||
| byrow = TRUE, | ||
| sparse = TRUE) | ||
| S <- as(S, "dgCMatrix") | ||
| colnames(S) <- as.character(1:2) | ||
| rownames(S) <- compartments | ||
|
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| v0 <- matrix(numeric(0), nrow = 0, ncol = nrow(u0)) | ||
| storage.mode(v0) <- "double" | ||
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| ldata <- matrix(numeric(0), nrow = 0, ncol = nrow(u0)) | ||
| storage.mode(ldata) <- "double" | ||
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| gdata <- c(beta, gamma) | ||
| storage.mode(gdata) <- "double" | ||
| names(gdata) <- c("beta", "gamma") | ||
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| model <- siminf_model(G = G, | ||
| S = S, | ||
| E = E, | ||
| N = N, | ||
| tspan = tspan, | ||
| events = events, | ||
| ldata = ldata, | ||
| gdata = gdata, | ||
| u0 = u0, | ||
| v0 = v0) | ||
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| return(as(model, "SIR")) | ||
| } | ||
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| ##' @rdname susceptible-methods | ||
| ##' @export | ||
| setMethod("susceptible", | ||
| signature("SIR"), | ||
| function(model, i = NULL, by = 1, ...) { | ||
| if (identical(dim(model@U), c(0L, 0L))) | ||
| stop("Please run the model first, the 'U' matrix is empty") | ||
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| ii <- seq(from = 1, to = dim(model@U)[1], by = 3) | ||
| if (!is.null(i)) | ||
| ii <- ii[i] | ||
| j <- seq(from = 1, to = dim(model@U)[2], by = by) | ||
| as.matrix(model@U[ii, j, drop = FALSE]) | ||
| } | ||
| ) | ||
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| ##' @rdname infected-methods | ||
| ##' @export | ||
| setMethod("infected", | ||
| signature("SIR"), | ||
| function(model, i = NULL, by = 1, ...) { | ||
| if (identical(dim(model@U), c(0L, 0L))) | ||
| stop("Please run the model first, the 'U' matrix is empty") | ||
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| ii <- seq(from = 2, to = dim(model@U)[1], by = 3) | ||
| if (!is.null(i)) | ||
| ii <- ii[i] | ||
| j <- seq(from = 1, to = dim(model@U)[2], by = by) | ||
| as.matrix(model@U[ii, j, drop = FALSE]) | ||
| } | ||
| ) | ||
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| ##' @rdname recovered-methods | ||
| ##' @export | ||
| setMethod("recovered", | ||
| signature("SIR"), | ||
| function(model, i = NULL, by = 1, ...) { | ||
| if (identical(dim(model@U), c(0L, 0L))) | ||
| stop("Please run the model first, the 'U' matrix is empty") | ||
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| ii <- seq(from = 3, to = dim(model@U)[1], by = 3) | ||
| if (!is.null(i)) | ||
| ii <- ii[i] | ||
| j <- seq(from = 1, to = dim(model@U)[2], by = by) | ||
| as.matrix(model@U[ii, j, drop = FALSE]) | ||
| } | ||
| ) | ||
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| ##' @name plot-methods | ||
| ##' @aliases plot plot-methods plot,SIR-method | ||
| ##' @importFrom graphics plot | ||
| ##' @export | ||
| setMethod("plot", | ||
| signature(x = "SIR"), | ||
| function(x, t0 = NULL, ...) | ||
| { | ||
| callNextMethod(x, t0 = t0, legend = c("S", "I", "R"), ...) | ||
| } | ||
| ) | ||
|
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| ##' Scheduled events example data for the \code{SIR} model | ||
| ##' | ||
| ##' Synthetic scheduled events data to demonstrate the \code{SIR} | ||
| ##' model. The data contains 466692 events for 1600 nodes over 365 * 4 | ||
| ##' days. | ||
| ##' @return A \code{data.frame} | ||
| ##' @keywords methods | ||
| ##' @importFrom utils data | ||
| ##' @export | ||
| events_SIR <- function() { | ||
| utils::data(events_SISe3, envir = environment()) | ||
| events_SISe3$select[events_SISe3$event == 0] <- 2 | ||
| events_SISe3$select[events_SISe3$event == 1] <- 1 | ||
| events_SISe3 <- events_SISe3[events_SISe3$event != 2,] | ||
| events_SISe3$select[events_SISe3$event == 3] <- 2 | ||
| events_SISe3 | ||
| } | ||
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| ##' Example data to initialize the \code{SIR} model | ||
| ##' | ||
| ##' Synthetic init data for 1600 nodes to demonstrate the \code{SIR} | ||
| ##' model. | ||
| ##' @return A \code{data.frame} | ||
| ##' @keywords methods | ||
| ##' @importFrom utils data | ||
| ##' @export | ||
| u0_SIR <- function() { | ||
| utils::data(u0_SISe3, envir = environment()) | ||
| u0_SISe3$S <- u0_SISe3$S_1 + u0_SISe3$S_2 + u0_SISe3$S_3 | ||
| u0_SISe3$I <- u0_SISe3$I_1 + u0_SISe3$I_2 + u0_SISe3$I_3 | ||
| u0_SISe3$R <- 0 | ||
| u0_SISe3[, c("S", "I", "R")] | ||
| } |
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