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Adding mixing models (need examples) (#16)
* Adding mixing models (need examples) * Updating readme with figures and list of models * Adding entity to the model * Adding new entity wrappers * Starting off with entity vignette * Working on the vignette * Updating version of epiworld * Updating README * Refactoring how virus and tools are added * Updating calling methods * Finally passing * Adding a note on the news file * Adding defunct message * Updating roxygen * Updating news and minor updates to README.md * Working on entity * Correcting mixing vignette * Adding the dist functions (starting to). Expected to fail [skip ci] * Updating interface * Updating version of acions * Updating epiworld c++ * Updating epiworld (warnings) * Removing dangling calls * Final check errors * Missed Rd file * Updating reference * Adding examples and cleaning docs. * Updating
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| FROM rocker/r-base:latest | ||
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| RUN \ | ||
| echo 'options(repos=c(CRAN="https://cloud.r-project.org"))' >> ~/.Rprofile && \ | ||
| Rscript --vanilla -e 'getOption("repos")' | ||
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| # Adding Git | ||
| RUN apt-get update && apt-get install -y --no-install-recommends git | ||
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| # Adding R packages | ||
| RUN \ | ||
| wget https://github.com/jgm/pandoc/releases/download/3.2.1/pandoc-3.2.1-1-amd64.deb && \ | ||
| dpkg -i pandoc-3.2.1-1-amd64.deb | ||
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| RUN install2.r cpp11 rmarkdown roxygen2 tinytest data.table netplot |
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| // For format details, see https://aka.ms/devcontainer.json. For config options, see the | ||
| // README at: https://github.com/devcontainers/templates/tree/main/src/cpp | ||
| { | ||
| "name": "epiworldR", | ||
| "build": { | ||
| "dockerfile": "Dockerfile" | ||
| }, | ||
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| // Features to add to the dev container. More info: https://containers.dev/features. | ||
| // "features": {}, | ||
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| // Use 'forwardPorts' to make a list of ports inside the container available locally. | ||
| // "forwardPorts": [], | ||
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| // Use 'postCreateCommand' to run commands after the container is created. | ||
| // "postCreateCommand": "gcc -v", | ||
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| // Configure tool-specific properties. | ||
| // "customizations": {}, | ||
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| // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root. | ||
| "remoteUser": "root" | ||
| } |
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| #' Susceptible Exposed Infected Removed model (SEIR) with mixing | ||
| #' @param name String. Name of the virus | ||
| #' @param prevalence Double. Initial proportion of individuals with the virus. | ||
| #' @param contact_rate Numeric scalar. Average number of contacts per step. | ||
| #' @param transmission_rate Numeric scalar between 0 and 1. Probability of | ||
| #' transmission. | ||
| #' @param incubation_days Numeric scalar. Average number of days in the | ||
| #' incubation period. | ||
| #' @param recovery_rate Numeric scalar between 0 and 1. Probability of recovery. | ||
| #' @param x Object of class SIRCONN. | ||
| #' @param ... Currently ignore. | ||
| #' @param n Number of individuals in the population. | ||
| #' @param contact_matrix Matrix of contact rates between individuals. | ||
| #' @export | ||
| #' @family Models | ||
| #' @details | ||
| #' The `contact_matrix` is a matrix of contact rates between entities. The | ||
| #' matrix should be of size `n x n`, where `n` is the number of entities. | ||
| #' This is a row-stochastic matrix, i.e., the sum of each row should be 1. | ||
| #' | ||
| #' The [initial_states] function allows the user to set the initial state of the | ||
| #' model. In particular, the user can specify how many of the non-infected | ||
| #' agents have been removed at the beginning of the simulation. | ||
| #' @returns | ||
| #' - The `ModelSEIRMixing`function returns a model of class [epiworld_model]. | ||
| #' @aliases epiworld_seirmixing | ||
| #' | ||
| #' @examples | ||
| #' | ||
| #' # Start off creating three entities. | ||
| #' # Individuals will be distribured randomly between the three. | ||
| #' e1 <- entity("Population 1", 3e3, as_proportion = FALSE) | ||
| #' e2 <- entity("Population 2", 3e3, as_proportion = FALSE) | ||
| #' e3 <- entity("Population 3", 3e3, as_proportion = FALSE) | ||
| #' | ||
| #' # Row-stochastic matrix (rowsums 1) | ||
| #' cmatrix <- c( | ||
| #' c(0.9, 0.05, 0.05), | ||
| #' c(0.1, 0.8, 0.1), | ||
| #' c(0.1, 0.2, 0.7) | ||
| #' ) |> matrix(byrow = TRUE, nrow = 3) | ||
| #' | ||
| #' N <- 9e3 | ||
| #' | ||
| #' flu_model <- ModelSEIRMixing( | ||
| #' name = "Flu", | ||
| #' n = N, | ||
| #' prevalence = 1 / N, | ||
| #' contact_rate = 20, | ||
| #' transmission_rate = 0.1, | ||
| #' recovery_rate = 1 / 7, | ||
| #' incubation_days = 7, | ||
| #' contact_matrix = cmatrix | ||
| #' ) | ||
| #' | ||
| #' # Adding the entities to the model | ||
| #' flu_model |> | ||
| #' add_entity(e1) |> | ||
| #' add_entity(e2) |> | ||
| #' add_entity(e3) | ||
| #' | ||
| #' set.seed(331) | ||
| #' run(flu_model, ndays = 100) | ||
| #' summary(flu_model) | ||
| #' plot_incidence(flu_model) | ||
| #' | ||
| #' @seealso epiworld-methods | ||
| ModelSEIRMixing <- function( | ||
| name, n, prevalence, contact_rate, transmission_rate, | ||
| incubation_days, recovery_rate, contact_matrix | ||
| ) { | ||
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| structure( | ||
| ModelSEIRMixing_cpp( | ||
| name, n, prevalence, contact_rate, | ||
| transmission_rate, incubation_days, | ||
| recovery_rate, as.vector(contact_matrix) | ||
| ), | ||
| class = c("epiworld_seirmixing", "epiworld_model") | ||
| ) | ||
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| } | ||
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| #' @rdname ModelSEIRMixing | ||
| #' @export | ||
| #' @returns The `plot` function returns a plot of the SEIRMixing model of class | ||
| #' [epiworld_model]. | ||
| #' @param main Title of the plot | ||
| plot.epiworld_seirmixing <- function(x, main = get_name(x), ...) { # col = NULL | ||
| plot_epi(x, main = main, ...) | ||
| } |
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