Adding mixing models (need examples)

.devcontainer/Dockerfile

@@ -0,0 +1,15 @@
+FROM rocker/r-base:latest
+
+RUN \
+  echo 'options(repos=c(CRAN="https://cloud.r-project.org"))' >> ~/.Rprofile && \
+  Rscript --vanilla -e 'getOption("repos")'
+
+# Adding Git
+RUN apt-get update && apt-get install -y --no-install-recommends git
+
+# 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
+
+RUN install2.r cpp11 rmarkdown roxygen2 tinytest data.table netplot

.devcontainer/devcontainer.json

@@ -0,0 +1,23 @@
+// 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"
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "gcc -v",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	"remoteUser": "root"
+}

.github/workflows/r.yml

@@ -36,7 +36,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -69,7 +69,7 @@ jobs:
           error-on: '"warning"'
 
       # Upload the built package as an artifact
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         if: ${{ matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release' }}
         with:
           name: ${{ matrix.config.os }}-pkg

.vscode/c_cpp_properties.json

@@ -7,7 +7,8 @@
                 "/usr/local/include",
                 "/usr/lib/R/site-library/cpp11/include",
                 "/usr/lib/R/site-library/Rcpp/include",
-                "/usr/share/R/include"
+                "/usr/share/R/include",
+                "inst/include/epiworld"
             ],
             "intelliSenseMode": "linux-gcc-x64",
             "compilerPath": "/usr/bin/gcc",

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: epiworldR
 Type: Package
 Title: Fast Agent-Based Epi Models
-Version: 0.1-1
-Date: 2024-04-07
+Version: 0.3-2
+Date: 2024-06-12
 Authors@R: c(
   person("Derek", "Meyer", role=c("aut","cre"), 
   email="[email protected]", comment = c(ORCID = "0009-0005-1350-6988")),
@@ -21,7 +21,7 @@ URL: https://github.com/UofUEpiBio/epiworldR,
     https://uofuepibio.github.io/epiworldR-workshop/ 
 BugReports: https://github.com/UofUEpiBio/epiworldR/issues
 License: MIT + file LICENSE
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 LinkingTo: cpp11

Makefile

@@ -1,6 +1,7 @@
 # Capture the current value of the version of the package in DESCRIPTION
 VERSION := $(shell grep Version DESCRIPTION | sed -e 's/Version: //')
 
+
 build: 
 	cd .. && R CMD build epiworldR
 

NAMESPACE

@@ -1,8 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method("[",epiworld_agents)
+S3method("[",epiworld_entities)
 S3method(add_tool,epiworld_model)
-S3method(add_tool_n,epiworld_model)
 S3method(add_virus,epiworld_model)
 S3method(add_virus,epiworld_seir)
 S3method(add_virus,epiworld_seirconn)
@@ -12,14 +12,10 @@ S3method(add_virus,epiworld_sir)
 S3method(add_virus,epiworld_sirconn)
 S3method(add_virus,epiworld_sird)
 S3method(add_virus,epiworld_sirdconn)
-S3method(add_virus_n,epiworld_model)
-S3method(add_virus_n,epiworld_seir)
-S3method(add_virus_n,epiworld_seirconn)
-S3method(add_virus_n,epiworld_sir)
-S3method(add_virus_n,epiworld_sirconn)
 S3method(agents_from_edgelist,epiworld_model)
 S3method(agents_smallworld,epiworld_model)
 S3method(as.array,epiworld_hist_transition)
+S3method(get_agents,epiworld_model)
 S3method(get_hist_tool,epiworld_model)
 S3method(get_hist_total,epiworld_model)
 S3method(get_hist_transition_matrix,epiworld_model)
@@ -48,16 +44,23 @@ S3method(plot,epiworld_seir)
 S3method(plot,epiworld_seirconn)
 S3method(plot,epiworld_seird)
 S3method(plot,epiworld_seirdconn)
+S3method(plot,epiworld_seirmixing)
 S3method(plot,epiworld_sir)
 S3method(plot,epiworld_sirconn)
 S3method(plot,epiworld_sird)
 S3method(plot,epiworld_sirdconn)
+S3method(plot,epiworld_sirmixing)
 S3method(plot,epiworld_sis)
 S3method(plot,epiworld_sisd)
 S3method(plot,epiworld_surv)
+S3method(plot_epi,epiworld_hist)
+S3method(plot_epi,epiworld_hist_virus)
+S3method(plot_epi,epiworld_model)
 S3method(print,epiworld_agent)
 S3method(print,epiworld_agents)
 S3method(print,epiworld_agents_tools)
+S3method(print,epiworld_entities)
+S3method(print,epiworld_entity)
 S3method(print,epiworld_globalevent)
 S3method(print,epiworld_model)
 S3method(print,epiworld_saver)
@@ -82,14 +85,17 @@ export(ModelSEIR)
 export(ModelSEIRCONN)
 export(ModelSEIRD)
 export(ModelSEIRDCONN)
+export(ModelSEIRMixing)
 export(ModelSIR)
 export(ModelSIRCONN)
 export(ModelSIRD)
 export(ModelSIRDCONN)
 export(ModelSIRLogit)
+export(ModelSIRMixing)
 export(ModelSIS)
 export(ModelSISD)
 export(ModelSURV)
+export(add_entity)
 export(add_globalevent)
 export(add_tool)
 export(add_tool_agent)
@@ -101,10 +107,22 @@ export(agents_from_edgelist)
 export(agents_smallworld)
 export(change_state)
 export(clone_model)
+export(distribute_entity_randomly)
+export(distribute_entity_to_set)
+export(distribute_tool_randomly)
+export(distribute_tool_to_set)
+export(distribute_virus_randomly)
+export(distribute_virus_set)
+export(entity)
+export(entity_add_agent)
+export(entity_get_agents)
 export(get_agents)
 export(get_agents_data_ncols)
 export(get_agents_states)
 export(get_agents_tools)
+export(get_entities)
+export(get_entity_name)
+export(get_entity_size)
 export(get_generation_time)
 export(get_hist_tool)
 export(get_hist_total)
@@ -138,12 +156,14 @@ export(globalevent_tool_logit)
 export(has_tool)
 export(has_virus)
 export(initial_states)
+export(load_agents_entities_ties)
 export(make_saver)
 export(plot_generation_time)
 export(plot_incidence)
 export(plot_reproductive_number)
 export(queuing_off)
 export(queuing_on)
+export(rm_entity)
 export(rm_tool)
 export(rm_virus)
 export(run)
@@ -153,6 +173,9 @@ export(set_agents_data)
 export(set_death_reduction)
 export(set_death_reduction_fun)
 export(set_death_reduction_ptr)
+export(set_distribution_entity)
+export(set_distribution_tool)
+export(set_distribution_virus)
 export(set_incubation)
 export(set_incubation_fun)
 export(set_incubation_ptr)

NEWS.md

@@ -1,3 +1,22 @@
+# epiworldR 0.3-2 (dev)
+
+* Starting version 0.3-0, `epiworldR` is versioned using the same version as the C++ library, `epiworld`.
+
+* Adds the new mixing models `ModelSIRMixing` and `ModelSEIRMixing`.
+
+* Ports the `Entity` class. Entities are used to group agents within a model.
+
+* Refactors `add_tool`, `add_virus`, and `add_entity` simplifying syntax. Now,
+  these functions only receive the model and object. Prevalence is 
+  specified in the object itself. `add_tool_n` and `add_virus_n` are now
+  deprecated.
+
+* `globalaction_*` are now defunct. Use `globalevent_*` instead.
+
+* New functions to specify how viruses, tools, and entities are distributed
+  among agents: `distribute_viruses`, `distribute_tools`, and `distribute_entities`.
+
+
 # epiworldR 0.1-0`
 
 * Force model to update agents' states when running a simulation.

R/ModelSEIRCONN.R

@@ -39,8 +39,8 @@
 #' plot(model_seirconn)
 #' 
 #' # Adding the flu
-#' flu <- virus("Flu", .9, 1/7)
-#' add_virus(model_seirconn, flu, .001)
+#' flu <- virus("Flu", .9, 1/7, prevalence = 0.001, as_proportion = TRUE)
+#' add_virus(model_seirconn, flu)
 #' 
 #' #' # Running and printing
 #' run(model_seirconn, ndays = 100, seed = 1912)

R/ModelSEIRDCONN.R

@@ -47,8 +47,12 @@
 #' plot(model_seirdconn)
 #' 
 #' # Adding the flu
-#' flu <- virus("Flu", prob_infecting = .3, recovery_rate = 1/7, prob_death = 0.001)
-#' add_virus(model = model_seirdconn, virus = flu, proportion = .001)
+#' flu <- virus(
+#'   "Flu", prob_infecting = .3, recovery_rate = 1/7,
+#'   prob_death = 0.001,
+#'   prevalence = 0.001, as_proportion = TRUE
+#' )
+#' add_virus(model = model_seirdconn, virus = flu)
 #' 
 #' #' # Running and printing
 #' run(model_seirdconn, ndays = 100, seed = 1912)

R/ModelSEIRMixing.R

@@ -0,0 +1,91 @@
+#' 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
+) {
+
+  structure(
+    ModelSEIRMixing_cpp(
+      name, n, prevalence, contact_rate, 
+      transmission_rate, incubation_days, 
+      recovery_rate, as.vector(contact_matrix)
+      ),
+    class = c("epiworld_seirmixing", "epiworld_model")
+  )
+
+}
+
+#' @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, ...)
+}