Adding initial states function

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: epiworldRdev
+Package: epiworldR
 Type: Package
 Title: Fast Agent-Based Epi Models
 Version: 0.0-3.9000

NAMESPACE

@@ -134,6 +134,7 @@ export(globalaction_tool)
 export(globalaction_tool_logit)
 export(has_tool)
 export(has_virus)
+export(initial_states)
 export(make_saver)
 export(plot_generation_time)
 export(plot_incidence)
@@ -189,4 +190,4 @@ importFrom(stats,aggregate)
 importFrom(stats,quantile)
 importFrom(stats,sd)
 importFrom(utils,read.table)
-useDynLib(epiworldRdev, .registration = TRUE)
+useDynLib(epiworldR, .registration = TRUE)

R/ModelSEIR.R

@@ -12,6 +12,11 @@
 #' @export
 #' @family Models
 #' @aliases epiworld_seir
+#' @details 
+#' The [initial_state] function allows the user to set the initial state of the
+#' model. The user must provide a vector of proportions indicating the following
+#' values: (1) Proportion of non-infected agents who are removed, and (2)
+#' Proportion of exposed agents to be set as infected.
 #' @returns
 #' - The `ModelSEIR`function returns a model of class [epiworld_model].
 #' @examples 

R/ModelSEIRD.R

@@ -11,6 +11,12 @@
 #' @param x Object of class SEIRD. 
 #' @param ... Currently ignore.
 #' @export
+#' @details 
+#' The [initial_state] function allows the user to set the initial state of the
+#' model. The user must provide a vector of proportions indicating the following
+#' values: (1) Proportion of exposed agents who are infected, (2)
+#' proportion of non-infected agents already removed, and (3) proportion of
+#' non-ifected agents already deceased.
 #' @family Models
 #' @aliases epiworld_seird
 #' @returns

R/ModelSEIRDCONN.R

@@ -17,6 +17,12 @@
 #' @param ... Currently ignore. 
 #' @param n Number of individuals in the population.
 #' @export
+#' @details 
+#' The [initial_state] function allows the user to set the initial state of the
+#' model. The user must provide a vector of proportions indicating the following
+#' values: (1) Proportion of exposed agents who are infected, (2)
+#' proportion of non-infected agents already removed, and (3) proportion of
+#' non-ifected agents already deceased.
 #' @family Models
 #' @aliases epiworld_seirdconn
 #' @returns

R/ModelSIR.R

@@ -13,6 +13,10 @@
 #' @param ... Additional arguments passed to [graphics::plot].
 #' @export
 #' @family Models
+#' @details 
+#' The [initial_state] 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.
 #' @aliases epiworld_sir
 #' @returns
 #' - The `ModelSIR` function returns a model of class [epiworld_model].

R/ModelSIRCONN.R

@@ -10,6 +10,10 @@
 #' @param n Number of individuals in the population.
 #' @export
 #' @family Models
+#' @details 
+#' The [initial_state] 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 `ModelSIRCONN`function returns a model of class [epiworld_model].
 #' @aliases epiworld_sirconn

R/ModelSIRD.R

@@ -13,6 +13,11 @@
 #' @param x Object of class SIR. 
 #' @param ... Additional arguments passed to [graphics::plot].
 #' @export
+#' @details
+#' The [initial_state] function allows the user to set the initial state of the
+#' model. The user must provide a vector of proportions indicating the following
+#' values: (1) proportion of non-infected agents already removed, and (2) proportion of
+#' non-ifected agents already deceased.
 #' @family Models
 #' @aliases epiworld_sird
 #' @returns

R/ModelSIRDCONN.R

@@ -10,6 +10,11 @@
 #' @param ... Currently ignore.
 #' @param n Number of individuals in the population.
 #' @export
+#' @details 
+#' The [initial_state] function allows the user to set the initial state of the
+#' model. The user must provide a vector of proportions indicating the following
+#' values: (1) proportion of non-infected agents already removed, and (2) proportion of
+#' non-ifected agents already deceased.
 #' @family Models
 #' @returns
 #' - The `ModelSIRDCONN`function returns a model of class [epiworld_model].

R/cpp11.R

@@ -256,6 +256,10 @@ get_network_cpp <- function(model) {
   .Call(`_epiworldR_get_network_cpp`, model)
 }
 
+initial_states_cpp <- function(model, proportions) {
+  .Call(`_epiworldR_initial_states_cpp`, model, proportions)
+}
+
 tool_cpp <- function(name, susceptibility_reduction, transmission_reduction, recovery_enhancer, death_reduction) {
   .Call(`_epiworldR_tool_cpp`, name, susceptibility_reduction, transmission_reduction, recovery_enhancer, death_reduction)
 }

R/epiworldR-package.R

@@ -1,5 +1,5 @@
-#' epiworldRdev
-#' @useDynLib epiworldRdev, .registration = TRUE
+#' epiworldR
+#' @useDynLib epiworldR, .registration = TRUE
 #' @importFrom graphics boxplot plot
 "_PACKAGE"
 

R/model-methods.R

@@ -351,3 +351,17 @@ get_tool <- function(model, tool_pos) {
     class = "epiworld_tool"
   )
 }
+
+#' @export 
+#' @param proportions Numeric vector. Proportions in which agents will be
+#' distributed (see details).
+#' @return 
+#' - `inital_states` returns the model with an updated initial state.
+#' @rdname epiworld-methods
+initial_states <- function(model, proportions) {
+
+  stopifnot_model(model)
+  invisible(initial_states_cpp(model, proportions))
+
+}
+

README.Rmd

@@ -67,7 +67,7 @@ This R package includes several popular epidemiological models including
 This Susceptible-Infected-Recovered model features a population of 100,000 agents simulated in a small-world network. Each agent is connected to ten other agents. One percent of the population has the virus, with a 70% chance of transmission. Infected individuals recover at a 0.3 rate:
 
 ```{r example}
-library(epiworldRdev)
+library(epiworldR)
 
 # Creating a SIR model
 sir <- ModelSIR(
@@ -204,8 +204,8 @@ sir <- ModelSIR(
 net <- get_transmissions(sir)
 
 # Plotting
-library(epiworldRdev)
-library(epiworldRdev)
+library(epiworldR)
+library(epiworldR)
 x <- graph_from_edgelist(as.matrix(net[,2:3]) + 1)
 
 nplot(x, edge.curvature = 0, edge.color = "gray", skip.vertex=TRUE)

README.md

@@ -87,7 +87,7 @@ virus, with a 70% chance of transmission. Infected individuals recover
 at a 0.3 rate:
 
 ``` r
-library(epiworldRdev)
+library(epiworldR)
 
 # Creating a SIR model
 sir <- ModelSIR(
@@ -345,9 +345,9 @@ sir <- ModelSIR(
 net <- get_transmissions(sir)
 
 # Plotting
-library(epiworldRdev)
+library(epiworldR)
 #> Loading required package: grid
-library(epiworldRdev)
+library(epiworldR)
 #> 
 #> Attaching package: 'igraph'
 #> The following object is masked from 'package:netplot':

configure

@@ -4519,7 +4519,7 @@ sed -i -E 's/^useDynLib\([a-zA-Z]+/useDynLib('"${epiworldname}"'/g' NAMESPACE
 
 sed -i -E 's/^Package:.+/Package: '"${epiworldname}"'/g' DESCRIPTION
 
-sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{'"${epiworldname}"'/g' man/epiworldRfaster-package.Rd
+sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{'"${epiworldname}"'/g' man/epiworldR-package.Rd
 
 
 # configure is writing to config.log, and then calls config.status.

configure.ac

@@ -192,7 +192,7 @@ AC_CONFIG_COMMANDS_POST(
     )
 
 AC_CONFIG_COMMANDS_POST(
-    [sed -i -E 's/^\\(name|alias|title)\{[[a-zA-Z]]+/\\\1{'"${epiworldname}"'/g' man/epiworldRfaster-package.Rd]
+    [sed -i -E 's/^\\(name|alias|title)\{[[a-zA-Z]]+/\\\1{'"${epiworldname}"'/g' man/epiworldR-package.Rd]
     )
 
 AC_OUTPUT

inst/include/epiworld/agent-bones.hpp

@@ -102,8 +102,6 @@ class Agent {
     std::vector< ToolPtr<TSeq> > tools;
     epiworld_fast_uint n_tools = 0u;
 
-    epiworld_fast_uint action_counter = 0u;
-
     std::vector< Agent<TSeq> * > sampled_agents;
     size_t sampled_agents_n      = 0u;
     std::vector< size_t > sampled_agents_left;

inst/include/epiworld/agent-meat.hpp

@@ -27,8 +27,7 @@ inline Agent<TSeq>::Agent(Agent<TSeq> && p) :
     state_last_changed(p.state_last_changed),
     id(p.id),
     tools(std::move(p.tools)), /// Needs to be adjusted
-    n_tools(p.n_tools),
-    action_counter(p.action_counter)
+    n_tools(p.n_tools)
 {
 
     state = p.state;
@@ -138,8 +137,6 @@ inline Agent<TSeq> & Agent<TSeq>::operator=(
         tools[i] = std::make_shared<Tool<TSeq>>(*other_agent.tools[i]);
         tools[i]->set_agent(this, i);
     }
-
-    action_counter      = other_agent.action_counter;
 
     return *this;