Merge pull request #10 from UofUEpiBio/main

Simplifies code and add initial_state

Makefile

@@ -11,9 +11,18 @@ docker-debug:
 	EPI_CONFIG="-DEPI_DEBUG -Wall -pedantic -g" R CMD INSTALL \
 		--no-docs --build .
 
-install: build 
-	which R
-	cd ../ && R CMD INSTALL epiworldR_*.tar.gz
+install-dev: clean
+	sed -i -E 's/@useDynLib\s+[a-zA-Z]+/@useDynLib epiworldRdev/g' R/epiworldR-package.R
+	sed -i -E 's/useDynLib\(+[a-zA-Z]+/useDynLib(epiworldRdev/g' NAMESPACE
+	sed -i -E 's/^Package:.+/Package: epiworldRdev/g' DESCRIPTION 
+	sed -i -E 's/^library\([a-zA-Z]+\)/library(epiworldRdev)/g' README.*
+	Rscript --vanilla -e 'roxygen2::roxygenize()'
+	EPI_DEV=yes R CMD INSTALL .& $(MAKE) clean
+
+install:
+	$(MAKE) clean
+	R CMD INSTALL .
+
 
 README.md: README.Rmd
 	Rscript --vanilla -e 'rmarkdown::render("README.Rmd")'
@@ -29,6 +38,11 @@ check: build
 
 clean: 
 	Rscript --vanilla -e 'devtools::clean_dll()'
+	sed -i -E 's/@useDynLib\s+[a-zA-Z]+/@useDynLib epiworldR/g' R/epiworldR-package.R
+	sed -i -E 's/useDynLib\(+[a-zA-Z]+/useDynLib(epiworldR/g' NAMESPACE
+	sed -i -E 's/^Package:.+/Package: epiworldR/g' DESCRIPTION 
+	# sed -i -E 's/^\\(name|alias|title)\{[a-zA-Z]+/\\\1{epiworldR/g' man/epiworldR-package.Rd
+	sed -i -E 's/^library\([a-zA-Z]+\)/library(epiworldR)/g' README.*
 
 docs:
 	Rscript --vanilla -e 'devtools::document()'

NAMESPACE

@@ -106,7 +106,6 @@ export(get_agents)
 export(get_agents_data_ncols)
 export(get_agents_states)
 export(get_agents_tools)
-export(get_agents_viruses)
 export(get_generation_time)
 export(get_hist_tool)
 export(get_hist_total)
@@ -135,6 +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)

R/ModelSEIR.R

@@ -12,6 +12,11 @@
 #' @export
 #' @family Models
 #' @aliases epiworld_seir
+#' @details 
+#' The [initial_states] 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_states] 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_states] 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_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.
 #' @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_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 `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_states] 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_states] 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)
 }
@@ -427,11 +431,3 @@ get_name_virus_cpp <- function(virus) {
 set_name_virus_cpp <- function(virus, name) {
   .Call(`_epiworldR_set_name_virus_cpp`, virus, name)
 }
-
-get_agents_viruses_cpp <- function(model) {
-  .Call(`_epiworldR_get_agents_viruses_cpp`, model)
-}
-
-print_agent_viruses_cpp <- function(viruses) {
-  .Call(`_epiworldR_print_agent_viruses_cpp`, viruses)
-}

R/epiworldR-package.R.in

@@ -0,0 +1,5 @@
+#' @EPIWORLD_NAME@
+#' @useDynLib @EPIWORLD_NAME@, .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))
+
+}
+

R/virus.R

@@ -536,25 +536,6 @@ set_incubation_fun <- function(virus, model, vfun) {
 
 }
 
-#' @export
-#' @rdname agents_smallworld
-#' @returns 
-#' - `get_agents_viruses` returns a list of class `epiworld_agents_viruses`
-#' with `epiworld_viruses` (list of lists).
-get_agents_viruses <- function(model) {
-
-  stopifnot_model(model)
-
-  res <- lapply(
-      get_agents_viruses_cpp(model),
-      `class<-`,
-      "epiworld_viruses"
-    )
-
-  structure(res, class = c("epiworld_agents_viruses", class(res)))
-
-}
-
 #' @export 
 #' @rdname virus
 #' @param max_print Numeric scalar. Maximum number of viruses to print.

README.Rmd

@@ -71,10 +71,10 @@ library(epiworldR)
 
 # Creating a SIR model
 sir <- ModelSIR(
-  name           = "COVID-19",
-  prevalence     = .01,
+  name              = "COVID-19",
+  prevalence        = .01,
   transmission_rate = .7,
-  recovery       = .3
+  recovery          = .3
   ) |>
   # Adding a Small world population 
   agents_smallworld(n = 100000, k = 10, d = FALSE, p = .01) |>
@@ -204,9 +204,11 @@ sir <- ModelSIR(
 net <- get_transmissions(sir)
 
 # Plotting
+library(epiworldR)
 library(netplot)
-library(igraph)
-x <- graph_from_edgelist(as.matrix(net[,2:3]) + 1)
+x <- igraph::graph_from_edgelist(
+  as.matrix(net[,2:3]) + 1
+  )
 
 nplot(x, edge.curvature = 0, edge.color = "gray", skip.vertex=TRUE)
 ```

README.md

@@ -91,10 +91,10 @@ library(epiworldR)
 
 # Creating a SIR model
 sir <- ModelSIR(
-  name           = "COVID-19",
-  prevalence     = .01,
+  name              = "COVID-19",
+  prevalence        = .01,
   transmission_rate = .7,
-  recovery       = .3
+  recovery          = .3
   ) |>
   # Adding a Small world population 
   agents_smallworld(n = 100000, k = 10, d = FALSE, p = .01) |>
@@ -127,8 +127,8 @@ summary(sir)
 #> Number of entities  : 0
 #> Days (duration)     : 50 (of 50)
 #> Number of viruses   : 1
-#> Last run elapsed t  : 196.00ms
-#> Last run speed      : 25.43 million agents x day / second
+#> Last run elapsed t  : 166.00ms
+#> Last run speed      : 30.01 million agents x day / second
 #> Rewiring            : off
 #> 
 #> Global actions:
@@ -303,16 +303,16 @@ rn <- get_reproductive_number(model_logit)
 # Looking into the agents
 get_agents(model_logit)
 #> Agents from the model "Susceptible-Infected-Removed (SIR) (logit)":
-#> Agent: 0, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 1, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 2, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 3, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 4, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 5, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 6, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 7, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 8, state: Susceptible (0), Nvirus: 0, NTools: 0, NNeigh: 8
-#> Agent: 9, state: Recovered (2), Nvirus: 0, NTools: 0, NNeigh: 8
+#> Agent: 0, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 1, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 2, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 3, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 4, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 5, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 6, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 7, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 8, state: Susceptible (0), Has virus: no, NTools: 0, NNeigh: 8
+#> Agent: 9, state: Recovered (2), Has virus: no, NTools: 0, NNeigh: 8
 #> ... 99990 more agents ...
 ```
 
@@ -345,21 +345,12 @@ sir <- ModelSIR(
 net <- get_transmissions(sir)
 
 # Plotting
+library(epiworldR)
 library(netplot)
 #> Loading required package: grid
-library(igraph)
-#> 
-#> Attaching package: 'igraph'
-#> The following object is masked from 'package:netplot':
-#> 
-#>     ego
-#> The following objects are masked from 'package:stats':
-#> 
-#>     decompose, spectrum
-#> The following object is masked from 'package:base':
-#> 
-#>     union
-x <- graph_from_edgelist(as.matrix(net[,2:3]) + 1)
+x <- igraph::graph_from_edgelist(
+  as.matrix(net[,2:3]) + 1
+  )
 
 nplot(x, edge.curvature = 0, edge.color = "gray", skip.vertex=TRUE)
 ```
@@ -411,10 +402,10 @@ head(ans$reproductive)
 #>   sim_num virus_id    virus source source_exposure_date rt
 #> 1       1        0 COVID-19    767                   11  0
 #> 2       1        0 COVID-19    835                   10  0
-#> 3       1        0 COVID-19    466                    9  0
+#> 3       1        0 COVID-19    793                    9  0
 #> 4       1        0 COVID-19    612                    9  0
-#> 5       1        0 COVID-19    793                    9  0
-#> 6       1        0 COVID-19     20                    8  0
+#> 5       1        0 COVID-19    466                    9  0
+#> 6       1        0 COVID-19    920                    8  0
 
 plot(ans$reproductive)
 ```

configure

@@ -617,6 +617,7 @@ PACKAGE_URL=''
 
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
+EPIWORLD_NAME
 OPENMP_FLAG
 CXXCPP
 OBJEXT
@@ -3365,11 +3366,24 @@ printf "%s\n" "found and suitable" >&6; }
     fi
 fi
 
+# Checking if the development version is being built
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether to build the dev version" >&5
+printf %s "checking whether to build the dev version... " >&6; }
+epiworldname="epiworldR"
+if test x"${EPI_DEV}" != x"" ; then
+    epiworldname="epiworldRdev"
+fi
 
 ## now use all these
 OPENMP_FLAG="${openmp_flag}"
 
-ac_config_files="$ac_config_files src/Makevars"
+EPIWORLD_NAME="${epiworldname}"
+
+ac_config_files="$ac_config_files src/Makevars R/epiworldR-package.R"
+
+
+# Use sed to replace the line useDynLib\([a-zA-Z]+ in the NAMESPACE
+# file with useDynLib(${epiworldname}
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -4072,6 +4086,7 @@ for ac_config_target in $ac_config_targets
 do
   case $ac_config_target in
     "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;;
+    "R/epiworldR-package.R") CONFIG_FILES="$CONFIG_FILES R/epiworldR-package.R" ;;
 
   *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
   esac

configure.ac

@@ -169,8 +169,19 @@ if test x"${can_use_openmp}" = x"yes"; then
     fi
 fi
 
+# Checking if the development version is being built
+AC_MSG_CHECKING([whether to build the dev version])
+epiworldname="epiworldR"
+if test x"${EPI_DEV}" != x"" ; then
+    epiworldname="epiworldRdev"
+fi
 
 ## now use all these
 AC_SUBST([OPENMP_FLAG], ["${openmp_flag}"])
-AC_CONFIG_FILES([src/Makevars])
+AC_SUBST([EPIWORLD_NAME], ["${epiworldname}"])
+AC_CONFIG_FILES([src/Makevars R/epiworldR-package.R])
+
+# Use sed to replace the line useDynLib\([a-zA-Z]+ in the NAMESPACE
+# file with useDynLib(${epiworldname}
+
 AC_OUTPUT