Adding defunct message

NAMESPACE

@@ -98,8 +98,10 @@ export(add_entity)
 export(add_globalevent)
 export(add_tool)
 export(add_tool_agent)
+export(add_tool_n)
 export(add_virus)
 export(add_virus_agent)
+export(add_virus_n)
 export(agents_from_edgelist)
 export(agents_smallworld)
 export(change_state)

NEWS.md

@@ -1,12 +1,15 @@
-# epiworldR 0.2-1 (dev)
+# epiworldR 0.3-0 (dev)
 
 * 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.
+  specified in the object itself. `add_tool_n` and `add_virus_n` are now
+  deprecated.
+
+* `globalaction_*` are now defunct. Use `globalevent_*` instead.
 
 
 # epiworldR 0.1-0`

R/functions-renamed.R

@@ -1,7 +1,34 @@
-#' Deprecated functions in epiworldR
+#' Deprecated and removed functions in epiworldR
 #' @description
 #' Starting version 0.0-4, epiworld changed how it refered to "actions."
 #' Following more traditional ABMs, actions are now called "events."
+#' 
 #' @param ... Arguments to be passed to the new function.
+#' @param model Model object of class `epiworld_model`.
+#' @param tool Tool object of class `epiworld_tool`.
+#' @param virus Virus object of class `epiworld_virus`.
 #' @name epiworldR-deprecated
-NULL
+NULL
+
+#' @param n Deprecated. Either set the prevalence during the tool/virus
+#' initialization or use `set_prevalence_tool`/`set_prevalence_virus`.
+#' @export 
+#' @rdname epiworldR-deprecated
+add_tool_n <- function(model, tool, n) {
+
+  .Deprecated(new = "add_tool")
+
+  set_prevalence_tool(tool, n, as_proportion = FALSE)
+  add_tool(model, tool)
+
+}
+
+#' @export 
+#' @rdname epiworldR-deprecated
+add_virus_n <- function(model, virus, n) {
+
+  .Deprecated(new = "add_virus")
+  set_prevalence_virus(virus, n, as_proportion = FALSE)
+  add_virus(model, virus)
+
+}

R/global-actions.R

@@ -91,12 +91,10 @@ globalevent_tool <- function(
 #' @rdname epiworldR-deprecated
 globalaction_tool <- function(...) {
 
-  .Deprecated(
+  .Defunct(
     new = "globalevent_tool"
-    )  
+    )
 
-  globalevent_tool(...)
-
 }
 
 #' @export
@@ -134,7 +132,7 @@ globalevent_tool_logit <- function(
 #' @rdname epiworldR-deprecated
 globalaction_tool_logit <- function(...) {
 
-  .Deprecated(
+  .Defunct(
     new = "globalevent_tool_logit"
     )  
 
@@ -172,7 +170,8 @@ globalevent_set_params <- function(
 #' @rdname epiworldR-deprecated
 globalaction_set_params <- function(...) {
 
-  .Deprecated(
+
+  .Defunct(
     new = "globalevent_set_params"
     )  
 
@@ -234,7 +233,7 @@ globalevent_fun <- function(
 #' @rdname epiworldR-deprecated
 globalaction_fun <- function(...) {
 
-  .Deprecated(
+  .Defunct(
     new = "globalevent_fun"
     )  
 

R/tool.R

@@ -142,14 +142,31 @@ get_name_tool <- function(tool) {
 
 #' @export
 #' @param tool An object of class `epiworld_tool`
+#' @param proportion Deprecated. Either set the prevalence during the tool
+#' initialization or use `set_prevalence_tool`.
 #' @details 
 #' The `add_tool` function adds the specified tool to the model of class 
 #' [epiworld_model] with specified proportion.
 #' @rdname tool
-add_tool <- function(model, tool) UseMethod("add_tool")
+add_tool <- function(model, tool, proportion) {
+
+  if (!missing(proportion)) {
+
+    warning(
+      "The 'proportion' argument is deprecated. ",
+      "Use 'set_prevalence_tool' instead."
+      )
+
+    set_prevalence_tool(tool, proportion, TRUE)
+
+  }
+
+  UseMethod("add_tool")
+
+}
 
 #' @export
-add_tool.epiworld_model <- function(model, tool) {
+add_tool.epiworld_model <- function(model, tool, proportion) {
 
   stopifnot_tool(tool)
   add_tool_cpp(model, tool)

R/virus.R

@@ -143,13 +143,30 @@ get_name_virus <- function(virus) {
 #' @rdname virus
 #' @param model An object of class `epiworld_model`.
 #' @param virus An object of class `epiworld_virus`
+#' @param proportion Deprecated. Either set the prevalence during the virus
+#' initialization or use `set_prevalence_virus`.
 #' @returns 
 #' - The `add_virus` function does not return a value, instead it adds the 
 #' virus of choice to the model object of class [epiworld_model].
-add_virus <- function(model, virus) UseMethod("add_virus")
+add_virus <- function(model, virus, proportion) {
+
+  if (!missing(proportion)) {
+
+    warning(
+      "The argument 'proportion' is deprecated and will be removed in ",
+      "the next version."
+      )
+
+    set_prevalence_virus(virus, proportion, as_proportion = TRUE)
+
+  }
+
+  UseMethod("add_virus")
+
+}
 
 #' @export
-add_virus.epiworld_model <- function(model, virus) {
+add_virus.epiworld_model <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   add_virus_cpp(model, virus)
@@ -158,7 +175,7 @@ add_virus.epiworld_model <- function(model, virus) {
 }
 
 #' @export
-add_virus.epiworld_sir <- function(model, virus) {
+add_virus.epiworld_sir <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   virus_set_state(virus, init = 1, end = 2, removed = 2)
@@ -167,7 +184,7 @@ add_virus.epiworld_sir <- function(model, virus) {
 }
 
 #' @export
-add_virus.epiworld_sird <- function(model, virus) {
+add_virus.epiworld_sird <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   virus_set_state(virus, init = 1, end = 2, removed = 3)
@@ -176,15 +193,15 @@ add_virus.epiworld_sird <- function(model, virus) {
 }
 
 #' @export
-add_virus.epiworld_sirconn <- function(model, virus) {
+add_virus.epiworld_sirconn <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   add_virus.epiworld_sir(model, virus)
 
 }
 
 #' @export
-add_virus.epiworld_sirdconn <- function(model, virus) {
+add_virus.epiworld_sirdconn <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   add_virus.epiworld_sird(model, virus)
@@ -193,7 +210,7 @@ add_virus.epiworld_sirdconn <- function(model, virus) {
 
 
 #' @export
-add_virus.epiworld_seir <- function(model, virus) {
+add_virus.epiworld_seir <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   virus_set_state(virus, init = 1, end = 3, removed = 3)
@@ -202,7 +219,7 @@ add_virus.epiworld_seir <- function(model, virus) {
 }
 
 #' @export
-add_virus.epiworld_seird <- function(model, virus) {
+add_virus.epiworld_seird <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   virus_set_state(virus, init = 1, end = 3, removed = 4)
@@ -211,15 +228,15 @@ add_virus.epiworld_seird <- function(model, virus) {
 }
 
 #' @export
-add_virus.epiworld_seirconn <- function(model, virus) {
+add_virus.epiworld_seirconn <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   add_virus.epiworld_seir(model, virus)
 
 }
 
 #' @export
-add_virus.epiworld_seirdconn <- function(model, virus) {
+add_virus.epiworld_seirdconn <- function(model, virus, proportion) {
 
   stopifnot_virus(virus)
   add_virus.epiworld_seird(model, virus)

README.md

@@ -140,8 +140,8 @@ summary(sir)
 #> Number of entities  : 0
 #> Days (duration)     : 50 (of 50)
 #> Number of viruses   : 1
-#> Last run elapsed t  : 162.00ms
-#> Last run speed      : 30.85 million agents x day / second
+#> Last run elapsed t  : 163.00ms
+#> Last run speed      : 30.49 million agents x day / second
 #> Rewiring            : off
 #> 
 #> Global events:
@@ -197,7 +197,16 @@ model_seirconn <- ModelSEIRCONN(
   incubation_days     = 7, 
   transmission_rate   = 0.1,
   recovery_rate       = 1/7
-) |> add_virus(virus("COVID-19", 0.01, 0.6, 0.5, 7), .5)
+) |> add_virus(
+    virus(
+      name = "COVID-19",
+      prevalence = 0.01,
+      as_proportion = TRUE,
+      prob_infecting = 0.01,
+      recovery_rate = 0.6,
+      prob_death = 0.5,
+      incubation = 7
+    ))
 
 set.seed(132)
 run(model_seirconn, ndays = 100)
@@ -219,16 +228,16 @@ summary(model_seirconn)
 #> Number of entities  : 0
 #> Days (duration)     : 100 (of 100)
 #> Number of viruses   : 2
-#> Last run elapsed t  : 34.00ms
-#> Last run speed      : 29.33 million agents x day / second
+#> Last run elapsed t  : 36.00ms
+#> Last run speed      : 27.62 million agents x day / second
 #> Rewiring            : off
 #> 
 #> Global events:
 #>  - Update infected individuals (runs daily)
 #> 
 #> Virus(es):
 #>  - COVID-19 (baseline prevalence: 1.00%)
-#>  - COVID-19 (baseline prevalence: 50.00%)
+#>  - COVID-19 (baseline prevalence: 1.00%)
 #> 
 #> Tool(s):
 #>  (none)
@@ -240,15 +249,15 @@ summary(model_seirconn)
 #>  - Prob. Transmission   : 0.1000
 #> 
 #> Distribution of the population at time 100:
-#>   - (0) Susceptible :  4900 -> 229
-#>   - (1) Exposed     :  5100 -> 8
-#>   - (2) Infected    :     0 -> 27
-#>   - (3) Recovered   :     0 -> 9736
+#>   - (0) Susceptible :  9800 -> 13
+#>   - (1) Exposed     :   200 -> 0
+#>   - (2) Infected    :     0 -> 1
+#>   - (3) Recovered   :     0 -> 9986
 #> 
 #> Transition Probabilities:
-#>  - Susceptible  0.97  0.03  0.00  0.00
+#>  - Susceptible  0.94  0.06  0.00  0.00
 #>  - Exposed      0.00  0.86  0.14  0.00
-#>  - Infected     0.00  0.00  0.78  0.22
+#>  - Infected     0.00  0.00  0.85  0.15
 #>  - Recovered    0.00  0.00  0.00  1.00
 ```
 
@@ -269,13 +278,13 @@ head(plot(repnum))
 
 <img src="man/figures/README-seir-conn-figures-2.png" width="100%" />
 
-    #>   virus_id    virus date      avg  n       sd lb   ub
-    #> 1        0 COVID-19    0 3.671053 76 3.012809  1 12.0
-    #> 2        0 COVID-19    2 2.714286  7 4.347961  0 10.8
-    #> 3        0 COVID-19    3 3.461538 13 4.539005  0 12.8
-    #> 4        0 COVID-19    4 3.307692 13 3.923957  0 12.1
-    #> 5        0 COVID-19    5 2.074074 27 2.615427  0  9.0
-    #> 6        0 COVID-19    6 3.421053 19 2.968647  0  9.1
+    #>   virus_id    virus date      avg  n       sd  lb   ub
+    #> 1        0 COVID-19    0 5.615385 91 4.832228 1.0 17.0
+    #> 2        0 COVID-19    2 5.000000  9 3.605551 0.2 10.4
+    #> 3        0 COVID-19    3 6.000000 13 5.049752 0.0 13.0
+    #> 4        0 COVID-19    4 4.592593 27 3.885469 0.0 12.7
+    #> 5        0 COVID-19    5 4.846154 26 4.920913 0.0 14.5
+    #> 6        0 COVID-19    6 4.236842 38 3.241906 0.0 12.0
 
 ``` r
 
@@ -284,13 +293,13 @@ head(plot_generation_time(model_seirconn))
 
 <img src="man/figures/README-seir-conn-figures-3.png" width="100%" />
 
-    #>   date       avg  n       sd ci_lower ci_upper    virus virus_id
-    #> 1    2  3.250000  4 1.258306    2.075    4.850 COVID-19        0
-    #> 2    3 11.600000 10 8.733079    2.000   26.975 COVID-19        0
-    #> 3    4 11.545455 11 6.890046    4.000   23.000 COVID-19        0
-    #> 4    5  9.666667 18 8.791707    2.425   30.775 COVID-19        0
-    #> 5    6  9.571429 14 6.618323    2.650   24.450 COVID-19        0
-    #> 6    7 10.045455 22 6.168100    2.525   25.900 COVID-19        0
+    #>   date      avg  n       sd ci_lower ci_upper    virus virus_id
+    #> 1    2 7.125000  8 2.474874      2.7    9.825 COVID-19        0
+    #> 2    3 8.090909 11 7.203534      2.0   23.750 COVID-19        0
+    #> 3    4 6.708333 24 4.338695      2.0   16.425 COVID-19        0
+    #> 4    5 7.428571 21 4.738897      2.0   15.500 COVID-19        0
+    #> 5    6 7.628571 35 4.173345      2.0   15.300 COVID-19        0
+    #> 6    7 6.921053 38 4.675304      2.0   16.150 COVID-19        0
 
 ## SIR Logit