update onset-to-event and risk args in sim_linelist and sim_outbreak …

…to use NULL instead of NA, closes #147

R/add_cols.R

@@ -97,8 +97,8 @@ NULL
   .data$hospitalisation[infected_lgl_idx] <- .data$time[infected_lgl_idx] +
     onset_to_hosp(num_infected)
 
-  # hosp_risk is either numeric or <data.frame> or NA
-  if (!rlang::is_lgl_na(hosp_risk)) {
+  # hosp_risk is either numeric or <data.frame> or NULL
+  if (!is.null(hosp_risk)) {
     if (is.numeric(hosp_risk)) {
       # size is converted to an integer internally in sample()
       pop_sample <- sample(
@@ -146,9 +146,9 @@ NULL
 
   # internal function only called in .add_outcome()
   # assign deaths using population or age-stratified death risk
-  # if risk is NA then no deaths are assigned
+  # if risk is NULL then no deaths are assigned
   apply_death_risk <- function(.data, risk, idx, config) {
-    if (!rlang::is_lgl_na(risk)) {
+    if (!is.null(risk)) {
       # single population risk is a special case of the age-strat risk
       # convert population risk to data.frame to apply the same operations
       if (is.numeric(risk)) {

R/checkers.R

@@ -159,13 +159,13 @@
         sum(case_type_probs) == 1,
       "hosp_risk must be a single numeric or a data.frame" =
         is.numeric(hosp_risk) || is.data.frame(hosp_risk) ||
-        rlang::is_lgl_na(hosp_risk),
+        is.null(hosp_risk),
       "hosp_death_risk must be a single numeric or a data.frame" =
         is.numeric(hosp_death_risk) || is.data.frame(hosp_death_risk) ||
-        rlang::is_lgl_na(hosp_death_risk),
+        is.null(hosp_death_risk),
       "non_hosp_death_risk must be a single numeric or a data.frame" =
         is.numeric(non_hosp_death_risk) || is.data.frame(non_hosp_death_risk) ||
-        rlang::is_lgl_na(non_hosp_death_risk)
+        is.null(non_hosp_death_risk)
     )
     if (is.numeric(hosp_risk)) {
       checkmate::assert_number(hosp_risk, lower = 0, upper = 1)
@@ -244,18 +244,18 @@
 #' @description
 #' There are two types of cross-checking:
 #' 1. If the onset-to-event distribution is specified but the corresponding risk
-#' is not specified (i.e. `NA`) the function will error ([stop()]).
-#' 2. If the onset-to-event distribution is not specified (i.e. `NA`) but the
+#' is not specified (i.e. `NULL`) the function will error ([stop()]).
+#' 2. If the onset-to-event distribution is not specified (i.e. `NULL`) but the
 #' corresponding risk is specified the function will throw a warning
 #' ([warning()]).
 #'
 #' The difference in condition handling is because in the case that the
-#' onset-to-event is `NA` the simulation can safely ignore the corresponding
+#' onset-to-event is `NULL` the simulation can safely ignore the corresponding
 #' risk, while throwing a warning, as there are no events. In other words, if
 #' the onset-to-hospitalisation is not specified, no infected individuals will
 #' go to hospital and the `date_admission` column in the line list will all be
 #' `NA`s. However, if the onset-to-event is specified and the corresponding
-#' risk is `NA` then the proportion of individuals infected that are
+#' risk is `NULL` then the proportion of individuals infected that are
 #' hospitalised or die cannot be calculated and therefore the simulation
 #' cannot run. It is in this latter case that the cross-checking throws an
 #' error.
@@ -272,7 +272,7 @@
                                    hosp_death_risk,
                                    non_hosp_death_risk) {
   # hosp_risk, hosp_death_risk and non_hosp_death_risk can assumed to be a
-  # number or a <data.frame> or NA as they will have been checked by
+  # number or a <data.frame> or NULL as they will have been checked by
   # .check_sim_input() before calling .cross_check_sim_input
   # onset_to_hosp and onset_to_death will be closures
 
@@ -281,23 +281,23 @@
   onset_to_death_eval <- onset_to_death(1)
 
   msg <- character(0)
-  # risks can only be NA when the onset to event is also NA
-  if (!rlang::is_lgl_na(onset_to_hosp_eval) && rlang::is_lgl_na(hosp_risk)) {
+  # risks can only be NULL when the onset to event is NA
+  if (!rlang::is_lgl_na(onset_to_hosp_eval) && is.null(hosp_risk)) {
     msg <- c(msg, paste(
-      "hosp_risk is set to NA but onset_to_hosp is specified \n",
+      "hosp_risk is set to NULL but onset_to_hosp is specified \n",
       "set hosp_risk to numeric value"
     ))
   }
   if (!rlang::is_lgl_na(onset_to_death_eval)) {
-    if (rlang::is_lgl_na(hosp_death_risk) && !rlang::is_lgl_na(hosp_risk)) {
+    if (is.null(hosp_death_risk) && !is.null(hosp_risk)) {
       msg <- c(msg, paste(
-        "hosp_death_risk is set to NA but hosp_risk and onset_to_death is",
+        "hosp_death_risk is set to NULL but hosp_risk and onset_to_death is",
         "specified \n set hosp_death_risk to numeric value"
       ))
     }
-    if (rlang::is_lgl_na(non_hosp_death_risk)) {
+    if (is.null(non_hosp_death_risk)) {
       msg <- c(msg, paste(
-        "non_hosp_death_risk is set to NA but onset_to_death is specified \n",
+        "non_hosp_death_risk is set to NULL but onset_to_death is specified \n",
         "set non_hosp_death_risk to numeric value"
       ))
     }
@@ -314,37 +314,37 @@
       checkmate::test_number(hosp_risk) ||
       rlang::is_lgl_na(onset_to_hosp_eval) && is.data.frame(hosp_risk)) {
     msg <- c(msg, paste(
-      "onset_to_hosp is set to NA but hosp_risk is specified \n",
-      "hosp_risk is being ignored, set hosp_risk to NA when",
-      "onset_to_hosp is NA"
+      "onset_to_hosp is set to NULL but hosp_risk is specified \n",
+      "hosp_risk is being ignored, set hosp_risk to NULL when",
+      "onset_to_hosp is NULL"
     ))
   }
   if (rlang::is_lgl_na(onset_to_hosp_eval) &&
       checkmate::test_number(hosp_death_risk) ||
       rlang::is_lgl_na(onset_to_hosp_eval) && is.data.frame(hosp_death_risk)) {
     msg <- c(msg, paste(
-      "onset_to_hosp is set to NA but hosp_death_risk is specified \n",
-      "hosp_death_risk is being ignored, set hosp_death_risk to NA when",
-      "onset_to_hosp is NA"
+      "onset_to_hosp is set to NULL but hosp_death_risk is specified \n",
+      "hosp_death_risk is being ignored, set hosp_death_risk to NULL when",
+      "onset_to_hosp is NULL"
     ))
   }
   if (rlang::is_lgl_na(onset_to_death_eval) &&
       checkmate::test_number(hosp_death_risk) ||
       rlang::is_lgl_na(onset_to_death_eval) && is.data.frame(hosp_death_risk)) {
     msg <- c(msg, paste(
-      "onset_to_death is set to NA but hosp_death_risk is specified \n",
-      "hosp_death_risk is being ignored, set hosp_death_risk to NA when",
-      "onset_to_death is NA"
+      "onset_to_death is set to NULL but hosp_death_risk is specified \n",
+      "hosp_death_risk is being ignored, set hosp_death_risk to NULL when",
+      "onset_to_death is NULL"
     ))
   }
   if (rlang::is_lgl_na(onset_to_death_eval) &&
       checkmate::test_number(non_hosp_death_risk) ||
       rlang::is_lgl_na(onset_to_death_eval) &&
       is.data.frame(non_hosp_death_risk)) {
     msg <- c(msg, paste(
-      "onset_to_death is set to NA but non_hosp_death_risk is specified \n",
-      "non_hosp_death_risk is being ignored, set non_hosp_death_risk to NA",
-      "when onset_to_death is NA"
+      "onset_to_death is set to NULL but non_hosp_death_risk is specified \n",
+      "non_hosp_death_risk is being ignored, set non_hosp_death_risk to NULL",
+      "when onset_to_death is NULL"
     ))
   }
   if (length(msg) > 0) {

R/sim_linelist.R

@@ -34,33 +34,33 @@
 #' @param prob_infection A single `numeric` for the probability of a secondary
 #' contact being infected by an infected primary contact.
 #' @param onset_to_hosp An `<epidist>` object, an anonymous function for
-#' the onset to hospitalisation delay distribution, or `NA` to not simulate
+#' the onset to hospitalisation delay distribution, or `NULL` to not simulate
 #' hospitalisation (admission) dates.
 #' @param onset_to_death An `<epidist>` object, an anonymous function for
-#' the onset to death delay distribution, or `NA` to not simulate dates for
+#' the onset to death delay distribution, or `NULL` to not simulate dates for
 #' individuals that died.
 #' @param onset_to_recovery An `<epidist>` object, an anonymous function for
-#' the onset to death delay distribution, or `NA` to not simulate dates for
-#' individuals that recovered. Default is `NA` so by default cases that
+#' the onset to death delay distribution, or `NULL` to not simulate dates for
+#' individuals that recovered. Default is `NULL` so by default cases that
 #' recover get an `NA` in the `$date_outcome` line list column.
 #' @param hosp_risk Either a single `numeric` for the hospitalisation risk of
 #' everyone in the population, or a `<data.frame>` with age specific
 #' hospitalisation risks Default is 20% hospitalisation (`0.2`) for the entire
-#' population. If the `onset_to_hosp` argument is set to `NA` this argument
-#' should also be set to `NA`. See details and examples for more information.
+#' population. If the `onset_to_hosp` argument is set to `NULL` this argument
+#' should also be set to `NULL`. See details and examples for more information.
 #' @param hosp_death_risk Either a single `numeric` for the death risk for
 #' hospitalised individuals across the population, or a `<data.frame>` with age
 #' specific hospitalised death risks Default is 50% death risk in hospitals
 #' (`0.5`) for the entire population. If the `onset_to_death` argument is set
-#' to `NA` this argument should also be set to `NA`. See details and examples
-#' for more information. If a time-varying death risk is specified in the
-#' `config` the `hosp_death_risk` is interpreted as the maximum risk across
+#' to `NULL` this argument should also be set to `NULL`. See details and
+#' examples for more information. If a time-varying death risk is specified in
+#' the `config` the `hosp_death_risk` is interpreted as the maximum risk across
 #' the epidemic.
 #' @param non_hosp_death_risk Either a single `numeric` for the death risk for
 #' outside of hospitals across the population, or a `<data.frame>` with age
 #' specific death risks outside of hospitals. Default is 5% death risk outside
 #' of hospitals  (`0.05`) for the entire population. If the `onset_to_death`
-#' argument is set to `NA` this argument should also be set to `NA`. See
+#' argument is set to `NULL` this argument should also be set to `NULL`. See
 #' details and examples for more information. If a time-varying death risk is
 #' specified in the `config` the `non_hosp_death_risk` is interpreted as the
 #' maximum risk across the epidemic.
@@ -157,7 +157,7 @@ sim_linelist <- function(contact_distribution,
                          prob_infection,
                          onset_to_hosp,
                          onset_to_death,
-                         onset_to_recovery = NA,
+                         onset_to_recovery = NULL,
                          hosp_risk = 0.2,
                          hosp_death_risk = 0.5,
                          non_hosp_death_risk = 0.05,

R/sim_outbreak.R

@@ -58,7 +58,7 @@ sim_outbreak <- function(contact_distribution,
                          prob_infection,
                          onset_to_hosp,
                          onset_to_death,
-                         onset_to_recovery = NA,
+                         onset_to_recovery = NULL,
                          hosp_risk = 0.2,
                          hosp_death_risk = 0.5,
                          non_hosp_death_risk = 0.05,

R/utils.R

@@ -120,11 +120,11 @@
   out
 }
 
-#' Convert `<epidist>` or `NA` to function
+#' Convert `<epidist>` or `NULL` to function
 #'
 #' @description
 #' An extension to [as.function()], particularly the \pkg{epiparameter}
-#' `as.function` S3 method, with the added feature that [`NA`]s are converted
+#' `as.function` S3 method, with the added feature that [`NULL`]s are converted
 #' into functions that generate a vector of `NA`s to behave equivalently to
 #' the generator functions output from
 #' `as.function(..., func_type = "generate")`.
@@ -133,9 +133,9 @@
 #' unchanged.
 #'
 #' There is also input checking to error if input is not an `<epidist>`,
-#' `function` ([closure]), or for onset-to-event distributions `NA`.
+#' `function` ([closure]), or for onset-to-event distributions `NULL`.
 #'
-#' @param x A named list containing either `<epidist>`, `function` or `NA`.
+#' @param x A named list containing either `<epidist>`, `function` or `NULL`.
 #' Named list elements are: `"contact_distribution"`, `"infectious_period"`,
 #' `"onset_to_hosp"`, `"onset_to_death"`, `"onset_to_recovery".`
 #'
@@ -147,29 +147,29 @@ as_function <- function(x) {
       inherits(x$contact_distribution, c("function", "epidist")) &&
       inherits(x$infectious_period, c("function", "epidist")),
     "onset_to_hosp, onset_to_death and onset_to_recovery need to be a function,
-    <epidist> or NA" =
-      inherits(x$onset_to_hosp, c("function", "epidist")) ||
-      rlang::is_lgl_na(x$onset_to_hosp) &&
-      inherits(x$onset_to_death, c("function", "epidist")) ||
-      rlang::is_lgl_na(x$onset_to_death)
+    <epidist> or NULL" =
+      (inherits(x$onset_to_hosp, c("function", "epidist")) ||
+      is.null(x$onset_to_hosp)) &&
+      (inherits(x$onset_to_death, c("function", "epidist")) ||
+      is.null(x$onset_to_death))
   )
   contact_distribution <- as.function(
     x$contact_distribution, func_type = "density"
   )
   infectious_period <- as.function(x$infectious_period, func_type = "generate")
-  if (rlang::is_lgl_na(x$onset_to_hosp)) {
+  if (is.null(x$onset_to_hosp)) {
     # function to generate NA instead of hospitalisation times
     onset_to_hosp <- function(x) rep(NA, times = x)
   } else {
     onset_to_hosp <- as.function(x$onset_to_hosp, func_type = "generate")
   }
-  if (rlang::is_lgl_na(x$onset_to_death)) {
+  if (is.null(x$onset_to_death)) {
     # function to generate NA instead of death times
     onset_to_death <- function(x) rep(NA, times = x)
   } else {
     onset_to_death <- as.function(x$onset_to_death, func_type = "generate")
   }
-  if (rlang::is_lgl_na(x$onset_to_recovery)) {
+  if (is.null(x$onset_to_recovery)) {
     # function to generate NA instead of recovery times
     onset_to_recovery <- function(x) rep(NA, times = x)
   } else {