restore sim.cs() and sim.cs.multi() to the export list

.gitignore

@@ -20,3 +20,4 @@ README_files
 NEWS.html
 NEWS_files
 **/.quarto/
+*.pdf

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.3.0.9019
+Version: 1.3.0.9020
 Authors@R: c(
     person("Peter", "Teunis", , "[email protected]", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

NAMESPACE

@@ -32,6 +32,8 @@ export(load_noise_params)
 export(load_pop_data)
 export(log_likelihood)
 export(serocalculator_example)
+export(sim.cs)
+export(sim.cs.multi)
 export(sim_pop_data)
 export(sim_pop_data_multi)
 export(strata)

NEWS.md

@@ -25,7 +25,7 @@
 * Extended `simulate_xsectionalData.Rmd` article to explore
 `renew_params = TRUE` vs `renew_params = FALSE` (#348)
 
-* Renamed variables for consistency (#281):
+* Renamed variables for consistency (#281, #373):
   - `sim.cs()` -> `sim_pop_data()` 
   - `sim.cs.multi()` -> `sim_pop_data_multi()`
 

R/sim_pop_data.R

@@ -93,7 +93,7 @@
     ...) {
   if (verbose > 1) {
     message("inputs to `sim_pop_data()`:")
-    print(environment() %>% as.list())
+    print(environment() |> as.list())
   }
 
 
@@ -105,18 +105,18 @@
   # and provide `curve_params` instead.
 
   predpar <-
-    curve_params %>%
-    filter(.data$antigen_iso %in% antigen_isos) %>%
-    droplevels() %>%
-    prep_curve_params_for_array() %>%
+    curve_params |>
+    filter(.data$antigen_iso %in% antigen_isos) |>
+    droplevels() |>
+    prep_curve_params_for_array() |>
     df_to_array(dim_var_names = c("antigen_iso", "parameter"))
 
   stopifnot(length(lambda) == 1)
 
   day2yr <- 365.25
   lambda <- lambda / day2yr
   age_range <- age_range * day2yr
-  npar <- dimnames(predpar)$parameter %>% length()
+  npar <- dimnames(predpar)$parameter |> length()
 
 
   baseline_limits <- noise_limits
@@ -149,8 +149,8 @@
   colnames(ysim) <- c("age", antigen_isos)
 
   to_return <-
-    ysim %>%
-    as_tibble() %>%
+    ysim |>
+    as_tibble() |>
     mutate(
       id = as.character(row_number()),
       age = round(.data$age / day2yr, 2)
@@ -159,15 +159,15 @@
   if (format == "long") {
     if (verbose) message("outputting long format data")
     to_return <-
-      to_return %>%
+      to_return |>
       pivot_longer(
         cols = all_of(antigen_isos),
         values_to = c("value"),
         names_to = c("antigen_iso")
-      ) %>%
+      ) |>
       structure(
         format = "long"
-      ) %>%
+      ) |>
       as_pop_data(
         value = "value",
         age = "age",
@@ -177,7 +177,7 @@
   } else {
     if (verbose) message("outputting wide format data")
     to_return <-
-      to_return %>%
+      to_return |>
       structure(
         class = c("pop_data_wide", class(to_return)),
         format = "wide"
@@ -194,21 +194,22 @@
 #'
 #' `sim.cs()` was renamed to [sim_pop_data()] to create a more
 #' consistent API.
-#'
 #' @keywords internal
-sim.cs <- function(
-    n.smpl,
-    age.rng,
-    n.mc,
-    renew.params,
-    add.noise,
-    ...) { # nolint: object_name_linter
+#' @export
+sim.cs <- function( # nolint: object_name_linter
+  n.smpl, # nolint: object_name_linter
+  age.rng, # nolint: object_name_linter
+  n.mc, # nolint: object_name_linter
+  renew.params, # nolint: object_name_linter
+  add.noise, # nolint: object_name_linter
+  ...) { # nolint: object_name_linter
   lifecycle::deprecate_soft("1.3.1", "sim.cs()", "sim_pop_data()")
   sim_pop_data(
     n_samples = n.smpl,
     age_range = age.rng,
     n_mcmc_samples = n.mc,
     renew_params = renew.params,
     add_noise = add.noise,
-    ...)
+    ...
+  )
 }

R/sim_pop_data_multi.R

@@ -57,7 +57,7 @@
     ...) {
   if (verbose) {
     message("inputs to `sim_pop_data_multi()`:")
-    print(environment() %>% as.list())
+    print(environment() |> as.list())
   }
 
   if (num_cores > 1L) {
@@ -69,7 +69,7 @@
       num_cores <- 2L
     } else {
       # use all cores in devtools::test()
-      num_cores <- num_cores %>% check_parallel_cores()
+      num_cores <- num_cores |> check_parallel_cores()
     }
 
 
@@ -104,7 +104,7 @@
       sim_pop_data(
         lambda = l,
         ...
-      ) %>%
+      ) |>
         mutate(lambda.sim = l, cluster = n)
     }
   doParallel::stopImplicitCluster()
@@ -121,6 +121,7 @@
 #' to create a more consistent API.
 #'
 #' @keywords internal
+#' @export
 sim.cs.multi <- function(...) { # nolint: object_name_linter
   lifecycle::deprecate_soft("1.3.1", "sim.cs.multi()", "sim_pop_data_multi()")
   sim_pop_data_multi(...)