Merge pull request #36 from UCD-SERG/sim.cs

Sim.cs
UCD-SERG · Nov 18, 2023 · 187140a · 187140a
2 parents 0f38691 + b740925
commit 187140a
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Showing 18 changed files with 140,591 additions and 1,650 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -33,7 +33,8 @@ Suggests:
     testthat (>= 3.0.0),
     readr,
     ggplot2,
-    bookdown
+    bookdown,
+    doParallel
 VignetteBuilder: knitr
 LazyData: true
 Encoding: UTF-8

diff --git a/NAMESPACE b/NAMESPACE
@@ -10,6 +10,7 @@ export(est.incidence.by)
 export(fdev)
 export(getAdditionalData)
 export(postprocess_fit)
+export(sim.cs)
 importFrom(Rcpp,sourceCpp)
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
@@ -21,6 +22,7 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,inner_join)
+importFrom(dplyr,is.grouped_df)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
 importFrom(dplyr,pull)
@@ -43,6 +45,7 @@ importFrom(stats,optim)
 importFrom(stats,pgamma)
 importFrom(stats,plnorm)
 importFrom(stats,qnorm)
+importFrom(stats,runif)
 importFrom(stats,xtabs)
 importFrom(tibble,as_tibble)
 importFrom(tibble,column_to_rownames)

diff --git a/R/df_to_array.R b/R/df_to_array.R
@@ -29,7 +29,7 @@ df_to_array = function(
   }
 
   all_factors  =
-    df |> select(dim_var_names) |> sapply(F = is.factor) |> all()
+    df |> select(dim_var_names) |> sapply(FUN = is.factor) |> all()
 
   if(!all_factors)
   {

diff --git a/R/prep_curve_params_for_array.R b/R/prep_curve_params_for_array.R
@@ -0,0 +1,13 @@
+prep_curve_params_for_array = function(data)
+{
+  data |>
+  mutate(y1 = .data$y1 - .data$y0) %>%
+    mutate(r = .data$r - 1) %>%
+    tidyr::pivot_longer(
+      names_to = "parameter",
+      cols = c("y0", "y1", "t1", "alpha", "r") ) |>
+    mutate(parameter = factor(.data$parameter, levels = unique(.data$parameter))) %>%
+    select(-any_of(c("Country", "ageCat"))) %>%
+    mutate(value = log(.data$value)) %>%
+    droplevels()
+}
diff --git a/R/serocalculator-package.R b/R/serocalculator-package.R
@@ -105,6 +105,7 @@
 #' @importFrom dplyr everything
 #' @importFrom dplyr filter
 #' @importFrom dplyr inner_join
+#' @importFrom dplyr is.grouped_df
 #' @importFrom dplyr mutate
 #' @importFrom dplyr n
 #' @importFrom dplyr pull
@@ -125,6 +126,7 @@
 #' @importFrom stats formula
 #' @importFrom stats nlm
 #' @importFrom stats qnorm
+#' @importFrom stats runif
 #' @importFrom stats xtabs
 #' @importFrom tibble as_tibble
 #' @importFrom tibble column_to_rownames