epiverse-trace · joshwlambert · Apr 29, 2024 · Apr 25, 2024 · Apr 25, 2024 · Apr 25, 2024
diff --git a/R/checkers.R b/R/checkers.R
@@ -123,7 +123,6 @@
                              onset_to_death = NULL,
                              onset_to_recovery = NULL,
                              add_names = NULL,
-                             add_ct = NULL,
                              case_type_probs = NULL,
                              contact_tracing_status_probs = NULL,
                              hosp_risk = NULL,
@@ -149,7 +148,6 @@
     .check_func_req_args(onset_to_death, func_name = "onset_to_death")
     .check_func_req_args(onset_to_recovery, func_name = "onset_to_recovery")
     checkmate::assert_logical(add_names, len = 1)
-    checkmate::assert_logical(add_ct, len = 1)
     checkmate::assert_numeric(case_type_probs, len = 3, lower = 0, upper = 1)
     checkmate::assert_names(
       names(case_type_probs),

diff --git a/R/sim_internal.R b/R/sim_internal.R
@@ -23,7 +23,6 @@
                           non_hosp_death_risk = NULL,
                           outbreak_start_date,
                           add_names = NULL,
-                          add_ct = NULL,
                           outbreak_size,
                           population_age,
                           case_type_probs = NULL,
@@ -142,14 +141,12 @@
     )
 
     # add Ct if confirmed
-    if (add_ct) {
-      .data <- .add_ct(
-        .data = .data,
-        distribution = config$ct_distribution,
-        config$ct_distribution_params
-      )
-      linelist_cols <- c(linelist_cols, "ct_value")
-    }
+    .data <- .add_ct(
+      .data = .data,
+      distribution = config$ct_distribution,
+      config$ct_distribution_params
+    )
+    linelist_cols <- c(linelist_cols, "ct_value")
   }
 
   if (sim_type %in% c("contacts", "outbreak")) {

diff --git a/R/sim_linelist.R b/R/sim_linelist.R
@@ -67,10 +67,6 @@
 #' @param outbreak_start_date A `date` for the start of the outbreak.
 #' @param add_names A `logical` boolean for whether to add names to each row
 #' of the line list. Default is `TRUE`.
-#' @param add_ct A `logical` boolean for whether to add Ct values to each
-#' confirmed case and `NA` otherwise for each case in the line list.
-#' Default is `TRUE`. Ct refers to the Cycle threshold from a Real-time
-#' PCR or quantitative PCR (qPCR).
 #' @param outbreak_size A `numeric` vector of length 2 defining the minimum and
 #' the maximum number of infected individuals for the simulated outbreak.
 #' Default is `c(10, 1e4)`, so the minimum outbreak size is 10 infected
@@ -92,7 +88,7 @@
 #' each case type. The names of the vector must be `"suspected"`, `"probable"`,
 #' `"confirmed"`. Values of each case type must sum to one.
 #' @param config A list of settings to adjust the randomly sampled delays and
-#' Ct values (if `add_ct = TRUE`). See [create_config()] for more information.
+#' Ct values. See [create_config()] for more information.
 #'
 #' @return A line list `<data.frame>`
 #' @export
@@ -167,7 +163,6 @@ sim_linelist <- function(contact_distribution,
                          non_hosp_death_risk = 0.05,
                          outbreak_start_date = as.Date("2023-01-01"),
                          add_names = TRUE,
-                         add_ct = TRUE,
                          outbreak_size = c(10, 1e4),
                          population_age = c(1, 90),
                          case_type_probs = c(
@@ -203,7 +198,6 @@ sim_linelist <- function(contact_distribution,
     onset_to_death = onset_to_death,
     onset_to_recovery = onset_to_recovery,
     add_names = add_names,
-    add_ct = add_ct,
     case_type_probs = case_type_probs,
     hosp_risk = hosp_risk,
     hosp_death_risk = hosp_death_risk,
@@ -261,7 +255,6 @@ sim_linelist <- function(contact_distribution,
     non_hosp_death_risk = non_hosp_death_risk,
     outbreak_start_date = outbreak_start_date,
     add_names = add_names,
-    add_ct = add_ct,
     outbreak_size = outbreak_size,
     population_age = population_age,
     case_type_probs = case_type_probs,

diff --git a/R/sim_outbreak.R b/R/sim_outbreak.R
@@ -64,7 +64,6 @@ sim_outbreak <- function(contact_distribution,
                          non_hosp_death_risk = 0.05,
                          outbreak_start_date = as.Date("2023-01-01"),
                          add_names = TRUE,
-                         add_ct = TRUE,
                          outbreak_size = c(10, 1e4),
                          population_age = c(1, 90),
                          case_type_probs = c(
@@ -105,7 +104,6 @@ sim_outbreak <- function(contact_distribution,
     onset_to_death = onset_to_death,
     onset_to_recovery = onset_to_recovery,
     add_names = add_names,
-    add_ct = add_ct,
     case_type_probs = case_type_probs,
     contact_tracing_status_probs = contact_tracing_status_probs,
     hosp_risk = hosp_risk,
@@ -164,7 +162,6 @@ sim_outbreak <- function(contact_distribution,
     non_hosp_death_risk = non_hosp_death_risk,
     outbreak_start_date = outbreak_start_date,
     add_names = add_names,
-    add_ct = add_ct,
     outbreak_size = outbreak_size,
     population_age = population_age,
     case_type_probs = case_type_probs,

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -18,12 +18,16 @@ reference:
     - create_config
 
 articles:
-- title: Package Vignettes
-  navbar: Package Vignettes
+- title: Customising simulated outbreak
+  navbar: Customising simulated outbreak
   contents:
   - age-strat-risks
   - age-struct-pop
   - time-varying-cfr
+- title: Wrangling and plotting data
+  navbar: Wrangling and plotting data
+  contents:
+  - wrangling-linelist
   - vis-linelist
 - title: Developer Documentation
   navbar: Developer Documentation

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -2,6 +2,7 @@ aes
 apyramid
 bookdown
 bw
+Çetinkaya
 cfr
 CMD
 codecov
@@ -13,6 +14,7 @@ COVID
 Ct
 ct
 db
+Deon
 df
 dist
 dplyr
@@ -27,6 +29,7 @@ facetted
 ggplot
 gh
 github
+Grolemund
 implmented
 infector
 integerish
@@ -36,6 +39,8 @@ lifecycle
 Lifecycle
 linelist
 lintr
+Lusseau
+Mancini
 md
 MERS
 olds
@@ -52,8 +57,9 @@ qPCR
 randomNames
 RECON
 redocumented
-rmarkdown
 resimulate
+rmarkdown
+Rundel
 SARS
 sensu
 sim
@@ -65,6 +71,7 @@ tabset
 testthat
 threejs
 tidyr
+tidyverse
 Tidyverse
 visNetwork
 yaml
diff --git a/man/dot-add_date.Rd b/man/dot-add_date.Rd
diff --git a/man/dot-check_sim_input.Rd b/man/dot-check_sim_input.Rd
diff --git a/man/dot-sim_internal.Rd b/man/dot-sim_internal.Rd
diff --git a/man/dot-sim_network_bp.Rd b/man/dot-sim_network_bp.Rd
diff --git a/man/sim_contacts.Rd b/man/sim_contacts.Rd
diff --git a/man/sim_linelist.Rd b/man/sim_linelist.Rd
diff --git a/man/sim_outbreak.Rd b/man/sim_outbreak.Rd
diff --git a/tests/testthat/_snaps/sim_linelist.md b/tests/testthat/_snaps/sim_linelist.md
@@ -66,40 +66,6 @@
       11         <NA>         2023-01-01        2023-01-04       NA
       12         <NA>         2023-01-01        2023-01-03       NA
 
-# sim_linelist works as expected without Ct
-
-    Code
-      sim_linelist(contact_distribution = contact_distribution, infect_period = infect_period,
-        prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death,
-        add_ct = FALSE)
-    Output
-         id              case_name case_type sex age date_onset date_admission
-      1   1        Dominic Sundara  probable   m  35 2023-01-01           <NA>
-      2   2     Preston Montgomery suspected   m  43 2023-01-01           <NA>
-      3   3          Reece Chittum  probable   m   1 2023-01-01           <NA>
-      4   5          Michael Cheek confirmed   m  78 2023-01-01           <NA>
-      5   6         Jennifer Smith confirmed   f  22 2023-01-01           <NA>
-      6   8         Erika Quintero confirmed   f  28 2023-01-01           <NA>
-      7  11       Isaiah Patterson suspected   m  46 2023-01-01     2023-01-13
-      8  12        Cicely Anderson suspected   f  67 2023-01-01           <NA>
-      9  13           Michael John  probable   m  86 2023-01-01     2023-01-01
-      10 18 Giovana Magana Aguirre suspected   f  60 2023-01-02           <NA>
-      11 20       Mudrik al-Hallal suspected   m  49 2023-01-02           <NA>
-      12 22          Tea Slaughter  probable   f   7 2023-01-02     2023-01-02
-           outcome date_outcome date_first_contact date_last_contact
-      1  recovered         <NA>               <NA>              <NA>
-      2  recovered         <NA>         2022-12-30        2023-01-05
-      3  recovered         <NA>         2022-12-30        2023-01-02
-      4  recovered         <NA>         2022-12-29        2023-01-02
-      5  recovered         <NA>         2023-01-01        2023-01-03
-      6  recovered         <NA>         2023-01-03        2023-01-04
-      7  recovered         <NA>         2023-01-04        2023-01-05
-      8  recovered         <NA>         2023-01-01        2023-01-04
-      9       died   2023-01-12         2022-12-31        2023-01-03
-      10 recovered         <NA>         2022-12-30        2023-01-03
-      11 recovered         <NA>         2023-01-01        2023-01-04
-      12 recovered         <NA>         2023-01-01        2023-01-03
-
 # sim_linelist works as expected with anonymous
 
     Code

diff --git a/tests/testthat/test-checkers.R b/tests/testthat/test-checkers.R
@@ -187,7 +187,6 @@ test_that(".check_sim_input works as expected", {
     onset_to_death = onset_to_death,
     onset_to_recovery = onset_to_recovery,
     add_names = TRUE,
-    add_ct = FALSE,
     case_type_probs = c(
       suspected = 0.2,
       probable = 0.3,
@@ -217,7 +216,6 @@ test_that(".check_sim_input works as expected", {
     onset_to_death = onset_to_death,
     onset_to_recovery = onset_to_recovery,
     add_names = TRUE,
-    add_ct = FALSE,
     case_type_probs = c(
       suspected = 0.2,
       probable = 0.3,
@@ -261,7 +259,6 @@ test_that(".check_sim_input works as expected with NA risks", {
     onset_to_death = onset_to_death,
     onset_to_recovery = onset_to_recovery,
     add_names = TRUE,
-    add_ct = FALSE,
     case_type_probs = c(
       suspected = 0.2,
       probable = 0.3,