Run {styler}

R/add_cols.R

@@ -223,7 +223,8 @@ NULL
  infector_names <- data.frame(id = .data$id, infector_name = .data$case_name)
  col_order <- c(colnames(.data), "infector_name")
  .data <- merge(
- .data, infector_names, by.x = "infector", by.y = "id", all.x = TRUE
+ .data, infector_names,
+ by.x = "infector", by.y = "id", all.x = TRUE
  )
  .data <- .data[order(is.na(.data$infector_name), decreasing = TRUE), ]
  .data <- .data[col_order]

R/checkers.R

@@ -57,7 +57,6 @@
 #' invalid.
 #' @keywords internal
 .check_age_df <- function(x) {
-
  # check input
  stopifnot(
  "column names should be 'age_range' & 'proportion'" =
@@ -140,7 +139,7 @@
  stopifnot(
  "population_age must be two numerics or a data.frame" =
  is.numeric(population_age) && length(population_age) == 2 ||
- is.data.frame(population_age)
+  is.data.frame(population_age)
  )
 
  if (sim_type == "linelist" || sim_type == "outbreak") {
@@ -159,13 +158,13 @@
  sum(case_type_probs) == 1,
  "hosp_rate must be a single numeric or a data.frame" =
  is.numeric(hosp_rate) && length(hosp_rate) == 1 ||
- is.data.frame(hosp_rate),
+  is.data.frame(hosp_rate),
  "hosp_death_rate must be a single numeric or a data.frame" =
  is.numeric(hosp_death_rate) && length(hosp_death_rate) == 1 ||
- is.data.frame(hosp_death_rate),
+  is.data.frame(hosp_death_rate),
  "non_hosp_death_rate must be a single numeric or a data.frame" =
  is.numeric(non_hosp_death_rate) && length(non_hosp_death_rate) == 1 ||
- is.data.frame(non_hosp_death_rate)
+  is.data.frame(non_hosp_death_rate)
  )
  }
 

R/create_linelist.R

@@ -56,7 +56,6 @@
 #' @return A `<data.frame>`.
 #' @keywords internal
 .create_linelist <- function(scenario) {
-
  scenario <- match.arg(
  arg = scenario,
  choices = c(

R/dev-utils.R

@@ -5,5 +5,4 @@ release_bullets <- function() { # nocov start
  "Run `goodpractice::gp()`",
  "Review [WORDLIST](https://docs.cran.dev/spelling#wordlist)"
  )
-
 } # nocov end

R/sim_contacts.R

@@ -49,7 +49,6 @@ sim_contacts <- function(R,
  ),
  config = create_config(),
  ...) {
-
  chkDots(...)
 
  .check_sim_input(

R/sim_contacts_tbl.R

@@ -11,7 +11,6 @@
  population_age,
  contact_tracing_status_probs,
  config) {
-
  if (!"infector_name" %in% colnames(.data)) {
  .data <- .add_names(.data = .data)
  }
@@ -20,7 +19,8 @@
  .data,
  select = c(
  "infector", "infector_name", "case_name", "age", "gender",
- "date_first_contact", "date_last_contact")
+ "date_first_contact", "date_last_contact"
+ )
  )
  colnames(contact_investigation) <- c(
  "infector", "from", "to", "cnt_age", "cnt_gender",
@@ -43,7 +43,7 @@
  nrow(other_contacts)
  )
 
- #Multiply row by times specified in frequency column V
+ # Multiply row by times specified in frequency column V
  other_contacts <-
  other_contacts[rep(row.names(other_contacts), contact_freq), ]
 
@@ -73,7 +73,7 @@
  replace = TRUE
  )
 
- #Add corresponding names acc to the gender V
+ # Add corresponding names acc to the gender V
  other_contacts$to <- randomNames::randomNames(
  which.names = "both",
  name.sep = " ",

R/sim_linelist.R

@@ -135,7 +135,6 @@ sim_linelist <- function(R,
  ),
  config = create_config(),
  ...) {
-
  chkDots(...)
 
  .check_sim_input(

README.Rmd

@@ -123,10 +123,10 @@ If both the line list and contacts table are required, they can be jointly simul
 
 ```{r, sim-outbreak}
 outbreak <- sim_outbreak(
- R = 1.1, 
- serial_interval = serial_interval, 
- onset_to_hosp = onset_to_hosp, 
- onset_to_death = onset_to_death, 
+ R = 1.1,
+ serial_interval = serial_interval,
+ onset_to_hosp = onset_to_hosp,
+ onset_to_death = onset_to_death,
  contact_distribution = contact_distribution
 )
 head(outbreak$linelist)

README.md

@@ -102,20 +102,20 @@ linelist <- sim_linelist(
  onset_to_death = onset_to_death
 )
 head(linelist)
-#> id case_name case_type gender age onset_date
-#> 1 1 Wajdi al-Matar probable  m 69 2023-01-01
-#> 2 2 Brandon Meeks confirmed m 14 2023-01-01
-#> 3 3 Darrien Fernandez confirmed  m 72 2023-01-02
-#> 4 4  Jalond Ramos probable   m 66 2023-01-02
-#> 5 5  Rudy Sanchez Vergara probable m 24 2023-01-03
-#> 6 6 Abdul Jabbaar al-Koroma suspected  m 86 2023-01-02
-#> hospitalisation_date date_first_contact date_last_contact
-#> 1  <NA> <NA> <NA>
-#> 2 2023-01-08  2022-12-28 2023-01-02
-#> 3  <NA> 2023-01-01 2023-01-04
-#> 4  2023-01-04 2023-01-01 2023-01-05
-#> 5  <NA> 2022-12-29 2023-01-04
-#> 6 2023-01-04  2022-12-31 2023-01-04
+#> id case_name case_type gender age date_onset date_admission
+#> 1 1  Aliyah Bunck suspected  f 84 2023-01-01 2023-01-03
+#> 2 2  Rayel Roman confirmed f 62 2023-01-01 <NA>
+#> 3 3   Alex Fuentes suspected m 53 2023-01-01  2023-01-02
+#> 4 4 Nusaiba al-Wahab confirmed f 6 2023-01-02 <NA>
+#> 5 5 Monica Alvarez Valentin probable f 86 2023-01-02 <NA>
+#> 6 6   Adelaide Weible confirmed f 39 2023-01-02 <NA>
+#> date_death date_first_contact date_last_contact
+#> 1 <NA> <NA> <NA>
+#> 2 <NA> 2022-12-30 2023-01-04
+#> 3 2023-01-26 2023-01-01 2023-01-04
+#> 4 <NA> 2023-01-01 2023-01-05
+#> 5 2023-01-19 2023-01-03 2023-01-04
+#> 6 <NA> 2023-01-05 2023-01-07
 ```
 
 In this example, the line list is simulated using the default values
@@ -134,20 +134,20 @@ linelist <- sim_linelist(
  outbreak_start_date = as.Date("2019-12-01")
 )
 head(linelist)
-#> id  case_name case_type gender age onset_date
-#> 1 1     Ghaazi al-Shad probable  m 5 2019-12-01
-#> 2 2     Uriel Vigil confirmed m 38 2019-12-01
-#> 3 3    Azhaar al-Mussa suspected m 21 2019-12-02
-#> 4 4    Kabeer el-Khatib suspected m 22 2019-12-01
-#> 5 5 Dhipthika Rezaie-Khodabandelou probable  f 52 2019-12-02
-#> 6 6    Kalyn Lovejoy suspected f 67 2019-12-03
-#> hospitalisation_date date_first_contact date_last_contact
-#> 1  <NA> <NA> <NA>
-#> 2  <NA> 2019-11-29 2019-12-04
-#> 3  <NA> 2019-11-26 2019-12-01
-#> 4  <NA> 2019-11-28 2019-12-01
-#> 5  <NA> 2019-11-30 2019-12-03
-#> 6  <NA> 2019-12-03 2019-12-04
+#> id case_name case_type gender age date_onset date_admission date_death
+#> 1 1 Melissa Moralez confirmed f 41 2019-12-01   <NA>   <NA>
+#> 2 2 Lorna Gries suspected f 72 2019-12-01   <NA> <NA>
+#> 3 3 Saood el-Salik suspected m 39 2019-12-01   <NA> <NA>
+#> 4 4 Antonio Trujillo probable m 61 2019-12-02   <NA> <NA>
+#> 5 5  Aaron Kimble confirmed  m 3 2019-12-01 <NA> <NA>
+#> 6 6 Gage Declaw confirmed m 6 2019-12-02   <NA> 2019-12-14
+#> date_first_contact date_last_contact
+#> 1 <NA> <NA>
+#> 2 2019-11-28 2019-12-03
+#> 3 2019-11-28 2019-12-01
+#> 4 2019-12-03 2019-12-06
+#> 5 2019-12-02 2019-12-03
+#> 6 2019-11-30 2019-12-04
 ```
 
 To simulate a table of contacts we can reuse the serial interval from
@@ -170,20 +170,20 @@ contacts <- sim_contacts(
  contact_distribution = contact_distribution
 )
 head(contacts)
-#>  part_name contact_name cnt_age cnt_gender date_first_contact
-#> 1 Macario Sandoval   David Torres  63  m 2022-12-29
-#> 2 Macario Sandoval Dong Sung Abraham 84  m  2022-12-31
-#> 3 Macario Sandoval  Callie Lakkaraju  59  f 2022-12-29
-#> 4 Macario Sandoval Isaac Pinedo Carrillo 39 m 2022-12-31
-#> 5  David Torres Aydee Luna Gonzalez 32  f 2022-12-28
-#> 6  David Torres  Ric Noble 74 m 2023-01-03
+#> from   to cnt_age cnt_gender date_first_contact
+#> 1 Ryan Xiong Fawz el-Noor  89 m 2023-01-03
+#> 2 Ryan Xiong  Oleta Knapp  2  f  2023-01-02
+#> 3 Ryan Xiong Yohana Bontrager  24 f 2022-12-31
+#> 4 Ryan Xiong Danyelle Dowdell  3 f 2023-01-03
+#> 5 Ryan Xiong Lorena Dominguez   66  f 2023-01-02
+#> 6 Ryan Xiong Jonathan Kercher  89 m 2023-01-03
 #> date_last_contact was_case status
-#> 1 2023-01-03 Y case
-#> 2 2023-01-02 N under_followup
+#> 1 2023-01-04 Y case
+#> 2 2023-01-03 Y  case
 #> 3 2023-01-04 N under_followup
-#> 4 2023-01-04 N  under_followup
-#> 5 2023-01-03 Y case
-#> 6 2023-01-05 N lost_to_followup
+#> 4 2023-01-06 N lost_to_followup
+#> 5 2023-01-05 N lost_to_followup
+#> 6 2023-01-06 N  under_followup
 ```
 
 If both the line list and contacts table are required, they can be
@@ -194,42 +194,42 @@ the same default settings as the other functions).
 
 ``` r
 outbreak <- sim_outbreak(
- R = 1.1, 
- serial_interval = serial_interval, 
- onset_to_hosp = onset_to_hosp, 
- onset_to_death = onset_to_death, 
+ R = 1.1,
+ serial_interval = serial_interval,
+ onset_to_hosp = onset_to_hosp,
+ onset_to_death = onset_to_death,
  contact_distribution = contact_distribution
 )
 head(outbreak$linelist)
-#> id  case_name case_type gender age onset_date
-#> 1 1   Simon Garver confirmed m 50 2023-01-01
-#> 2 2   Anthony Tomas suspected m 78 2023-01-01
-#> 3 3 Abdul Maalik al-Mahdavi probable m 40 2023-01-02
-#> 4 4   Saabiqa al-Pour suspected  f 4 2023-01-02
-#> 5 5   Alexis Martin probable  f 68 2023-01-02
-#> 6 6  Desiree Shackelford confirmed f 82 2023-01-02
-#> hospitalisation_date date_first_contact date_last_contact
-#> 1  2023-01-07 <NA> <NA>
-#> 2  <NA> 2023-01-06 2023-01-07
-#> 3  <NA> 2023-01-01 2023-01-04
-#> 4  <NA> 2022-12-28 2023-01-03
-#> 5  2023-01-03 2022-12-30 2023-01-03
-#> 6  <NA> 2022-12-29 2023-01-04
+#> id case_name case_type gender age date_onset date_admission
+#> 1 1 Albert Brown suspected  m 78 2023-01-01 <NA>
+#> 2 2 Martin Menning probable  m 32 2023-01-01 <NA>
+#> 3 3  Drayas Fenton probable m 85 2023-01-01 <NA>
+#> 4 4 Michael Wilkerson suspected m 60 2023-01-02 2023-01-07
+#> 5 5 Essence Fadler probable  f 86 2023-01-01  <NA>
+#> 6 6 Erika Trujillo confirmed f 15 2023-01-02 <NA>
+#> date_death date_first_contact date_last_contact
+#> 1 2023-01-23 <NA> <NA>
+#> 2 2023-01-11 2022-12-31 2023-01-03
+#> 3 <NA> 2023-01-02 2023-01-07
+#> 4 2023-01-18 2022-12-28 2023-01-02
+#> 5 2023-01-12 2023-01-05 2023-01-05
+#> 6 <NA> 2023-01-02 2023-01-06
 head(outbreak$contacts)
-#> part_name contact_name cnt_age cnt_gender date_first_contact
-#> 1 Simon Garver    Anthony Tomas  78  m 2023-01-06
-#> 2 Simon Garver Abdul Maalik al-Mahdavi  40 m 2023-01-01
-#> 3 Simon Garver   Katherine Smit 42 f 2022-12-31
-#> 4 Simon Garver   Judy Ragoschke  6  f  2023-01-02
-#> 5 Simon Garver   Zuhair al-Ishak  70  m  2023-01-01
-#> 6 Simon Garver   Donna Cummings 20  f 2022-12-31
-#> date_last_contact was_case  status
-#> 1 2023-01-07 Y  case
-#> 2 2023-01-04 Y  case
-#> 3 2023-01-03 N  under_followup
-#> 4 2023-01-03 N  under_followup
-#> 5 2023-01-04 N lost_to_followup
-#> 6 2023-01-04 N lost_to_followup
+#> from  to cnt_age cnt_gender date_first_contact
+#> 1  Albert Brown Martin Menning  32 m 2022-12-31
+#> 2  Albert Brown  Drayas Fenton  85  m 2023-01-02
+#> 3  Albert Brown Areli Vigil  6 f 2022-12-30
+#> 4  Albert Brown Long Farley  25  m  2023-01-01
+#> 5  Albert Brown Abigail Zagal  17  f  2023-01-03
+#> 6 Martin Menning Michael Wilkerson 60   m 2022-12-28
+#> date_last_contact was_case status
+#> 1 2023-01-03 Y case
+#> 2 2023-01-07 Y case
+#> 3 2023-01-03 N under_followup
+#> 4 2023-01-04 N under_followup
+#> 5 2023-01-05 N under_followup
+#> 6 2023-01-02 Y case
 ```
 
 ## Help
@@ -257,16 +257,18 @@ citation("simulist")
 #> To cite package 'simulist' in publications use:
 #> 
 #> Lambert J, Tamayo C (2023). _simulist: Tools to Simulated Line list
-#> Data_. https://github.com/epiverse-trace/simulist,
-#> https://epiverse-trace.github.io/simulist/.
+#> Data_. R package version 0.0.0.9000,
+#> https://epiverse-trace.github.io/simulist/,
+#> <https://github.com/epiverse-trace/simulist>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #> @Manual{,
 #> title = {simulist: Tools to Simulated Line list Data},
 #> author = {Joshua W. Lambert and Carmen Tamayo},
 #> year = {2023},
-#> note = {https://github.com/epiverse-trace/simulist,
+#> note = {R package version 0.0.0.9000, 
 #> https://epiverse-trace.github.io/simulist/},
+#> url = {https://github.com/epiverse-trace/simulist},
 #> }
 ```

tests/testthat/test-create_config.R

@@ -4,9 +4,11 @@ test_that("create_config works as expected with defaults", {
  expect_length(config, 6)
  expect_named(
  config,
- c("last_contact_distribution", "last_contact_distribution_params",
+ c(
+ "last_contact_distribution", "last_contact_distribution_params",
  "first_contact_distribution", "first_contact_distribution_params",
- "ct_distribution", "ct_distribution_params")
+ "ct_distribution", "ct_distribution_params"
+ )
  )
 })
 
@@ -16,9 +18,11 @@ test_that("create_config works as expected modifying element", {
  expect_length(config, 6)
  expect_named(
  config,
- c("last_contact_distribution", "last_contact_distribution_params",
+ c(
+ "last_contact_distribution", "last_contact_distribution_params",
  "first_contact_distribution", "first_contact_distribution_params",
- "ct_distribution", "ct_distribution_params")
+ "ct_distribution", "ct_distribution_params"
+ )
  )
  expect_identical(config$last_contact_distribution, "geom")
 })
@@ -30,9 +34,11 @@ test_that("create_config works as expected misspelling modifying element", {
  expect_length(config, 6)
  expect_named(
  config,
- c("last_contact_distribution", "last_contact_distribution_params",
+ c(
+ "last_contact_distribution", "last_contact_distribution_params",
  "first_contact_distribution", "first_contact_distribution_params",
- "ct_distribution", "ct_distribution_params")
+ "ct_distribution", "ct_distribution_params"
+ )
  )
  expect_identical(config$last_contact_distribution, "pois")
 })