Merge branch 'main' into new-formula-for-proposed-transmission

R/probability_contain.R

@@ -70,13 +70,16 @@ probability_contain <- function(R,
 
   input_params <- missing(R) && missing(k)
   if (!xor(input_params, missing(offspring_dist))) {
-    stop("Only one of R and k or <epidist> must be supplied.", call. = FALSE)
+    stop(
+      "Only one of R and k or <epiparameter> must be supplied.",
+      call. = FALSE
+    )
   }
   # check inputs
   if (input_params) {
-    checkmate::assert_class(offspring_dist, classes = "epidist")
-    R <- get_epidist_param(epidist = offspring_dist, parameter = "R")
-    k <- get_epidist_param(epidist = offspring_dist, parameter = "k")
+    checkmate::assert_class(offspring_dist, classes = "epiparameter")
+    R <- get_epiparameter_param(epiparameter = offspring_dist, parameter = "R")
+    k <- get_epiparameter_param(epiparameter = offspring_dist, parameter = "k")
   }
   checkmate::assert_number(R, lower = 0, finite = TRUE)
   checkmate::assert_number(k, lower = 0)

R/probability_epidemic.R

@@ -20,8 +20,9 @@
 #' default optimisation settings. Currently only `"fit_method"` is accepted
 #' and can be either `"optim"` (default) or `"grid"` for numerical
 #' optimisation routine or grid search, respectively.
-#' @param offspring_dist An `<epidist>` object. An S3 class for working with
-#' epidemiological parameters/distributions, see [epiparameter::epidist()].
+#' @param offspring_dist An `<epiparameter>` object. An S3 class for working
+#' with epidemiological parameters/distributions, see
+#' [epiparameter::epiparameter()].
 #'
 #' @return A value with the probability of a large epidemic.
 #' @export
@@ -89,14 +90,17 @@ probability_extinct <- function(R,
                                 offspring_dist) {
   input_params <- missing(R) && missing(k)
   if (!xor(input_params, missing(offspring_dist))) {
-    stop("Only one of R and k or <epidist> must be supplied.", call. = FALSE)
+    stop(
+      "Only one of R and k or <epiparameter> must be supplied.",
+      call. = FALSE
+    )
   }
 
   # check inputs
   if (input_params) {
-    checkmate::assert_class(offspring_dist, classes = "epidist")
-    R <- get_epidist_param(epidist = offspring_dist, parameter = "R")
-    k <- get_epidist_param(epidist = offspring_dist, parameter = "k")
+    checkmate::assert_class(offspring_dist, classes = "epiparameter")
+    R <- get_epiparameter_param(epiparameter = offspring_dist, parameter = "R")
+    k <- get_epiparameter_param(epiparameter = offspring_dist, parameter = "k")
   }
 
   checkmate::assert_number(R, lower = 0, finite = TRUE)

R/proportion_cluster_size.R

@@ -44,15 +44,18 @@ proportion_cluster_size <- function(R, k, cluster_size, ..., offspring_dist,
                                     format_prop = TRUE) {
   input_params <- missing(R) && missing(k)
   if (!xor(input_params, missing(offspring_dist))) {
-    stop("Only one of R and k or <epidist> must be supplied.", call. = FALSE)
+    stop(
+      "Only one of R and k or <epiparameter> must be supplied.",
+      call. = FALSE
+    )
   }
 
   # check inputs
   chkDots(...)
   if (input_params) {
-    checkmate::assert_class(offspring_dist, classes = "epidist")
-    R <- get_epidist_param(epidist = offspring_dist, parameter = "R")
-    k <- get_epidist_param(epidist = offspring_dist, parameter = "k")
+    checkmate::assert_class(offspring_dist, classes = "epiparameter")
+    R <- get_epiparameter_param(epiparameter = offspring_dist, parameter = "R")
+    k <- get_epiparameter_param(epiparameter = offspring_dist, parameter = "k")
   }
   checkmate::assert_numeric(R, lower = 0, finite = TRUE)
   checkmate::assert_numeric(k, lower = 0)

R/proportion_transmission.R

@@ -131,16 +131,19 @@ proportion_transmission <- function(R, k,
                                     format_prop = TRUE) {
   input_params <- missing(R) && missing(k)
   if (!xor(input_params, missing(offspring_dist))) {
-    stop("Only one of R and k or <epidist> must be supplied.", call. = FALSE)
+    stop(
+      "Only one of R and k or <epiparameter> must be supplied.",
+      call. = FALSE
+    )
   }
   method <- match.arg(method)
 
   # check inputs
   chkDots(...)
   if (input_params) {
-    checkmate::assert_class(offspring_dist, classes = "epidist")
-    R <- get_epidist_param(epidist = offspring_dist, parameter = "R")
-    k <- get_epidist_param(epidist = offspring_dist, parameter = "k")
+    checkmate::assert_class(offspring_dist, classes = "epiparameter")
+    R <- get_epiparameter_param(epiparameter = offspring_dist, parameter = "R")
+    k <- get_epiparameter_param(epiparameter = offspring_dist, parameter = "k")
   }
   checkmate::assert_numeric(R, lower = 0, finite = TRUE)
   checkmate::assert_numeric(k, lower = 0)

R/utils.R

@@ -1,18 +1,18 @@
-#' Get a parameter out of <epidist>
+#' Get a parameter out of <epiparameter>
 #'
 #' @inheritParams probability_epidemic
 #' @param parameter A character string, either `"R"` or `"k"`.
 #'
 #' @return An unnamed numeric.
 #' @keywords internal
 #' @noRd
-get_epidist_param <- function(epidist,
-                              parameter = c("R", "k")) {
-  # check inputs (<epidist> already checked)
+get_epiparameter_param <- function(epiparameter,
+                                   parameter = c("R", "k")) {
+  # check inputs (<epiparameter> already checked)
   parameter <- match.arg(parameter)
 
-  # extract parameters from <epidist>
-  params <- epiparameter::get_parameters(epidist)
+  # extract parameters from <epiparameter>
+  params <- epiparameter::get_parameters(epiparameter)
 
   regexpr_pattern <- switch(parameter,
     R = "^r$|^r0$|^mean$",
@@ -28,7 +28,10 @@ get_epidist_param <- function(epidist,
   if (length(idx) == 0) {
     stop(
       sprintf(
-        "Cannot find %s in <epidist>, check if parameters have correct names.",
+        paste(
+          "Cannot find %s in <epiparameter>,",
+          "check if parameters have correct names."
+        ),
         parameter
       ),
       call. = FALSE

tests/testthat/_snaps/probability_contain.md

@@ -73,25 +73,25 @@
       "value": [0.7636]
     }
 
-# probability_contain works with <epidist>
+# probability_contain works with <epiparameter>
 
     Code
-      probability_contain(num_init_infect = 1, pop_control = 0.1, offspring_dist = edist)
+      probability_contain(num_init_infect = 1, pop_control = 0.1, offspring_dist = od)
     Output
       [1] 0.9037105
 
 ---
 
     Code
-      probability_contain(num_init_infect = 1, ind_control = 0.1, offspring_dist = edist)
+      probability_contain(num_init_infect = 1, ind_control = 0.1, offspring_dist = od)
     Output
       [1] 0.9133394
 
 ---
 
     Code
       probability_contain(num_init_infect = 5, ind_control = 0.1, pop_control = 0.1,
-        offspring_dist = edist)
+        offspring_dist = od)
     Output
       [1] 0.7168911
 

tests/testthat/_snaps/probability_epidemic.md

@@ -41,10 +41,10 @@
     Output
       [1] 0.1084924
 
-# probability_epidemic works with <epidist>
+# probability_epidemic works with <epiparameter>
 
     Code
-      probability_epidemic(num_init_infect = 1, offspring_dist = edist)
+      probability_epidemic(num_init_infect = 1, offspring_dist = od)
     Output
       [1] 0.1198705
 

tests/testthat/_snaps/proportion_transmission.md

@@ -65,10 +65,10 @@
     Output
       [1] 0.264419
 
-# proportion_transmission works with <epidist>
+# proportion_transmission works with <epiparameter>
 
     Code
-      proportion_transmission(percent_transmission = 0.8, offspring_dist = edist)
+      proportion_transmission(percent_transmission = 0.8, offspring_dist = od)
     Output
            R    k prop_80
       1 1.63 0.16     13%

tests/testthat/test-probability_contain.R

@@ -91,29 +91,29 @@ test_that("probability_contain works as when using dots", {
   )
 })
 
-test_that("probability_contain works with <epidist>", {
+test_that("probability_contain works with <epiparameter>", {
   skip_if_not_installed(pkg = "epiparameter")
-  edist <- suppressMessages(
-    epiparameter::epidist_db(
+  od <- suppressMessages(
+    epiparameter::epiparameter_db(
       disease = "SARS",
       epi_dist = "offspring distribution",
       author = "Lloyd-Smith",
-      single_epidist = TRUE
+      single_epiparameter = TRUE
     )
   )
   expect_snapshot(
     probability_contain(
       num_init_infect = 1,
       pop_control = 0.1,
-      offspring_dist = edist
+      offspring_dist = od
     )
   )
 
   expect_snapshot(
     probability_contain(
       num_init_infect = 1,
       ind_control = 0.1,
-      offspring_dist = edist
+      offspring_dist = od
     )
   )
 
@@ -122,7 +122,7 @@ test_that("probability_contain works with <epidist>", {
       num_init_infect = 5,
       ind_control = 0.1,
       pop_control = 0.1,
-      offspring_dist = edist
+      offspring_dist = od
     )
   )
 })
@@ -148,9 +148,9 @@ test_that("probability_contain fails using dots with incorrect name", {
   )
 })
 
-test_that("probability_contain fails without R and k or <epidist>", {
+test_that("probability_contain fails without R and k or <epiparameter>", {
   expect_error(
     probability_contain(num_init_infect = 1, pop_control = 0.5),
-    regexp = "Only one of R and k or <epidist> must be supplied."
+    regexp = "Only one of R and k or <epiparameter> must be supplied."
   )
 })

tests/testthat/test-probability_epidemic.R

@@ -94,25 +94,25 @@ test_that("probability_epidemic works for R > 1", {
   )
 })
 
-test_that("probability_epidemic works with <epidist>", {
+test_that("probability_epidemic works with <epiparameter>", {
   skip_if_not_installed(pkg = "epiparameter")
-  edist <- suppressMessages(
-    epiparameter::epidist_db(
+  od <- suppressMessages(
+    epiparameter::epiparameter_db(
       disease = "SARS",
       epi_dist = "offspring distribution",
       author = "Lloyd-Smith",
-      single_epidist = TRUE
+      single_epiparameter = TRUE
     )
   )
   expect_snapshot(
-    probability_epidemic(num_init_infect = 1, offspring_dist = edist)
+    probability_epidemic(num_init_infect = 1, offspring_dist = od)
   )
 })
 
-test_that("probability_epidemic fails without R and k or <epidist>", {
+test_that("probability_epidemic fails without R and k or <epiparameter>", {
   expect_error(
     probability_epidemic(num_init_infect = 1),
-    regexp = "Only one of R and k or <epidist> must be supplied."
+    regexp = "Only one of R and k or <epiparameter> must be supplied."
   )
 })
 

tests/testthat/test-proportion_cluster_size.R

@@ -84,17 +84,17 @@ test_that("proportion_cluster_size fails as expected", {
   )
 })
 
-test_that("proportion_cluster_size works with <epidist>", {
+test_that("proportion_cluster_size works with <epiparameter>", {
   skip_if_not_installed(pkg = "epiparameter")
-  edist <- suppressMessages(
-    epiparameter::epidist_db(
+  od <- suppressMessages(
+    epiparameter::epiparameter_db(
       disease = "SARS",
       epi_dist = "offspring distribution",
       author = "Lloyd-Smith",
-      single_epidist = TRUE
+      single_epiparameter = TRUE
     )
   )
-  res <- proportion_cluster_size(cluster_size = 20, offspring_dist = edist)
+  res <- proportion_cluster_size(cluster_size = 20, offspring_dist = od)
 
   expect_s3_class(res, "data.frame")
   expect_identical(dim(res), c(1L, 3L))
@@ -104,9 +104,9 @@ test_that("proportion_cluster_size works with <epidist>", {
   )
 })
 
-test_that("proportion_cluster_size fails without R and k or <epidist>", {
+test_that("proportion_cluster_size fails without R and k or <epiparameter>", {
   expect_error(
     proportion_cluster_size(cluster_size = 10),
-    regexp = "Only one of R and k or <epidist> must be supplied."
+    regexp = "Only one of R and k or <epiparameter> must be supplied."
   )
 })