update tests and snapshots using new epiparameter constructor signature

tests/testthat/_snaps/epiparameter.md

@@ -1,8 +1,8 @@
 # epiparameter.print works as expected
 
     Code
-      epiparameter(disease = "ebola", epi_dist = "incubation", prob_distribution = "gamma",
-        prob_distribution_params = c(shape = 1, scale = 1))
+      epiparameter(disease = "ebola", epi_dist = "incubation", prob_distribution = create_prob_distribution(
+        prob_distribution = "gamma", prob_distribution_params = c(shape = 1, scale = 1)))
     Message
       Citation cannot be created as author, year, journal or title is missing
     Output
@@ -18,8 +18,9 @@
 ---
 
     Code
-      epiparameter(disease = "ebola", epi_dist = "incubation", prob_distribution = "gamma",
-        prob_distribution_params = c(shape = 1, scale = 1), discretise = TRUE)
+      epiparameter(disease = "ebola", epi_dist = "incubation", prob_distribution = create_prob_distribution(
+        prob_distribution = "gamma", prob_distribution_params = c(shape = 1, scale = 1),
+        discretise = TRUE))
     Message
       Citation cannot be created as author, year, journal or title is missing
     Output

tests/testthat/_snaps/print.md

@@ -23,8 +23,8 @@
       <https://doi.org/10.1016/S1473-3099%2809%2970069-6>.
       Distribution: lnorm
       Parameters:
-        meanlog: 1.247
-        sdlog: 0.975
+        meanlog: 1.723
+        sdlog: 0.231
       
       [[2]]
       Disease: Human Coronavirus
@@ -37,8 +37,8 @@
       <https://doi.org/10.1016/S1473-3099%2809%2970069-7>.
       Distribution: lnorm
       Parameters:
-        meanlog: 0.742
-        sdlog: 0.918
+        meanlog: 1.163
+        sdlog: 0.140
       
       [[3]]
       Disease: SARS
@@ -51,8 +51,8 @@
       <https://doi.org/10.1016/S1473-3099%2809%2970069-8>.
       Distribution: lnorm
       Parameters:
-        meanlog: 0.660
-        sdlog: 1.205
+        meanlog: 1.386
+        sdlog: 0.593
       
       # i 122 more elements
       # i Use `print(n = ...)` to see more elements.

tests/testthat/test-accessors.R

@@ -11,7 +11,7 @@ test_that("get_parameters works as expected for unparameterised epiparameter", {
     epiparameter(
       disease = "Ebola",
       epi_dist = "incubation period",
-      prob_distribution = "gamma"
+      prob_distribution = create_prob_distribution(prob_distribution = "gamma")
     )
   )
   expect_true(is.na(get_parameters(ep)))
@@ -22,8 +22,10 @@ test_that("get_parameters works as expected for continuous epiparameter", {
     epiparameter(
       disease = "Ebola",
       epi_dist = "incubation period",
-      prob_distribution = "gamma",
-      prob_distribution_params = c(shape = 1, scale = 1)
+      prob_distribution = create_prob_distribution(
+        prob_distribution = "gamma",
+        prob_distribution_params = c(shape = 1, scale = 1)
+      )
     )
   )
   params <- get_parameters(ep)
@@ -36,9 +38,11 @@ test_that("get_parameters works as expected for discretised epiparameter", {
     epiparameter(
       disease = "Ebola",
       epi_dist = "incubation period",
-      prob_distribution = "gamma",
-      prob_distribution_params = c(shape = 1, scale = 1),
-      discretise = TRUE
+      prob_distribution = create_prob_distribution(
+        prob_distribution = "gamma",
+        prob_distribution_params = c(shape = 1, scale = 1),
+        discretise = TRUE
+      )
     )
   )
   params <- get_parameters(ep)
@@ -66,8 +70,10 @@ test_that("get_citation works as expected for manual epiparameter", {
     epiparameter(
       disease = "ebola",
       epi_dist = "incubation_period",
-      prob_distribution = "gamma",
-      prob_distribution_params = c(shape = 1, scale = 1),
+      prob_distribution = create_prob_distribution(
+        prob_distribution = "gamma",
+        prob_distribution_params = c(shape = 1, scale = 1)
+      ),
       citation = create_citation(
         author = person(given = "John F.", family = "Smith"),
         year = 2000,
@@ -86,8 +92,10 @@ test_that("get_citation works as expected for epiparameter missing citation", {
     epiparameter(
       disease = "ebola",
       epi_dist = "incubation_period",
-      prob_distribution = "gamma",
-      prob_distribution_params = c(shape = 1, scale = 1)
+      prob_distribution = create_prob_distribution(
+        prob_distribution = "gamma",
+        prob_distribution_params = c(shape = 1, scale = 1)
+      )
     )
   )
   citation <- get_citation(ep)

tests/testthat/test-checkers.R

@@ -3,8 +3,10 @@ test_that("is_parameterised works as expected with epiparameter parameters", {
   ep <- suppressMessages(epiparameter(
     disease = "ebola",
     epi_dist = "incubation_period",
-    prob_distribution = "gamma",
-    prob_distribution_params = c(shape = 1, scale = 1)
+    prob_distribution = create_prob_distribution(
+      prob_distribution = "gamma",
+      prob_distribution_params = c(shape = 1, scale = 1)
+    )
   ))
   expect_true(is_parameterised(ep))
 })

tests/testthat/test-convert_params.R

@@ -2,8 +2,10 @@ ep <- suppressMessages(
   epiparameter(
     disease = "Ebola",
     epi_dist = "incubation period",
-    prob_distribution = "lnorm",
-    prob_distribution_params = c(meanlog = 1, sdlog = 1),
+    prob_distribution = create_prob_distribution(
+      prob_distribution = "lnorm",
+      prob_distribution_params = c(meanlog = 1, sdlog = 1)
+    ),
     summary_stats = create_summary_stats(mean = 1, sd = 1)
   )
 )
@@ -196,7 +198,7 @@ test_that("convert_params_to_summary_stats.character fails as expected", {
 })
 
 test_that("convert_params_to_summary_stats.epiparameter fails as expected", {
-  ep$prob_dist <- "lnorm"
+  ep$prob_distribution <- "lnorm"
   expect_error(
     convert_params_to_summary_stats(ep),
     regexp = "<epiparameter> supplied has no parameters and none are suppled"