remove {epiparameter} usage from tests

epiverse-trace · Jan 20, 2025 · 49007c1 · 49007c1
1 parent af076ff
commit 49007c1
Show file tree

Hide file tree

Showing 7 changed files with 46 additions and 238 deletions.
diff --git a/tests/testthat/test-add_cols.R b/tests/testthat/test-add_cols.R
@@ -1,25 +1,10 @@
-suppressMessages({
-  # get onset to hospital admission from {epiparameter} database &
-  # convert to function
-  onset_to_hosp <- as.function(
-    epiparameter::epiparameter_db(
-      disease = "COVID-19",
-      epi_name = "onset to hospitalisation",
-      single_epiparameter = TRUE
-    )
-  )
-
-  # get onset to death from {epiparameter} database
-  onset_to_death <- as.function(
-    epiparameter::epiparameter_db(
-      disease = "COVID-19",
-      epi_name = "onset to death",
-      single_epiparameter = TRUE
-    )
-  )
-
-  onset_to_recovery <- function(x) rep(NA, times = x)
-})
+onset_to_hosp <- function(x) {
+  stats::rlnorm(n = x, meanlog = 0.947, sdlog = 1.628)
+}
+onset_to_death <- function(x) {
+  stats::rlnorm(n = x, meanlog = 2.863, sdlog = 0.534)
+}
+onset_to_recovery <- function(x) rep(NA, times = x)
 
 test_that(".add_date_contact works as expected with contact_type = 'last'", {
   ll <- readRDS(file = file.path("testdata", "pre_date_last_contact.rds"))

diff --git a/tests/testthat/test-checkers.R b/tests/testthat/test-checkers.R
@@ -137,57 +137,15 @@ test_that(".check_age_df fails as expected", {
   )
 })
 
-suppressMessages({
-  library(epiparameter)
-  contact_distribution <- as.function(
-    epiparameter(
-      disease = "COVID-19",
-      epi_name = "contact distribution",
-      prob_distribution = create_prob_distribution(
-        prob_distribution = "pois",
-        prob_distribution_params = c(mean = 2)
-      )
-    )
-  )
-
-  infectious_period <- as.function(
-    epiparameter(
-      disease = "COVID-19",
-      epi_name = "infectious period",
-      prob_distribution = create_prob_distribution(
-        prob_distribution = "gamma",
-        prob_distribution_params = c(shape = 1, scale = 1)
-      )
-    )
-  )
-
-  # get onset to hospital admission from {epiparameter} database
-  onset_to_hosp <- as.function(
-    epiparameter_db(
-      disease = "COVID-19",
-      epi_name = "onset to hospitalisation",
-      single_epiparameter = TRUE
-    )
-  )
-
-  # get onset to death from {epiparameter} database
-  onset_to_death <- as.function(
-    epiparameter_db(
-      disease = "COVID-19",
-      epi_name = "onset to death",
-      single_epiparameter = TRUE
-    )
-  )
-
-  onset_to_recovery <- as.function(epiparameter(
-    disease = "COVID-19",
-    epi_name = "onset to recovery",
-    prob_distribution = create_prob_distribution(
-      prob_distribution = "lnorm",
-      prob_distribution_params = c(meanlog = 3, sdlog = 1)
-    )
-  ))
-})
+contact_distribution <- function(x) stats::dpois(x = x, lambda = 2)
+infectious_period <- function(x) stats::rgamma(n = x, shape = 1, scale = 1)
+onset_to_hosp <- function(x) {
+  stats::rlnorm(n = x, meanlog = 0.947, sdlog = 1.628)
+}
+onset_to_death <- function(x) {
+  stats::rlnorm(n = x, meanlog = 2.863, sdlog = 0.534)
+}
+onset_to_recovery <- function(x) stats::rlnorm(n = x, meanlog = 3, sdlog = 1)
 
 test_that(".check_sim_input works as expected", {
   chk <- .check_sim_input(

diff --git a/tests/testthat/test-sim_contacts.R b/tests/testthat/test-sim_contacts.R
@@ -3,25 +3,8 @@ test_that("sim_contacts works as expected with defaults", {
   expect_snapshot(sim_contacts())
 })
 
-suppressMessages({
-  contact_distribution <- epiparameter::epiparameter(
-    disease = "COVID-19",
-    epi_name = "contact distribution",
-    prob_distribution = create_prob_distribution(
-      prob_distribution = "pois",
-      prob_distribution_params = c(mean = 2)
-    )
-  )
-
-  infectious_period <- epiparameter::epiparameter(
-    disease = "COVID-19",
-    epi_name = "infectious period",
-    prob_distribution = create_prob_distribution(
-      prob_distribution = "gamma",
-      prob_distribution_params = c(shape = 1, scale = 1)
-    )
-  )
-})
+contact_distribution <- function(x) stats::dpois(x = x, lambda = 2)
+infectious_period <- function(x) stats::rgamma(n = x, shape = 1, scale = 1)
 
 test_that("sim_contacts works as expected", {
   set.seed(1)

diff --git a/tests/testthat/test-sim_linelist.R b/tests/testthat/test-sim_linelist.R
@@ -3,40 +3,14 @@ test_that("sim_linelist works as expected with defaults", {
   expect_snapshot(sim_linelist())
 })
 
-suppressMessages({
-  library(epiparameter)
-  contact_distribution <- epiparameter(
-    disease = "COVID-19",
-    epi_name = "contact distribution",
-    prob_distribution = create_prob_distribution(
-      prob_distribution = "pois",
-      prob_distribution_params = c(mean = 2)
-    )
-  )
-
-  infectious_period <- epiparameter(
-    disease = "COVID-19",
-    epi_name = "infectious period",
-    prob_distribution = create_prob_distribution(
-      prob_distribution = "gamma",
-      prob_distribution_params = c(shape = 1, scale = 1)
-    )
-  )
-
-  # get onset to hospital admission from {epiparameter} database
-  onset_to_hosp <- epiparameter_db(
-    disease = "COVID-19",
-    epi_name = "onset to hospitalisation",
-    single_epiparameter = TRUE
-  )
-
-  # get onset to death from {epiparameter} database
-  onset_to_death <- epiparameter_db(
-    disease = "COVID-19",
-    epi_name = "onset to death",
-    single_epiparameter = TRUE
-  )
-})
+contact_distribution <- function(x) stats::dpois(x = x, lambda = 2)
+infectious_period <- function(x) stats::rgamma(n = x, shape = 1, scale = 1)
+onset_to_hosp <- function(x) {
+  stats::rlnorm(n = x, meanlog = 0.947, sdlog = 1.628)
+}
+onset_to_death <- function(x) {
+  stats::rlnorm(n = x, meanlog = 2.863, sdlog = 0.534)
+}
 
 test_that("sim_linelist works as expected", {
   set.seed(1)

diff --git a/tests/testthat/test-sim_network_bp.R b/tests/testthat/test-sim_network_bp.R
@@ -1,28 +1,5 @@
-suppressMessages({
-  library(epiparameter)
-  contact_distribution <- as.function(
-    epiparameter(
-      disease = "COVID-19",
-      epi_name = "contact distribution",
-      prob_distribution = create_prob_distribution(
-        prob_distribution = "pois",
-        prob_distribution_params = c(mean = 2)
-      )
-    )
-  )
-
-  infectious_period <- as.function(
-    epiparameter(
-      disease = "COVID-19",
-      epi_name = "infectious period",
-      prob_distribution = create_prob_distribution(
-        prob_distribution = "gamma",
-        prob_distribution_params = c(shape = 1, scale = 1)
-      )
-    ),
-    func_type = "generate"
-  )
-})
+contact_distribution <- function(x) stats::dpois(x = x, lambda = 2)
+infectious_period <- function(x) stats::rgamma(n = x, shape = 1, scale = 1)
 
 test_that(".sim_network_bp works as expected", {
   set.seed(1)
@@ -38,18 +15,7 @@ test_that(".sim_network_bp works as expected", {
 })
 
 test_that(".sim_network_bp works as expected with no contacts", {
-  suppressMessages(
-    contact_distribution <- as.function(
-      epiparameter(
-        disease = "COVID-19",
-        epi_name = "contact distribution",
-        prob_distribution = create_prob_distribution(
-          prob_distribution = "pois",
-          prob_distribution_params = c(mean = 1)
-        )
-      )
-    )
-  )
+  contact_distribution <- function(x) stats::dpois(x = x, lambda = 1)
   set.seed(1)
   expect_snapshot(
     .sim_network_bp(
@@ -90,19 +56,7 @@ test_that(".sim_network_bp warns as expected", {
 })
 
 test_that(".sim_network_bp errors with negative infectious period", {
-  suppressMessages({
-    infectious_period <- as.function(
-      epiparameter(
-        disease = "COVID-19",
-        epi_name = "infectious period",
-        prob_distribution = create_prob_distribution(
-          prob_distribution = "norm",
-          prob_distribution_params = c(mean = 10, sd = 5)
-        )
-      ),
-      func_type = "generate"
-    )
-  })
+  infectious_period <- function(x) stats::rnorm(n = x, mean = 10, sd = 5)
   set.seed(3)
   expect_error(
     .sim_network_bp(

diff --git a/tests/testthat/test-sim_outbreak.R b/tests/testthat/test-sim_outbreak.R
@@ -3,39 +3,15 @@ test_that("sim_outbreak works as expected with defaults", {
   expect_snapshot(sim_outbreak())
 })
 
-suppressMessages({
-  contact_distribution <- epiparameter::epiparameter(
-    disease = "COVID-19",
-    epi_name = "contact distribution",
-    prob_distribution = create_prob_distribution(
-      prob_distribution = "pois",
-      prob_distribution_params = c(mean = 2)
-    )
-  )
-
-  infectious_period <- epiparameter::epiparameter(
-    disease = "COVID-19",
-    epi_name = "infectious period",
-    prob_distribution = create_prob_distribution(
-      prob_distribution = "gamma",
-      prob_distribution_params = c(shape = 1, scale = 1)
-    )
-  )
 
-  # get onset to hospital admission from {epiparameter} database
-  onset_to_hosp <- epiparameter::epiparameter_db(
-    disease = "COVID-19",
-    epi_name = "onset to hospitalisation",
-    single_epiparameter = TRUE
-  )
-
-  # get onset to death from {epiparameter} database
-  onset_to_death <- epiparameter::epiparameter_db(
-    disease = "COVID-19",
-    epi_name = "onset to death",
-    single_epiparameter = TRUE
-  )
-})
+contact_distribution <- function(x) stats::dpois(x = x, lambda = 2)
+infectious_period <- function(x) stats::rgamma(n = x, shape = 1, scale = 1)
+onset_to_hosp <- function(x) {
+  stats::rlnorm(n = x, meanlog = 0.947, sdlog = 1.628)
+}
+onset_to_death <- function(x) {
+  stats::rlnorm(n = x, meanlog = 2.863, sdlog = 0.534)
+}
 
 test_that("sim_outbreak works as expected", {
   set.seed(1)

diff --git a/tests/testthat/testdata/README.md b/tests/testthat/testdata/README.md
@@ -18,37 +18,15 @@ The script to reproduce the data is:
 
 ``` r
 # load data required to simulate line list
-contact_distribution <- epiparameter::epiparameter(
-  disease = "COVID-19",
-  epi_name = "contact distribution",
-  prob_distribution = create_prob_distribution(
-    prob_distribution = "pois",
-    prob_distribution_params = c(mean = 2)
-  )
-)
-
-infectious_period <- epiparameter::epiparameter(
-  disease = "COVID-19",
-  epi_name = "infectious period",
-  prob_distribution = create_prob_distribution(
-    prob_distribution = "gamma",
-    prob_distribution_params = c(shape = 1, scale = 1)
-  )
-)
+contact_distribution <- function(x) stats::dpois(x = x, lambda = 2)
+infectious_period <- function(x) stats::rgamma(n = x, shape = 1, scale = 1)
+onset_to_hosp <- function(x) {
+  stats::rlnorm(n = x, meanlog = 0.947, sdlog = 1.628)
+}
+onset_to_death <- function(x) {
+  stats::rlnorm(n = x, meanlog = 2.863, sdlog = 0.534)
+}
 
-# get onset to hospital admission from {epiparameter} database
-onset_to_hosp <- epiparameter::epiparameter_db(
-  disease = "COVID-19",
-  epi_name = "onset to hospitalisation",
-  single_epiparameter = TRUE
-)
-
-# get onset to death from {epiparameter} database
-onset_to_death <- epiparameter::epiparameter_db(
-  disease = "COVID-19",
-  epi_name = "onset to death",
-  single_epiparameter = TRUE
-)
 set.seed(1)
 
 linelist <- sim_linelist(