reduce tests

UCD-SERG · Oct 22, 2024 · 98c881d · 98c881d
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diff --git a/tests/testthat/_snaps/est.incidence.by.md b/tests/testthat/_snaps/est.incidence.by.md
diff --git a/tests/testthat/_snaps/est.incidence.by.new.md b/tests/testthat/_snaps/est.incidence.by.new.md
diff --git a/tests/testthat/test-est.incidence.by.R b/tests/testthat/test-est.incidence.by.R
@@ -1,90 +1,3 @@
-test_that(
-  "est.incidence.by() produces expected results for typhoid data",
-  {
-    library(dplyr)
-    # get pop data
-    xs_data <- load_pop_data(
-      file_path = "https://osf.io/download//n6cp3/",
-      age = "Age",
-      value = "result",
-      id = "index_id",
-      standardize = TRUE
-    ) %>%
-      filter(Country == "Pakistan") %>%
-      slice_head(n = 100)
-
-    # get noise data
-    noise <- load_noise_params("https://osf.io/download//hqy4v/") %>%
-      filter(Country == "Pakistan")
-
-    # get curve data
-    curve <- load_curve_params("https://osf.io/download/rtw5k/") # slice if test is too slow (.by = antigen_iso))
-
-    # set start
-    start <- .05
-
-    typhoid_results <- est.incidence.by(
-      strata = c("catchment"),
-      pop_data = xs_data,
-      curve_param = curve,
-      curve_strata_varnames = "catchment",
-      noise_strata_varnames = "catchment",
-      noise_param = noise,
-      antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
-      num_cores = 8 # Allow for parallel processing to decrease run time
-    )
-
-    expect_snapshot(x = typhoid_results)
-
-    expect_snapshot_value(typhoid_results, style = "deparse")
-  }
-)
-
-test_that("`est.incidence.by()` produces expected results", {
-  curves <- load_curve_params("https://osf.io/download/rtw5k/")
-  noise <- load_noise_params("https://osf.io/download//hqy4v/")
-  xs_data_true <- load_pop_data(
-    file_path = "https://osf.io/download//n6cp3/",
-    age = "Age",
-    value = "result",
-    id = "index_id",
-    standardize = TRUE
-  ) %>%
-    filter(Country == "Pakistan") %>%
-    slice_head(n = 100)
-
-
-  est_true <- est.incidence.by(
-    strata = c("catchment"),
-    pop_data = xs_data_true,
-    curve_params = curves,
-    noise_params = noise %>% filter(Country == "Pakistan"),
-    antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
-    num_cores = 8 # Allow for parallel processing to decrease run time
-  )
-
-  xs_data_false <- load_pop_data(
-    file_path = "https://osf.io/download//n6cp3/",
-    age = "Age",
-    value = "result",
-    id = "index_id",
-    standardize = FALSE
-  ) %>%
-    filter(Country == "Pakistan") %>%
-    slice_head(n = 100)
-
-
-  est_false <- est.incidence.by(
-    strata = c("catchment"),
-    pop_data = xs_data_false,
-    curve_params = curves,
-    noise_params = noise %>% filter(Country == "Pakistan"),
-    antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
-    num_cores = 8 # Allow for parallel processing to decrease run time
-  )
-
-  expect_equal(est_true, est_false)
-})
 
 test_that("est.incidence.by() issues warning when strata is missing", {