Merge pull request #10 from kenmawer/km-issue_22_tests

Km issue 22: added tests

Author: kenmawer

tests/testthat/test-epi_shift_internal.R

@@ -0,0 +1,89 @@
+# Loading
+library(tidyverse)
+library(covidcast)
+library(delphi.epidata)
+library(epiprocess)
+library(tidymodels)
+
+# Taken from example-recipe
+x <- covidcast(
+  data_source = "jhu-csse",
+  signals = "confirmed_7dav_incidence_prop",
+  time_type = "day",
+  geo_type = "state",
+  time_values = epirange(20200301, 20211231),
+  geo_values = "*"
+) %>%
+  fetch_tbl() %>%
+  select(geo_value, time_value, case_rate = value)
+
+y <- covidcast(
+  data_source = "jhu-csse",
+  signals = "deaths_7dav_incidence_prop",
+  time_type = "day",
+  geo_type = "state",
+  time_values = epirange(20200301, 20211231),
+  geo_values = "*"
+) %>%
+  fetch_tbl() %>%
+  select(geo_value, time_value, death_rate = value)
+
+x <- x %>%
+  full_join(y, by = c("geo_value", "time_value")) %>%
+  as_epi_df()
+rm(y)
+
+xx <- x %>% filter(time_value > "2021-12-01")
+
+slm_fit <- function(recipe, data = x) {
+  workflow() %>%
+    add_recipe(recipe) %>%
+    add_model(linear_reg()) %>%
+    fit(data = data)
+}
+
+# Tests
+test_that("Check that epi_ahead shifts properly", {
+  r1 <- epi_recipe(x) %>%
+    step_epi_ahead(death_rate, ahead = 7) %>%
+    step_epi_lag(death_rate, lag = -7) %>%
+    step_naomit(all_predictors()) %>%
+    step_naomit(all_outcomes(), skip = TRUE)
+
+  slm_fit1 <- slm_fit(r1)
+
+  slope_ahead <- slm_fit1$fit$fit$fit$coefficients[[2]]
+  expect_equal(slope_ahead,1)
+})
+
+test_that("Check that epi_lag shifts properly", {
+  r2 <- epi_recipe(x) %>%
+    step_epi_ahead(death_rate, ahead = -7) %>%
+    step_epi_lag(death_rate, lag = 7) %>%
+    step_naomit(all_predictors()) %>%
+    step_naomit(all_outcomes(), skip = TRUE)
+
+  slm_fit2 <- slm_fit(r2)
+
+  slope_lag <- slm_fit2$fit$fit$fit$coefficients[[2]]
+  expect_equal(slope_lag,1)
+})
+
+test_that("Check for non-integer values", {
+  r3 <- epi_recipe(x) %>%
+    step_epi_ahead(death_rate, ahead = 3.6) %>%
+    step_epi_lag(death_rate, lag = 1.9)
+  expect_error(
+    slm_fit(r3)
+  )
+})
+
+test_that("Check for duplicate values", {
+  r4 <- epi_recipe(x) %>%
+    step_epi_ahead(death_rate, ahead = 7) %>%
+    step_epi_lag(death_rate, lag = 7) %>%
+    step_epi_lag(death_rate, lag = 7)
+  expect_error(
+    slm_fit(r4)
+  )
+})