fix failing tests

dajmcdon · dajmcdon · commit 244dacb9eb7f · 2024-10-18T17:05:54.000-07:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -40,7 +40,6 @@ Imports:
     magrittr,
     recipes (>= 1.0.4),
     rlang (>= 1.1.0),
-    purrr,
     stats,
     tibble,
     tidyr,
diff --git a/R/layer_population_scaling.R b/R/layer_population_scaling.R
@@ -48,7 +48,7 @@
 #' @export
 #' @examples
 #' library(dplyr)
-#' jhu <- jhu_csse_daily_subset %>%
+#' jhu <- cases_deaths_subset %>%
 #'   filter(time_value > "2021-11-01", geo_value %in% c("ca", "ny")) %>%
 #'   select(geo_value, time_value, cases)
 #'
diff --git a/R/step_population_scaling.R b/R/step_population_scaling.R
@@ -45,7 +45,7 @@
 #' @export
 #' @examples
 #' library(dplyr)
-#' jhu <- jhu_csse_daily_subset %>%
+#' jhu <- cases_deaths_subset %>%
 #'   filter(time_value > "2021-11-01", geo_value %in% c("ca", "ny")) %>%
 #'   select(geo_value, time_value, cases)
 #'
diff --git a/man/layer_population_scaling.Rd b/man/layer_population_scaling.Rd
diff --git a/man/step_adjust_latency.Rd b/man/step_adjust_latency.Rd
diff --git a/man/step_population_scaling.Rd b/man/step_population_scaling.Rd
diff --git a/tests/testthat/_snaps/arg_is_.md b/tests/testthat/_snaps/arg_is_.md
@@ -377,7 +377,7 @@
 # simple surface step test
 
     Code
-      epi_recipe(jhu_csse_daily_subset) %>% step_epi_lag(death_rate, lag = "hello")
+      epi_recipe(case_death_rate_subset) %>% step_epi_lag(death_rate, lag = "hello")
     Condition
       Error in `step_epi_lag()`:
       ! `lag` must be a non-negative integer.
diff --git a/tests/testthat/_snaps/snapshots.md b/tests/testthat/_snaps/snapshots.md
@@ -1034,8 +1034,8 @@
 ---
 
     structure(list(geo_value = c("ca", "fl", "ga", "ny", "pa", "tx"
-    ), .pred = c(0.303244704017743, 0.531332853311082, 0.588827944685979, 
-    0.988690249216229, 0.794801997001639, 0.306895457225321), .pred_distn = structure(list(
+    ), .pred = c(0.303244704017742, 0.531332853311081, 0.58882794468598, 
+    0.98869024921623, 0.79480199700164, 0.306895457225321), .pred_distn = structure(list(
         structure(list(values = c(0.136509784083987, 0.469979623951498
         ), quantile_levels = c(0.05, 0.95)), class = c("dist_quantiles", 
         "dist_default", "vctrs_rcrd", "vctrs_vctr")), structure(list(
@@ -1044,10 +1044,10 @@
         "vctrs_vctr")), structure(list(values = c(0.422093024752224, 
         0.755562864619735), quantile_levels = c(0.05, 0.95)), class = c("dist_quantiles", 
         "dist_default", "vctrs_rcrd", "vctrs_vctr")), structure(list(
-            values = c(0.821955329282474, 1.15542516914998), quantile_levels = c(0.05, 
+            values = c(0.821955329282475, 1.15542516914999), quantile_levels = c(0.05, 
             0.95)), class = c("dist_quantiles", "dist_default", "vctrs_rcrd", 
-        "vctrs_vctr")), structure(list(values = c(0.628067077067883, 
-        0.961536916935394), quantile_levels = c(0.05, 0.95)), class = c("dist_quantiles", 
+        "vctrs_vctr")), structure(list(values = c(0.628067077067884, 
+        0.961536916935395), quantile_levels = c(0.05, 0.95)), class = c("dist_quantiles", 
         "dist_default", "vctrs_rcrd", "vctrs_vctr")), structure(list(
             values = c(0.140160537291566, 0.473630377159077), quantile_levels = c(0.05, 
             0.95)), class = c("dist_quantiles", "dist_default", "vctrs_rcrd", 
@@ -1060,8 +1060,8 @@
 ---
 
     structure(list(geo_value = c("ca", "fl", "ga", "ny", "pa", "tx"
-    ), .pred = c(0.303244704017743, 0.531332853311082, 0.588827944685979, 
-    0.988690249216229, 0.794801997001639, 0.306895457225321), .pred_distn = structure(list(
+    ), .pred = c(0.303244704017742, 0.531332853311081, 0.58882794468598, 
+    0.98869024921623, 0.79480199700164, 0.306895457225321), .pred_distn = structure(list(
         structure(list(values = c(0.136509784083987, 0.469979623951498
         ), quantile_levels = c(0.05, 0.95)), class = c("dist_quantiles", 
         "dist_default", "vctrs_rcrd", "vctrs_vctr")), structure(list(
@@ -1070,10 +1070,10 @@
         "vctrs_vctr")), structure(list(values = c(0.422093024752224, 
         0.755562864619735), quantile_levels = c(0.05, 0.95)), class = c("dist_quantiles", 
         "dist_default", "vctrs_rcrd", "vctrs_vctr")), structure(list(
-            values = c(0.821955329282474, 1.15542516914998), quantile_levels = c(0.05, 
+            values = c(0.821955329282475, 1.15542516914999), quantile_levels = c(0.05, 
             0.95)), class = c("dist_quantiles", "dist_default", "vctrs_rcrd", 
-        "vctrs_vctr")), structure(list(values = c(0.628067077067883, 
-        0.961536916935394), quantile_levels = c(0.05, 0.95)), class = c("dist_quantiles", 
+        "vctrs_vctr")), structure(list(values = c(0.628067077067884, 
+        0.961536916935395), quantile_levels = c(0.05, 0.95)), class = c("dist_quantiles", 
         "dist_default", "vctrs_rcrd", "vctrs_vctr")), structure(list(
             values = c(0.140160537291566, 0.473630377159077), quantile_levels = c(0.05, 
             0.95)), class = c("dist_quantiles", "dist_default", "vctrs_rcrd", 
@@ -1090,7 +1090,7 @@
     Message
       == A basic forecaster of type ARX Forecaster ===================================
       
-      This forecaster was fit on 999-01-01.
+      This forecaster was fit on 0999-01-01.
       
       Training data was an <epi_df> with:
       * Geography: state,
@@ -1113,7 +1113,7 @@
     Message
       == A basic forecaster of type ARX Forecaster ===================================
       
-      This forecaster was fit on 999-01-01.
+      This forecaster was fit on 0999-01-01.
       
       Training data was an <epi_df> with:
       * Geography: state,
@@ -1137,7 +1137,7 @@
     Message
       == A basic forecaster of type ARX Forecaster ===================================
       
-      This forecaster was fit on 999-01-01.
+      This forecaster was fit on 0999-01-01.
       
       Training data was an <epi_df> with:
       * Geography: state,
diff --git a/tests/testthat/test-arg_is_.R b/tests/testthat/test-arg_is_.R
@@ -149,6 +149,7 @@ test_that("coerce scalar to date", {
 test_that("simple surface step test", {
   expect_snapshot(
     error = TRUE,
-    epi_recipe(jhu_csse_daily_subset) %>% step_epi_lag(death_rate, lag = "hello")
+    epi_recipe(case_death_rate_subset) %>%
+      step_epi_lag(death_rate, lag = "hello")
   )
 })
diff --git a/tests/testthat/test-arx_forecaster.R b/tests/testthat/test-arx_forecaster.R
@@ -1,4 +1,4 @@
-train_data <- jhu_csse_daily_subset
+train_data <- cases_deaths_subset
 test_that("arx_forecaster warns if forecast date beyond the implicit one", {
   bad_date <- max(train_data$time_value) + 300
   expect_warning(
diff --git a/tests/testthat/test-check-training-set.R b/tests/testthat/test-check-training-set.R
@@ -1,5 +1,5 @@
 test_that("training set validation works", {
-  template <- jhu_csse_daily_subset[1, ]
+  template <- cases_deaths_subset[1, ]
   rec <- list(template = template)
   t1 <- template
 
diff --git a/tests/testthat/test-population_scaling.R b/tests/testthat/test-population_scaling.R
@@ -90,7 +90,7 @@ test_that("Number of columns and column names returned correctly, Upper and lowe
 
 ## Postprocessing
 test_that("Postprocessing workflow works and values correct", {
-  jhu <- jhu_csse_daily_subset %>%
+  jhu <- cases_deaths_subset %>%
     dplyr::filter(time_value > "2021-11-01", geo_value %in% c("ca", "ny")) %>%
     dplyr::select(geo_value, time_value, cases)
 
diff --git a/tests/testthat/test-snapshots.R b/tests/testthat/test-snapshots.R
@@ -1,4 +1,4 @@
-train_data <- jhu_csse_daily_subset
+train_data <- cases_deaths_subset
 expect_snapshot_tibble <- function(x) {
   expect_snapshot_value(x, style = "deparse", cran = FALSE)
 }
diff --git a/tests/testthat/test-target_date_bug.R b/tests/testthat/test-target_date_bug.R
@@ -2,7 +2,7 @@
 # https://github.com/cmu-delphi/epipredict/issues/290
 
 library(dplyr)
-train <- jhu_csse_daily_subset |>
+train <- cases_deaths_subset |>
   filter(time_value >= as.Date("2021-10-01")) |>
   select(geo_value, time_value, cr = case_rate_7d_av, dr = death_rate_7d_av)
 ngeos <- n_distinct(train$geo_value)

Original file line number	Diff line number	Diff line change
`@@ -149,6 +149,7 @@ test_that("coerce scalar to date", {`
`149`	`149`	`test_that("simple surface step test", {`
`150`	`150`	`expect_snapshot(`
`151`	`151`	`error = TRUE,`
`152`		`- epi_recipe(jhu_csse_daily_subset) %>% step_epi_lag(death_rate, lag = "hello")`
	`152`	`+ epi_recipe(case_death_rate_subset) %>%`
	`153`	`+ step_epi_lag(death_rate, lag = "hello")`
`153`	`154`	`)`
`154`	`155`	`})`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-train_data <- jhu_csse_daily_subset`
	`1`	`+train_data <- cases_deaths_subset`
`2`	`2`	`test_that("arx_forecaster warns if forecast date beyond the implicit one", {`
`3`	`3`	`bad_date <- max(train_data$time_value) + 300`
`4`	`4`	`expect_warning(`