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bugs seemingly squashed
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3 files changed

+31
-25
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R/epi_recipe.R

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -113,7 +113,7 @@ epi_recipe.epi_df <-
113113
)
114114

115115
## Add types
116-
var_info <- dplyr::full_join(get_types(x), var_info, by = "variable")
116+
var_info <- dplyr::full_join(recipes:::get_types(x), var_info, by = "variable")
117117
var_info$source <- "original"
118118

119119
## arrange to easy order
@@ -371,7 +371,7 @@ prep.epi_recipe <- function(
371371
dplyr::group_by(variable) %>%
372372
dplyr::arrange(dplyr::desc(number)) %>%
373373
dplyr::summarise(
374-
type = dplyr::first(type),
374+
type = list(dplyr::first(type)),
375375
role = as.list(unique(unlist(role))),
376376
source = dplyr::first(source),
377377
number = dplyr::first(number),

tests/testthat/test-epi_recipe.R

Lines changed: 21 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -36,19 +36,21 @@ test_that("epi_recipe formula works", {
3636
r <- epi_recipe(y ~ x, tib)
3737
ref_var_info <- tibble::tribble(
3838
~ variable, ~ type, ~ role, ~ source,
39-
"x", "numeric", "predictor", "original",
40-
"y", "numeric", "outcome", "original",
39+
"x", c("integer", "numeric"), "predictor", "original",
40+
"y", c("integer", "numeric"), "outcome", "original",
4141
"time_value", "date", "time_value", "original",
42-
"geo_value", "nominal", "geo_value", "original"
42+
"geo_value", c("string", "unordered", "nominal"), "geo_value", "original"
4343
)
4444
expect_identical(r$var_info, ref_var_info)
4545
expect_equal(nrow(r$template), 1L)
4646

4747
# with an epi_key as a predictor
4848
r <- epi_recipe(y ~ x + geo_value, tib)
49-
ref_var_info <- ref_var_info %>% tibble::add_row(
50-
variable = "geo_value", type = "nominal", role = "predictor",
51-
source = "original", .after = 1)
49+
ref_var_info <- ref_var_info %>%
50+
tibble::add_row(
51+
variable = "geo_value", type = list(c("string", "unordered", "nominal")),
52+
role = "predictor",
53+
source = "original", .after = 1)
5254
expect_identical(r$var_info, ref_var_info)
5355
expect_equal(nrow(r$template), 1L)
5456

@@ -61,11 +63,13 @@ test_that("epi_recipe formula works", {
6163

6264
# with an additional key
6365
r <- epi_recipe(y ~ x + geo_value, tib)
64-
ref_var_info <- ref_var_info %>% tibble::add_row(
65-
variable = "z", type = "nominal", role = "key",
66-
source = "original")
66+
ref_var_info <- ref_var_info %>%
67+
tibble::add_row(
68+
variable = "z", type = list(c("string", "unordered", "nominal")),
69+
role = "key",
70+
source = "original")
6771

68-
#expect_identical(r$var_info, ref_var_info)
72+
expect_identical(r$var_info, ref_var_info)
6973

7074
})
7175

@@ -81,20 +85,20 @@ test_that("epi_recipe epi_df works", {
8185
ref_var_info <- tibble::tribble(
8286
~ variable, ~ type, ~ role, ~ source,
8387
"time_value", "date", "time_value", "original",
84-
"geo_value", "nominal", "geo_value", "original",
85-
"x", "numeric", "raw", "original",
86-
"y", "numeric", "raw", "original"
88+
"geo_value", c("string", "unordered", "nominal"), "geo_value", "original",
89+
"x", c("integer", "numeric"), "raw", "original",
90+
"y", c("integer", "numeric"), "raw", "original"
8791
)
8892
expect_identical(r$var_info, ref_var_info)
8993
expect_equal(nrow(r$template), 1L)
9094

9195
r <- epi_recipe(tib, formula = y ~ x)
9296
ref_var_info <- tibble::tribble(
9397
~ variable, ~ type, ~ role, ~ source,
94-
"x", "numeric", "predictor", "original",
95-
"y", "numeric", "outcome", "original",
98+
"x", c("integer", "numeric"), "predictor", "original",
99+
"y", c("integer", "numeric"), "outcome", "original",
96100
"time_value", "date", "time_value", "original",
97-
"geo_value", "nominal", "geo_value", "original"
101+
"geo_value", c("string", "unordered", "nominal"), "geo_value", "original"
98102
)
99103
expect_identical(r$var_info, ref_var_info)
100104
expect_equal(nrow(r$template), 1L)
@@ -106,7 +110,7 @@ test_that("epi_recipe epi_df works", {
106110
)
107111
ref_var_info <- ref_var_info %>%
108112
tibble::add_row(
109-
variable = "time_value", type = "date", role = "funny_business",
113+
variable = "time_value", type = list("date"), role = "funny_business",
110114
source = "original"
111115
)
112116
expect_identical(r$var_info, ref_var_info)

vignettes/preprocessing-and-models.Rmd

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -549,14 +549,16 @@ Notice the difference in number of rows `b1` and `b2` returns. This is because
549549
the second version, the one that doesn't use `step_epi_ahead` and `step_epi_lag`,
550550
has omitted dates compared to the one that used the `epipredict` functions.
551551
```{r}
552-
dates_used_in_training1 <-
553-
b1 %>% select(- ahead_7_death_rate) %>% na.omit() %>% select(time_value)
554-
552+
dates_used_in_training1 <- b1 %>%
553+
select(- ahead_7_death_rate) %>%
554+
na.omit() %>%
555+
select(time_value)
555556
dates_used_in_training1
556557
557-
dates_used_in_training2 <-
558-
b2 %>% select(- ahead7death_rate) %>% na.omit() %>% select(time_value)
559-
558+
dates_used_in_training2 <- b2 %>%
559+
select(- ahead7death_rate) %>%
560+
na.omit() %>%
561+
select(time_value)
560562
dates_used_in_training2
561563
```
562564

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