diff --git a/R/epi_recipe.R b/R/epi_recipe.R
index 57272ee88..abcb06167 100644
--- a/R/epi_recipe.R
+++ b/R/epi_recipe.R
@@ -45,10 +45,9 @@ epi_recipe.default <- function(x, ...) {
#' library(dplyr)
#' library(recipes)
#'
-#' jhu <- jhu_csse_daily_subset %>%
+#' jhu <- case_death_rate_subset %>%
#' filter(time_value > "2021-08-01") %>%
-#' select(geo_value:death_rate_7d_av) %>%
-#' rename(case_rate = case_rate_7d_av, death_rate = death_rate_7d_av)
+#' dplyr::arrange(geo_value, time_value)
#'
#' r <- epi_recipe(jhu) %>%
#' step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
@@ -257,10 +256,9 @@ is_epi_recipe <- function(x) {
#' library(dplyr)
#' library(recipes)
#'
-#' jhu <- jhu_csse_daily_subset %>%
+#' jhu <- case_death_rate_subset %>%
#' filter(time_value > "2021-08-01") %>%
-#' select(geo_value:death_rate_7d_av) %>%
-#' rename(case_rate = case_rate_7d_av, death_rate = death_rate_7d_av)
+#' dplyr::arrange(geo_value, time_value)
#'
#' r <- epi_recipe(jhu) %>%
#' step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
diff --git a/R/epi_workflow.R b/R/epi_workflow.R
index 72fe2b1f3..4be82dcc6 100644
--- a/R/epi_workflow.R
+++ b/R/epi_workflow.R
@@ -42,7 +42,7 @@ epi_workflow <- function(preprocessor = NULL, spec = NULL, postprocessor = NULL)
if (is_epi_recipe(preprocessor)) {
out <- add_epi_recipe(out, preprocessor)
- }else if (!is_null(preprocessor)) {
+ } else if (!is_null(preprocessor)) {
out <- workflows:::add_preprocessor(out, preprocessor)
}
if (!is_null(postprocessor)) {
diff --git a/R/frosting.R b/R/frosting.R
index b8bb75e8a..436ea2319 100644
--- a/R/frosting.R
+++ b/R/frosting.R
@@ -35,10 +35,23 @@
add_frosting <- function(x, frosting, ...) {
rlang::check_dots_empty()
action <- workflows:::new_action_post(frosting = frosting)
- workflows:::add_action(x, action, "frosting")
+ epi_add_action(x, action, "frosting")
}
-order_stage_post <- function() "frosting"
+
+# Hacks around workflows `order_stage_post <- charcter(0)` ----------------
+epi_add_action <- function(x, action, name, ..., call = caller_env()) {
+ workflows:::validate_is_workflow(x, call = call)
+ add_action_frosting(x, action, name, ..., call = call)
+}
+add_action_frosting <- function(x, action, name, ..., call = caller_env()) {
+ workflows:::check_singleton(x$post$actions, name, call = call)
+ x$post <- workflows:::add_action_to_stage(x$post, action, name, order_stage_frosting())
+ x
+}
+order_stage_frosting <- function() "frosting"
+# End hacks. See cmu-delphi/epipredict#75
+
#' @rdname add_frosting
#' @export
diff --git a/man/add_epi_recipe.Rd b/man/add_epi_recipe.Rd
index 6202e4670..55508eefb 100644
--- a/man/add_epi_recipe.Rd
+++ b/man/add_epi_recipe.Rd
@@ -35,10 +35,9 @@ library(epiprocess)
library(dplyr)
library(recipes)
-jhu <- jhu_csse_daily_subset \%>\%
+jhu <- case_death_rate_subset \%>\%
filter(time_value > "2021-08-01") \%>\%
- select(geo_value:death_rate_7d_av) \%>\%
- rename(case_rate = case_rate_7d_av, death_rate = death_rate_7d_av)
+ dplyr::arrange(geo_value, time_value)
r <- epi_recipe(jhu) \%>\%
step_epi_lag(death_rate, lag = c(0, 7, 14)) \%>\%
diff --git a/man/create_layer.Rd b/man/create_layer.Rd
index 81f5e33b0..7917e8854 100644
--- a/man/create_layer.Rd
+++ b/man/create_layer.Rd
@@ -9,9 +9,9 @@ create_layer(name = NULL, open = rlang::is_interactive())
\arguments{
\item{name}{Either a name without extension, or \code{NULL} to create the
paired file based on currently open file in the script editor. If
-the \verb{R/} file is open, \code{use_test()} will create/open the corresponding
+the R file is open, \code{use_test()} will create/open the corresponding
test file; if the test file is open, \code{use_r()} will create/open the
-corresponding \verb{R/} file.}
+corresponding R file.}
\item{open}{Whether to open the file for interactive editing.}
}
diff --git a/man/epi_recipe.Rd b/man/epi_recipe.Rd
index 8f5eb4e11..1c74426bf 100644
--- a/man/epi_recipe.Rd
+++ b/man/epi_recipe.Rd
@@ -61,10 +61,9 @@ library(epiprocess)
library(dplyr)
library(recipes)
-jhu <- jhu_csse_daily_subset \%>\%
+jhu <- case_death_rate_subset \%>\%
filter(time_value > "2021-08-01") \%>\%
- select(geo_value:death_rate_7d_av) \%>\%
- rename(case_rate = case_rate_7d_av, death_rate = death_rate_7d_av)
+ dplyr::arrange(geo_value, time_value)
r <- epi_recipe(jhu) \%>\%
step_epi_lag(death_rate, lag = c(0, 7, 14)) \%>\%
diff --git a/musings/example-recipe.R b/musings/example-recipe.R
index d2bf9f46c..00458e3ca 100644
--- a/musings/example-recipe.R
+++ b/musings/example-recipe.R
@@ -2,8 +2,8 @@ library(tidyverse)
library(covidcast)
library(delphi.epidata)
library(epiprocess)
-# library(epipredict)
library(tidymodels)
+
x <- covidcast(
data_source = "jhu-csse",
signals = "confirmed_7dav_incidence_prop",
@@ -40,10 +40,7 @@ r <- epi_recipe(x) %>% # if we add this as a class, maybe we get better
step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
step_epi_ahead(death_rate, ahead = 7) %>%
step_epi_lag(case_rate, lag = c(0, 7, 14)) %>%
- step_naomit(all_predictors()) %>%
- # below, `skip` means we don't do this at predict time
- # we should probably do something useful here to avoid user error
- step_naomit(all_outcomes(), skip = TRUE)
+ step_epi_naomit()
# specify trainer, this uses stats::lm() by default, but doing
# slm <- linear_reg() %>% use_engine("glmnet", penalty = 0.1)
diff --git a/musings/updated-example.Rmd b/musings/updated-example.Rmd
index 84b8ea803..6191cce04 100644
--- a/musings/updated-example.Rmd
+++ b/musings/updated-example.Rmd
@@ -10,15 +10,14 @@ knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(tidymodels)
library(epiprocess)
+# devtools::install_github("cmu-delphi/epipredict")
library(epipredict)
-
```
```{r small-data}
-jhu <- jhu_csse_daily_subset %>%
+jhu <- case_death_rate_subset %>%
filter(time_value > "2021-08-01") %>%
- select(geo_value:death_rate_7d_av) %>%
- rename(case_rate = case_rate_7d_av, death_rate = death_rate_7d_av)
+ dplyr::arrange(geo_value, time_value)
jhu_latest <- jhu %>%
filter(!is.na(case_rate), !is.na(death_rate)) %>%
@@ -58,13 +57,19 @@ Predict gives a new `epi_df`
```{r predict}
pp <- predict(wf, new_data = jhu_latest)
-pp
+pp
```
Can add a `forecast_date` (should be a post processing step)
```{r predict2}
-predict(wf, new_data = jhu_latest, forecast_date = "2021-12-31") %>%
+# Want:
+# predict(wf, new_data = jhu_latest, forecast_date = "2021-12-31") %>%
+# filter(!is.na(.pred))
+
+# Intended output:
+predict(wf, new_data = jhu_latest) %>%
+ mutate(forecast_date = as.Date("2021-12-31")) %>%
filter(!is.na(.pred))
```
diff --git a/musings/updated-example.html b/musings/updated-example.html
index c88fb95ba..eb9a039b4 100644
--- a/musings/updated-example.html
+++ b/musings/updated-example.html
@@ -15,24 +15,11 @@
Untitled
-
-