much more complete guts example, branching flatline fixes

Author: dsweber2

R/step_epi_shift.R

@@ -33,6 +33,12 @@
 #' @details The step assumes that the data are already _in the proper sequential
 #'  order_ for shifting.
 #'
+#'  While `{recipes}` provides a function `step_lag()`, it assumes that the data
+#'  have no breaks in the sequence of `time_values`, and has no ability to group by
+#'  `geo_value` or other keys. Our `lag/ahead` functions also appropriately adjust
+#'  the amount of data to avoid accidentally dropping recent predictors from the
+#'  test data.
+#'
 #' The `prefix` and `id` arguments are unchangeable to ensure that the code runs
 #' properly and to avoid inconsistency with naming. For `step_epi_ahead`, they
 #' are always set to `"ahead_"` and `"epi_ahead"` respectively, while for

README.md

@@ -105,7 +105,8 @@ cases_deaths |>
   facet_grid(
     rows = vars(.response_name),
     cols = vars(geo_value),
-    scale = "free") +
+    scale = "free"
+  ) +
   scale_x_date(date_breaks = "3 months", date_labels = "%Y %b") +
   theme(axis.text.x = element_text(angle = 90, hjust = 1))
 ```
@@ -177,7 +178,8 @@ forecast_date_label <-
     heights = c(rep(150, 4), rep(0.75, 4))
   )
 processed_data_plot <-
-  covid_case_death_rates |> filter(geo_value %in% used_locations) |>
+  covid_case_death_rates |>
+  filter(geo_value %in% used_locations) |>
   autoplot(
     case_rate,
     death_rate,
@@ -186,7 +188,8 @@ processed_data_plot <-
   facet_grid(
     rows = vars(.response_name),
     cols = vars(geo_value),
-    scale = "free") +
+    scale = "free"
+  ) +
   geom_vline(aes(xintercept = forecast_date)) +
   geom_text(
     data = forecast_date_label,
@@ -219,7 +222,7 @@ four_week_ahead <- arx_forecaster(
 four_week_ahead
 #> ══ A basic forecaster of type ARX Forecaster ════════════════════════════════
 #> 
-#> This forecaster was fit on 2025-01-31 10:46:32.
+#> This forecaster was fit on 2025-02-05 17:01:43.
 #> 
 #> Training data was an <epi_df> with:
 #> • Geography: state,

_pkgdown.yml

@@ -11,6 +11,7 @@ articles:
     navbar: ~
     contents:
       - epipredict
+      - custom_epiworkflows
       - preprocessing-and-models
       - backtesting
       - arx-classifier

man/figures/README-show-processed-data-1.png

@@ -8,7 +8,7 @@ vignette: >
 ---
 
 ```{r, include = FALSE}
-source("_common.R")
+source(here::here("vignettes/_common.R"))
 ```
 
 ## Load required packages

vignettes/arx-classifier.Rmd

@@ -8,7 +8,7 @@ vignette: >
 ---
 
 ```{r, include = FALSE}
-source("_common.R")
+source(here::here("vignettes/_common.R"))
 ```
 
 ```{r pkgs, include=FALSE, echo=TRUE}