From e7028ef9b6a46e2f44e88ce412bd6153d4f90d71 Mon Sep 17 00:00:00 2001
From: Dmitry Shemetov <dshemetov@ucdavis.edu>
Date: Wed, 25 Sep 2024 17:15:42 -0700
Subject: [PATCH] doc: fix examples, vignettes, add waldo

---
 .Rbuildignore           | 2 ++
 .gitignore              | 1 +
 DESCRIPTION             | 3 ++-
 R/methods-epi_archive.R | 4 ++--
 R/outliers.R            | 8 +++-----
 R/slide.R               | 2 +-
 man/detect_outlr_rm.Rd  | 3 +--
 man/detect_outlr_stl.Rd | 5 ++---
 man/epix_slide.Rd       | 4 ++--
 vignettes/archive.Rmd   | 2 +-
 10 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 0582014a6..cb0b7ed2b 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -16,3 +16,5 @@
 ^.lintr$
 ^DEVELOPMENT.md$
 man-roxygen
+^.venv$
+^sandbox.R$
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index de393a316..8dc001be4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,4 @@ docs
 renv/
 renv.lock
 .Rprofile
+sandbox.R
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index 333bf13cd..790b36a54 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -50,7 +50,8 @@ Imports:
     tidyselect (>= 1.2.0),
     tsibble,
     utils,
-    vctrs
+    vctrs,
+    waldo
 Suggests:
     covidcast,
     devtools,
diff --git a/R/methods-epi_archive.R b/R/methods-epi_archive.R
index be34211b8..0304d9a60 100644
--- a/R/methods-epi_archive.R
+++ b/R/methods-epi_archive.R
@@ -731,7 +731,7 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #' library(dplyr)
 #'
 #' # Reference time points for which we want to compute slide values:
-#' versions <- seq(as.Date("2020-06-01"),
+#' versions <- seq(as.Date("2020-06-02"),
 #'   as.Date("2020-06-15"),
 #'   by = "1 day"
 #' )
@@ -780,7 +780,7 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
 #'     .versions = versions
 #'   ) %>%
 #'   ungroup() %>%
-#'   arrange(geo_value, time_value)
+#'   arrange(geo_value, version)
 #'
 #' # --- Advanced: ---
 #'
diff --git a/R/outliers.R b/R/outliers.R
index 56cac3849..c2187de0a 100644
--- a/R/outliers.R
+++ b/R/outliers.R
@@ -161,8 +161,7 @@ detect_outlr <- function(x = seq_along(y), y,
 #'   group_by(geo_value) %>%
 #'   mutate(outlier_info = detect_outlr_rm(
 #'     x = time_value, y = cases
-#'   )) %>%
-#'   unnest(outlier_info)
+#'   ))
 detect_outlr_rm <- function(x = seq_along(y), y, n = 21,
                             log_transform = FALSE,
                             detect_negatives = FALSE,
@@ -256,9 +255,8 @@ detect_outlr_rm <- function(x = seq_along(y), y, n = 21,
 #'   group_by(geo_value) %>%
 #'   mutate(outlier_info = detect_outlr_stl(
 #'     x = time_value, y = cases,
-#'     seasonal_period = 7
-#'   )) %>% # weekly seasonality for daily data
-#'   unnest(outlier_info)
+#'     seasonal_period = 7 # weekly seasonality for daily data
+#'   ))
 detect_outlr_stl <- function(x = seq_along(y), y,
                              n_trend = 21,
                              n_seasonal = 21,
diff --git a/R/slide.R b/R/slide.R
index 50c8acf42..5a7fbd6aa 100644
--- a/R/slide.R
+++ b/R/slide.R
@@ -728,7 +728,7 @@ epi_slide_opt <- function(
   # positions of user-provided `col_names` into string column names. We avoid
   # using `names(pos)` directly for robustness and in case we later want to
   # allow users to rename fields via tidyselection.
-  if (class(quo_get_expr(enquo(.col_names))) == "character") {
+  if (inherits(quo_get_expr(enquo(.col_names)), "character")) {
     pos <- eval_select(dplyr::all_of(.col_names), data = .x, allow_rename = FALSE)
   } else {
     pos <- eval_select(enquo(.col_names), data = .x, allow_rename = FALSE)
diff --git a/man/detect_outlr_rm.Rd b/man/detect_outlr_rm.Rd
index 333c4a7b5..b57c44450 100644
--- a/man/detect_outlr_rm.Rd
+++ b/man/detect_outlr_rm.Rd
@@ -65,6 +65,5 @@ incidence_num_outlier_example \%>\%
   group_by(geo_value) \%>\%
   mutate(outlier_info = detect_outlr_rm(
     x = time_value, y = cases
-  )) \%>\%
-  unnest(outlier_info)
+  ))
 }
diff --git a/man/detect_outlr_stl.Rd b/man/detect_outlr_stl.Rd
index 695c2de78..fb69e8da3 100644
--- a/man/detect_outlr_stl.Rd
+++ b/man/detect_outlr_stl.Rd
@@ -96,7 +96,6 @@ incidence_num_outlier_example \%>\%
   group_by(geo_value) \%>\%
   mutate(outlier_info = detect_outlr_stl(
     x = time_value, y = cases,
-    seasonal_period = 7
-  )) \%>\% # weekly seasonality for daily data
-  unnest(outlier_info)
+    seasonal_period = 7 # weekly seasonality for daily data
+  ))
 }
diff --git a/man/epix_slide.Rd b/man/epix_slide.Rd
index 1f3018460..1326cc185 100644
--- a/man/epix_slide.Rd
+++ b/man/epix_slide.Rd
@@ -170,7 +170,7 @@ necessary (as it its purpose).
 library(dplyr)
 
 # Reference time points for which we want to compute slide values:
-versions <- seq(as.Date("2020-06-01"),
+versions <- seq(as.Date("2020-06-02"),
   as.Date("2020-06-15"),
   by = "1 day"
 )
@@ -219,7 +219,7 @@ archive_cases_dv_subset \%>\%
     .versions = versions
   ) \%>\%
   ungroup() \%>\%
-  arrange(geo_value, time_value)
+  arrange(geo_value, version)
 
 # --- Advanced: ---
 
diff --git a/vignettes/archive.Rmd b/vignettes/archive.Rmd
index 38707d7a6..62eea2aa5 100644
--- a/vignettes/archive.Rmd
+++ b/vignettes/archive.Rmd
@@ -76,7 +76,7 @@ format, with `issue` playing the role of `version`. We can now use
 redundant version updates in `as_epi_archive` using compactify, please refer to
 the [compactify vignette](articles/compactify.html).
 
-```{r, eval=FALSE}
+```{r}
 x <- dv %>%
   select(geo_value, time_value, version = issue, percent_cli = value) %>%
   as_epi_archive(compactify = TRUE)