doc: fix examples, vignettes, add waldo

.Rbuildignore

@@ -16,3 +16,5 @@
 ^.lintr$
 ^DEVELOPMENT.md$
 man-roxygen
+^.venv$
+^sandbox.R$

.gitignore

@@ -13,3 +13,4 @@ docs
 renv/
 renv.lock
 .Rprofile
+sandbox.R

DESCRIPTION

@@ -50,7 +50,8 @@ Imports:
     tidyselect (>= 1.2.0),
     tsibble,
     utils,
-    vctrs
+    vctrs,
+    waldo
 Suggests:
     covidcast,
     devtools,

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: ---
 #'

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,

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)

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)