wip: fix vignettes

cmu-delphi · Sep 25, 2024 · f481bd7 · f481bd7
1 parent 60aa7e6
commit f481bd7
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Showing 6 changed files with 301 additions and 293 deletions.
diff --git a/R/outliers.R b/R/outliers.R
@@ -189,7 +189,7 @@ detect_outlr_rm <- function(x = seq_along(y), y, n = 21,
 
   # Calculate lower and upper thresholds and replacement value
   z <- z %>%
-    epi_slide(fitted = median(y), .window_size = n, .align = "center") %>%
+    epi_slide(fitted = median(y, na.rm = TRUE), .window_size = n, .align = "center") %>%
     dplyr::mutate(resid = y - fitted) %>%
     roll_iqr(
       n = n,
@@ -359,7 +359,7 @@ roll_iqr <- function(z, n, detection_multiplier, min_radius,
 
   z %>%
     epi_slide(
-      roll_iqr = stats::IQR(resid),
+      roll_iqr = stats::IQR(resid, na.rm = TRUE),
       .window_size = n, .align = "center"
     ) %>%
     dplyr::mutate(

diff --git a/R/revision_analysis.R b/R/revision_analysis.R
@@ -99,11 +99,9 @@ revision_summary <- function(epi_arch,
   #
   # revision_tibble
   keys <- key_colnames(epi_arch)
-  names(epi_arch$DT)
 
-  revision_behavior <-
-    epi_arch$DT %>%
-    select(c(geo_value, time_value, all_of(keys), version, !!arg))
+  revision_behavior <- epi_arch$DT %>%
+    select(all_of(unique(c("geo_value", "time_value", keys, "version", arg))))
   if (!is.null(min_waiting_period)) {
     revision_behavior <- revision_behavior %>%
       filter(abs(time_value - as.Date(epi_arch$versions_end)) >= min_waiting_period)

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -48,7 +48,6 @@ articles:
       - aggregation
       - outliers
       - archive
-      - advanced
       - compactify
 
 repo: