Updated before that was a number too low.

Author: kenmawer

R/archive.R

@@ -599,8 +599,8 @@ epi_archive =
             }
 
             # If a custom time step is specified, then redefine units 
-            before_num = before-1
-            if (!missing(time_step)) before_num = time_step(before-1)
+            before_num = before
+            if (!missing(time_step)) before_num = time_step(before)
 
             # What to group by? If missing, set according to internal keys;
             # otherwise, tidyselect.

R/methods-epi_archive.R

@@ -422,11 +422,11 @@ epix_merge = function(x, y,
 #' Finally, this is simply a wrapper around the `slide()` method of the
 #'   `epi_archive` class, so if `x` is an `epi_archive` object, then:
 #'   ```
-#'   epix_slide(x, new_var = comp(old_var), before = 120)
+#'   epix_slide(x, new_var = comp(old_var), before = 119)
 #'   ```
 #'   is equivalent to:
 #'   ```
-#'   x$slide(new_var = comp(old_var), before = 120)
+#'   x$slide(new_var = comp(old_var), before = 119)
 #'   ```
 #'
 #' @importFrom rlang enquo
@@ -444,7 +444,7 @@ epix_merge = function(x, y,
 #'                       by = "1 day")
 #' epix_slide(x = archive_cases_dv_subset,
 #'            f = ~ mean(.x$case_rate_7d_av),
-#'            before = 3,
+#'            before = 2,
 #'            group_by = geo_value,
 #'            ref_time_values = time_values,
 #'            new_col_name = 'case_rate_3d_av')

man/epix_slide.Rd

@@ -17,7 +17,7 @@ test_that("epix_slide works as intended",{
 
   xx1 <- epix_slide(x = xx,
                     f = ~ sum(.x$binary),
-                    before = 3,
+                    before = 2,
                     group_by = geo_value,
                     new_col_name = "sum_binary")
 
@@ -32,7 +32,7 @@ test_that("epix_slide works as intended",{
   expect_identical(xx1,xx2) # *
 
   xx3 <- xx$slide(f = ~ sum(.x$binary),
-                  before = 3,
+                  before = 2,
                   group_by = "geo_value",
                   new_col_name = 'sum_binary')
 

tests/testthat/test-epix_slide.R

@@ -71,21 +71,21 @@ test_that("quosure passing issue in epix_slide is resolved + other potential iss
                       compactify = TRUE)
   reference_by_modulus = epix_slide(x = ea,
                                       f = ~ mean(.x$case_rate_7d_av),
-                                      before = 3,
+                                      before = 2,
                                       group_by = modulus,
                                       ref_time_values = time_values,
                                       new_col_name = 'case_rate_3d_av')
   reference_by_both = epix_slide(x = ea,
                                  f = ~ mean(.x$case_rate_7d_av),
-                                 before = 3,
+                                 before = 2,
                                  group_by = c(geo_value, modulus),
                                  ref_time_values = time_values,
                                  new_col_name = 'case_rate_3d_av')
   # test the passing-something-that-must-be-enquosed behavior:
   expect_identical(
     ea$slide(
       f = ~ mean(.x$case_rate_7d_av),
-      before = 3,
+      before = 2,
       group_by = modulus,
       ref_time_values = time_values,
       new_col_name = 'case_rate_3d_av'
@@ -96,7 +96,7 @@ test_that("quosure passing issue in epix_slide is resolved + other potential iss
   expect_identical(
     epix_slide(x = ea,
                f = ~ mean(.x$case_rate_7d_av),
-               before = 3,
+               before = 2,
                group_by = "modulus",
                ref_time_values = time_values,
                new_col_name = 'case_rate_3d_av'),
@@ -105,7 +105,7 @@ test_that("quosure passing issue in epix_slide is resolved + other potential iss
   expect_identical(
     ea$slide(
       f = ~ mean(.x$case_rate_7d_av),
-      before = 3,
+      before = 2,
       group_by = "modulus",
       ref_time_values = time_values,
       new_col_name = 'case_rate_3d_av'
@@ -121,7 +121,7 @@ test_that("quosure passing issue in epix_slide is resolved + other potential iss
   expect_identical(
     epix_slide(x = ea,
                f = ~ mean(.x$case_rate_7d_av),
-               before = 3,
+               before = 2,
                group_by = tidyselect::all_of(my_group_by),
                ref_time_values = time_values,
                new_col_name = 'case_rate_3d_av'),
@@ -130,7 +130,7 @@ test_that("quosure passing issue in epix_slide is resolved + other potential iss
   expect_identical(
     ea$slide(
       f = ~ mean(.x$case_rate_7d_av),
-      before = 3,
+      before = 2,
       group_by = tidyselect::all_of(my_group_by),
       ref_time_values = time_values,
       new_col_name = 'case_rate_3d_av'
@@ -141,15 +141,15 @@ test_that("quosure passing issue in epix_slide is resolved + other potential iss
   expect_identical(
     epix_slide(x = ea,
                f = ~ mean(.x$case_rate_7d_av),
-               before = 3,
+               before = 2,
                ref_time_values = time_values,
                new_col_name = 'case_rate_3d_av'),
     reference_by_both
   )
   expect_identical(
     ea$slide(
       f = ~ mean(.x$case_rate_7d_av),
-      before = 3,
+      before = 2,
       ref_time_values = time_values,
       new_col_name = 'case_rate_3d_av'
     ),

tests/testthat/test-methods-epi_archive.R

@@ -61,12 +61,12 @@ df %>%
 df %>% 
   mutate(version = time_value) %>% 
   as_epi_archive() %>%
-  epix_slide(x_2dav = mean(x), before = 2, ref_time_values = as.Date("2020-06-02"))
+  epix_slide(x_2dav = mean(x), before = 1, ref_time_values = as.Date("2020-06-02"))
 
 df %>% 
   mutate(version = time_value) %>% 
   as_epi_archive() %>%
-  epix_slide(~ mean(.x$x), before = 2, ref_time_values = as.Date("2020-06-02"))
+  epix_slide(~ mean(.x$x), before = 1, ref_time_values = as.Date("2020-06-02"))
 ```
 
 When the slide computation returns an atomic vector (rather than a single value)
@@ -153,7 +153,7 @@ df %>%
   as_epi_archive() %>%
   epix_slide(a = data.frame(x_2dav = mean(x), x_2dma = mad(x)),
              ref_time_values = as.Date("2020-06-02"),
-             before = 2, as_list_col = FALSE, names_sep = NULL)
+             before = 1, as_list_col = FALSE, names_sep = NULL)
 ```
 
 ## Multi-row outputs
@@ -354,7 +354,7 @@ k_week_ahead <- function(x, ahead = 7, as_of = TRUE) {
     x %>%
       epix_slide(fc = prob_arx(percent_cli, case_rate_7d_av, geo_value, time_value, 
                                args = prob_arx_args(ahead = ahead)), 
-                 before = 120, ref_time_values = fc_time_values) %>%
+                 before = 119, ref_time_values = fc_time_values) %>%
       mutate(target_date = time_value + ahead, as_of = TRUE, 
              geo_value = fc_geo_value)
   }

vignettes/advanced.Rmd

@@ -358,7 +358,7 @@ fc_time_values <- seq(as.Date("2020-08-01"),
                       by = "1 month")
 
 z <- epix_slide(x, fc = prob_arx(x = percent_cli, y = case_rate_7d_av),
-                before  = 120, ref_time_values = fc_time_values,
+                before  = 119, ref_time_values = fc_time_values,
                 group_by = geo_value)
 
 head(z, 10)
@@ -388,7 +388,7 @@ x_latest <- epix_as_of(x, max_version = max(x$DT$version))
 k_week_ahead <- function(x, ahead = 7, as_of = TRUE) {
   if (as_of) {
     x %>%
-      epix_slide(fc = prob_arx(percent_cli, case_rate_7d_av, ahead = ahead), before = 120,
+      epix_slide(fc = prob_arx(percent_cli, case_rate_7d_av, ahead = ahead), before = 119,
                  ref_time_values = fc_time_values, group_by = geo_value) %>%
       mutate(target_date = time_value + ahead, as_of = TRUE) 
   }