validate function: updated quick horizontal check to include ducks, g…

…eese, and coots_snipe only; these 3 bags are the only ones applicable to all 49 states

R/validate.R

@@ -30,7 +30,7 @@
 #'  \item vertical - Checks for repetition vertically in species and/or bag fields, grouped by dl_state and dl_date
 #'  \item horizontal - Checks for repetition horizontally, across each record
 #'  }
-#' @param all Should all species groups be checked (TRUE)? If set to FALSE (default), then only ducks will be vertically checked and only ducks, geese, doves, and woodcock will be horizontally checked.
+#' @param all Should all species groups be checked (TRUE)? If set to FALSE (default), then only ducks will be vertically checked and only ducks, geese, and coots_snipe will be horizontally checked.
 #' @param period Time period in which to group the data. The function uses dl_date automatically, but either of the following may be supplied:
 #'  \itemize{
 #'  \item dl_date - Date the HIP data were downloaded
@@ -184,12 +184,12 @@ validate <-
 
       # Horizontal validation
 
-      # Quick check (duck, goose, dove, and woodcock check only)
+      # Quick check (duck, goose, & coots_snipe only)
       if(all == FALSE){
         h_test <-
           x %>%
           # Subset the data
-          select(source_file, ducks_bag, geese_bag, dove_bag, woodcock_bag) %>%
+          select(source_file, ducks_bag, geese_bag, coots_snipe) %>%
           group_by(source_file) %>%
           # Paste all of the species group values together
           unite(h_string, !contains("source"), sep = "-") %>%

vignettes/migbirdHIP_workflow.Rmd

@@ -276,6 +276,13 @@ Note: This function replaces "." values with NA in non-permit species columns fo
 DL1301_fixed <- fixDuplicates(DL1301_clean)
 ```
 
+```
+## Error in `slice_sample()`:
+## ! Problem while computing indices.
+## Caused by error in `sample.int()`:
+## ! invalid first argument
+```
+
 ### strataCheck
 
 Running `strataCheck` ensures species "bag" values are in order. This function searches for values in species group columns that are not typical or expected by the FWS. If a value outside of the normal range is detected, an output tibble is created. Each row in the output contains the state, species, unusual stratum value, and a list of the normal values we would expect.
@@ -308,28 +315,28 @@ strataCheck(DL1301_fixed)
 
 The `validate` function looks for repeated values in two dimensions, both horizontally and vertically.
 
-<b>Horizontally.</b> The horizontal check for repetition looks across records and finds any rows with same value in each species group column. Details in the output tibble include: the repeated value (h_value), number of records with repeats (h_rep), total number of records (h_total), and proportion of repeated values per file (prop_repeat). The default version of this function (`all = FALSE`) only checks ducks, geese, dove, and woodcock bags. If the parameter is set to `all = TRUE`, every species group will be checked.
+<b>Horizontally.</b> The horizontal check for repetition looks across records and finds any rows with same value in each species group column. Details in the output tibble include: the repeated value (h_value), number of records with repeats (h_rep), total number of records (h_total), and proportion of repeated values per file (prop_repeat). The default version of this function (`all = FALSE`) only checks ducks, geese, and coots_snipe bags. If the parameter is set to `all = TRUE`, every species group will be checked.
 
 
 ```r
 validate(DL1301_fixed, type = "horizontal")
 ```
 
 ```
-## # A tibble: 43 × 5
+## # A tibble: 47 × 5
 ##    source_file    h_value h_rep h_total prop_repeat
 ##    <chr>          <chr>   <int>   <int>       <dbl>
-##  1 WI20211229.txt 1         276     323       0.854
-##  2 AL20211229.txt 1        3995    4790       0.834
-##  3 MO20211229.txt 1        2680    3604       0.744
-##  4 WV20211229.txt 2         183     294       0.622
-##  5 IN20211229.txt 1         406     690       0.588
-##  6 MN20211229.txt 1         171     297       0.576
-##  7 WA20211229.txt 1         815    1460       0.558
-##  8 WA20211215.txt 1         937    1737       0.539
-##  9 KY20211228.txt 1         528     984       0.537
-## 10 NE20211217.txt 1         477     903       0.528
-## # … with 33 more rows
+##  1 IA20211215.txt 0        2841    3175       0.895
+##  2 AL20211229.txt 1        4223    4790       0.882
+##  3 WI20211229.txt 1         273     323       0.845
+##  4 MO20211229.txt 1        2697    3604       0.748
+##  5 ME20211229.txt 1         112     151       0.742
+##  6 NM20211229.txt 1         208     295       0.705
+##  7 ID20211229.txt 1        1763    2588       0.681
+##  8 ND20211215.txt 1         130     204       0.637
+##  9 CA20211229.txt 1        2003    3211       0.624
+## 10 IN20211229.txt 1         416     690       0.603
+## # … with 37 more rows
 ```
 
 <b>Vertically.</b> The vertical check searches within each column for repetition. Any species group column with the same value in all rows will be detected. *Coming soon:* States that do not have a hunting season for one or more species groups (e.g. seaducks) will not be returned using this function for reporting all zero values. The default version of this function (`all = FALSE`) only checks duck bags. If the parameter is set to `all = TRUE`, every species group will be checked.

vignettes/migbirdHIP_workflow.Rmd.orig

@@ -229,7 +229,7 @@ strataCheck(DL1301_fixed)
 
 The `validate` function looks for repeated values in two dimensions, both horizontally and vertically.
 
-<b>Horizontally.</b> The horizontal check for repetition looks across records and finds any rows with same value in each species group column. Details in the output tibble include: the repeated value (h_value), number of records with repeats (h_rep), total number of records (h_total), and proportion of repeated values per file (prop_repeat). The default version of this function (`all = FALSE`) only checks ducks, geese, dove, and woodcock bags. If the parameter is set to `all = TRUE`, every species group will be checked.
+<b>Horizontally.</b> The horizontal check for repetition looks across records and finds any rows with same value in each species group column. Details in the output tibble include: the repeated value (h_value), number of records with repeats (h_rep), total number of records (h_total), and proportion of repeated values per file (prop_repeat). The default version of this function (`all = FALSE`) only checks ducks, geese, and coots_snipe bags. If the parameter is set to `all = TRUE`, every species group will be checked.
 
 ```{r, validate_h}
 validate(DL1301_fixed, type = "horizontal")