moving the taxa renaming routine to chkinp

Author: Robert Butler

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ASCI
 Type: Package
 Title: Calculate scores for the Algal Stream Condition Index
-Version: 2.5.0
+Version: 2.5.1
 Date: 2020-08-05
 Description: Calculate ASCI scores using diatom, soft-bodied algae, or a 
     hybrid appproach. Scores are used for bioassessment of California perennial 

R/ASCI.R

@@ -44,20 +44,6 @@ ASCI <- function(taxa, stations){
   txrmv <- dat$txrmv
   dat <- dat$taxa
 
-  dat <- dat %>%
-    left_join(
-      taxa_crosswalk %>% 
-      rename(FinalID = NewName)
-      ,
-      by = 'FinalID'
-    ) %>% 
-    mutate(
-      FinalID = case_when(
-        is.na(OldName_in_ASCI_Calculator) ~ FinalID,
-        T ~ OldName_in_ASCI_Calculator
-      )
-    ) %>%
-    select(-OldName_in_ASCI_Calculator)
 
   # calculate GIS from stations
   # calcgis calculates required gismetrics which are not provided, from the ones that were provided in the station data

R/chkinp.R

@@ -105,6 +105,23 @@ chkinp <- function(taxa, station, getval = FALSE){
     stop(msg, call. = FALSE)
   }
 
+  taxa <- taxa %>%
+    left_join(
+      taxa_crosswalk %>% 
+        rename(FinalID = NewName)
+      ,
+      by = 'FinalID'
+    ) %>% 
+    mutate(
+      FinalID = case_when(
+        is.na(OldName_in_ASCI_Calculator) ~ FinalID,
+        T ~ OldName_in_ASCI_Calculator
+      )
+    ) %>%
+    select(-OldName_in_ASCI_Calculator)
+  
+  
+  
   # Reassure that all columns are the correct datatype
   taxa <- taxa %>%
     dplyr::mutate(