moving the taxa renaming routine to chkinp

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(