path<-"/Users/kylielanglois/SCCWRP/eDNA Sample Management - eDNA/mASCI"
path.local<-"/Users/kylielanglois/OneDrive - SCCWRP/algae/mASCI"

dat.in<-read_excel(file.path(path, "eDNAmaster_inventory_mASCI.xlsx"), 
                   sheet = 2)
colnames(dat.in)<-dat.in[1, ]
dat.in<-dat.in[-1, ]
colnames(dat.in)<-gsub("\r\n", "\\.", colnames(dat.in)) 
#turn "new line" in excel format to period
colnames(dat.in)<-gsub(" ", "\\.", colnames(dat.in)) 

dat.ex<-read_excel(file.path(path, "eDNAmaster_extraction_mASCI.xlsx"), 
                   sheet=2)

dat.seq<-read_excel(file.path(path, "eDNAmaster_extraction_mASCI.xlsx"), 
                              sheet = 3)
today<-format(Sys.Date(), "%m/%d/%y")

ceden<-read_excel(file.path(path.local, "CEDEN_stationLU.xlsx"), sheet = 1)
ceden<-ceden[!duplicated(ceden$StationCode), ]

lustations_df<-read.csv(file.path(path.local, "lustations_081925.csv"))
ref.status<-read.csv(file.path(path.local, "ref_screens_final_09222025.csv"))
#only do if no access to SMC database

get years collected

total samples processed by SCCWRP

get impact status and PSA region

from Rafi Mazor code “0_targeting sites for sampling.R” accessed 7/25/25

do once then export read files in at beginning of code

from Jeff Brown code “ASCI_Algae taxonomy_GIS metrics.R” accessed 9/8/25

do once then export

match to CEDEN and SCCWRP lustations

get masterid to match with SCCWRP databases

organize by region

organize by reference