subset recruits and old stems so not flagged as duplicated #31

R_scripts/CI_QAQC_reports.R

@@ -17,15 +17,19 @@ library(curl)
 old_tree <- fread("raw_data/old_trees/tree_table_0.csv")
 recruits_tree <-  fread("raw_data/recruits/tree_table_0.csv")
 
-old_stem <-  fread("raw_data/old_trees/stem_table_1.csv")
-recruits_stem <- fread("raw_data/recruits/stem_table_1.csv")
+old_stem <-  fread("raw_data/old_trees/stem_table_1.csv")# this is essentially the same as recruits_stem, so will subset
+recruits_stem <- fread("raw_data/recruits/stem_table_1.csv") # this is essentially the same as old_stem, so will subset
 
 
 tree <- rbind(data.table(table = "old_trees", old_tree), data.table(table = "recruits", recruits_tree))
 if( any(duplicated(tree$tag))) stop("there are duplicated tags in tree! double check how to bring in recuits")
 
 
-recruits_stem$dbh_2018_mm <- old_stem$dbh_2018_mm[match(paste(recruits_stem$tag, recruits_stem$StemTag), paste(old_stem$tag, old_stem$StemTag))] # have to add this as it is missing in the recruits
+old_stem <- old_stem[tag %in% old_tree$tag, ]
+recruits_stem <- recruits_stem[tag %in% recruits_tree$tag, ]
+
+recruits_stem$dbh_2018_mm <- NA
+
 stem <- rbind(data.table(table = "old_trees", old_stem), data.table(table = "recruits", recruits_stem[, names(old_stem), with = F]))
 
 cat("New census data loaded") # this is to troubleshoot CI on GitHub actions (see where errors happen)