figure out Dead_but_now_alive #52 #54

R_scripts/X_check_trees_with_warnings.R

@@ -0,0 +1,46 @@
+
+#############################################################################
+# Purpose: check trees with warnings
+# Developped by: Valentine Herrmann - HerrmannV@si.edu
+##########################################################################
+
+# Clean environment ####
+rm(list = ls())
+
+# Set working directory ####
+setwd(".")
+
+# Load libraries ####
+
+
+# Load data ####
+
+## warning files
+w <- read.csv("testthat/reports/trace_of_reports/warnings_file.csv")
+
+
+## previous mortality census files
+
+# mort_files <- list.files("data/", pattern = "\\d\\d.csv", full.names = T)
+#
+# mort_files <- sapply(mort_files, read.csv)
+# names(mort_files) <- regmatches(names(mort_files), regexpr("\\d{4}", names(mort_files))) # give year as name
+
+## load allmort data 
+load("C:/Users/herrmannV/Dropbox (Smithsonian)/GitHub/SCBI-ForestGEO/SCBImortality/data/allmort.rdata") # load allmort data
+
+## look at types of warnings #### 
+table(w$warning_name) # add code if some are not adressed below
+
+# check status history of status issues ####
+st <- w[w$warning_name %in% "Dead_but_now_alive", ]
+
+status_history <- cbind(st[, c("Quad", "Tag", "StemTag", "DBH")], allmort[match(paste(st$Tag, st$StemTag), paste(allmort$tag, allmort$StemTag)), sort(grep("status", names(allmort), value = T))], "/" = "/", st[,grep("Status", names(st))], st$Notes.2021)
+
+status_history$status.2018.1 <- NULL
+
+status_history <- status_history[order(status_history$Status.2018), ]
+
+View(status_history)
+
+write.table(status_history, "temporary_files_for_QA_QC/status_history_Dead_but_now_alive.csv", sep = "|", quote = F, row.names = F)