MoveTraitsDatabase/02e_remove_studies_manually.R at main · annescharf/MoveTraitsDatabase · GitHub

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# ---
# title: "MoveTraits Database"
# author: "Anne Hertel"
# date: "March 2025"
# ---

### in this script:
## open access studies where owners have not approved reuse are set to "exclude = yes" in reference table

library(lubridate);library(metafor);library(tidyverse);library(amt);library(Hmisc)
library(adehabitatHR); library(move2); library(epitools); library(suncalc); library(purrr); library(bit64)

## ----Import movement data per individual-------------------------------------------------------------
pathTOfolder <- "./DATA/MoveTraitsData/"

metadata <- readRDS(paste0(pathTOfolder,"/referenceTableStudies_ALL_excludedColumn.rds"))
metadata[metadata$MBid %in% 1541820092,"excluded"] <- "yes" # exclude Cagan study

metadata[metadata$fileName %in%  c("1120749252_3069649656.rds",
                                   "1120749252_3069649678.rds",
                                   "1120749252_3069649685.rds",
                                   "2950149_2950167.rds") ,"excluded"] <- "yes" # exclude coaties

## ---- Studies to remove - manual cleaning -------------------------------------------------------------
myremove <- read.csv(paste0(pathTOfolder,"/manual_remove.csv"))
myremove <- paste(myremove$study_id,myremove$animal_id,sep="_")
myremove <- paste0(myremove,".rds")

metadata[metadata$fileName %in%  myremove ,"excluded"] <- "yes"

saveRDS(metadata, paste0(pathTOfolder,"/referenceTableStudies_ALL_excludedColumn_excludedStudies.rds"))