README.md

In LDalby/loggr: Handling and Analyzing Data From Loggers

loggr

loggr is in very early development. Use with caution.

Installation

Installing the latest version of loggr requires having the devtools package installed. Make sure you have that (on Win you need to install RTools first) and then simply run the lines below:

library(devtools)
install_github('LDalby/loggr')

Use

A short example of using the CleanRawFile function to clean output from HOBO data loggers. In this example you have a bunch of data logger files sitting in a folder containing only logger files. It is assumed that all the characters before the last underscore is the logger ID. If this is not the case you might get funky stuff out...

The beginendfile file is a file with the three columns: BiotopID, start & stop. It is indicating the start and stop dates for each logger. To avoid the data which may have been recorded before deployment of the device.

# Clean HOBO loggers
library(loggr)
pathtologgers = INSERT PATH TO DIRECTORY
files = dir(pathtologgers)
LoggerList = vector('list', length(files))
beginendfile = fread(INSERT PATH TO START STOP)
for (i in seq_along(files)) {
    path = paste0(pathtologgers, files[i])
    temp = CleanRawFile(file = path, type = 'hobo')
    uscorelocs = stringr::str_locate_all(files[i], '_')
    lastuscore = max(unlist(uscorelocs))
    id = stringr::str_sub(files[i], end = lastuscore-1)
    temp[, ID:=id]
    start = beginendfile[BiotopID == id, start]
    stop = beginendfile[BiotopID == id, stop]
    LoggerList[[i]] = temp[Date >= mdy(start) & Date <= mdy(stop),]
}
final = do.call('rbind', LoggerList)
write.table(final, file = PATH AND FILE NAME, sep = '\t',
    row.names = FALSE, quote = FALSE)

LDalby/loggr documentation built on May 8, 2019, 5:48 p.m.