mt_read: Reading files downloaded from movebank

Description

Reading files downloaded from movebank

Usage

mt_read(file, ...)

Value

An object of the class move2

Arguments

file: The file path to read or a R connection (for details see connections). Files can either be csv files from movebank or zip files that are created using Env-DATA.
...: Arguments passed on to vroom, for example col_select

Details

Files can be gz compressed and if the same columns are present multiple files can be read simultaneously. Using the pipe command in R and some command line tools it is possible to select specific days or months.

When using the col_select argument of vroom it is possible to speed up file reading considerably while reducing memory consumption. Especially columns containing acceleration values can become quite large.

For files that contain both a individual-local-identifier and a tag-local-identifier column a check is preformed if individuals have been wearing multiple tags over time. If this is the case tracks are created based on the combination of both id's. A new column names individual-tag-local-identifier in created, which will correspond to the track ids. This somewhat resembles the movebank logic however the track ids do not necessarily correspond to the deployments in movebank as this information is not contained in exported csv's.

Examples

Run this code

path_fishers <- mt_example()
mt_read(path_fishers)

## Reduce the mount of data read this might provide memory advantages
## and speed up reading
mt_read(path_fishers, col_select = c(
  "location-long", "location-lat",
  "timestamp", "individual-local-identifier"
))
## Read Galapagos Albatross data that has been annotated
mt_read(mt_example("Galapagos_Albatrosses-1332012225316982996.zip"))
## Notice this produces a warning as some units are not recognized
## This can be prevented by installing the units
if (FALSE) {
units::install_unit("gC", "g", "Grams of carbon")
}

if (FALSE) {
## Reading can also be manipulted to speed up or reduce memory consumption
## Here we assume the Galapagos albatross data has been downloaded
mt_read("~/Downloads/Galapagos Albatrosses.csv")
## Exclude the column 'eobs:accelerations-raw'
mt_read("~/Downloads/Galapagos Albatrosses.csv",
  col_select = (!`eobs:accelerations-raw`)
)
## Only read records from July 2008 using a system pipe where the data
## is already filtered before reading into R
mt_read(pipe('cat "~/Downloads/Galapagos Albatrosses.csv" | grep "2008-07\\|time"'))
}