ctmm: as.telemetry – R documentation

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as.telemetry

Import, coerce, and summarize MoveBank data

Description

Functions to import MoveBank csv files, data.frame, and Move objects, coerce them into telemetry objects, and summarize them.

Usage

as.telemetry(object,timeformat="",timezone="UTC",projection=NULL,datum=NULL,timeout=Inf,
             na.rm="row",mark.rm=FALSE,keep=FALSE,drop=TRUE,...)

## S3 method for class 'character'
as.telemetry(object,timeformat="",timezone="UTC",projection=NULL,datum=NULL,timeout=Inf,
             na.rm="row",mark.rm=FALSE,keep=FALSE,drop=TRUE,...)

## S3 method for class 'data.frame'
as.telemetry(object,timeformat="",timezone="UTC",projection=NULL,datum=NULL,timeout=Inf,
             na.rm="row",mark.rm=FALSE,keep=FALSE,drop=TRUE,...)

## S3 method for class 'Move'
as.telemetry(object,timeformat="",timezone="UTC",projection=NULL,datum=NULL,timeout=Inf,
             na.rm="row",mark.rm=FALSE,keep=FALSE,drop=TRUE,...)

## S3 method for class 'telemetry'
summary(object,...)

head(x,...)

## S3 method for class 'telemetry'
head(x,n=6L,...)

tail(x,...)

## S3 method for class 'telemetry'
tail(x,n=6L,...)

Arguments

`object`	A MoveBank CSV filename, MoveBank `data.frame` object, or `Move` object to coerce, or a `telemetry` object to summarize.
`timeformat`	Format argument for `strptime`, corresponding to the input data.
`timezone`	Timezone argument for `strptime`, corresponding to the input data.
`projection`	Optional PROJ.4 projection argument to be fed to `spTransform`, for the output telemetry object.
`datum`	Optional PROJ.4 projection argument to specify the input longitude-latitude datum. The default is WGS84.
`timeout`	GPS location fix timeout value (seconds) for assigning a `"timed-out"` location class.

`na.rm`	If some values are `NA` in the data frame, are the rows (times) deleted or are the columns (data types) deleted.
`mark.rm`	Delete Movebank manually marked outliers. Also see `outlie`.
`keep`	Retain additonal columns after coercion. `keep=TRUE` retains all columns, while individual columns to retain can be specified by name.
`drop`	Only return a `telemetry` object for one individual if `TRUE`. Always return a `list` of telemetry objects if `FALSE`.
`...`	Optional arguments to be fed to `fread` or `read.csv`, in the case of compressed files.
`x`	`telemetry` object.
`n`	Number of rows to return, if positive, or number of rows to omit, if negative.

Details

If no projection argument is specified, a two-point equidistant projection is calculated that should be good for most range resident and migratory species. Global migrations that are not along one geodesic (locally straight line) will probably suffer distortion.

as.telemetry assumes Movebank naming conventions. Sufficient MoveBank columns include individual.local.identifier (or tag.local.identifier), timestamp, location.long and location.lat, while the optional Movebank columns include (E-OBS) eobs.horizontal.accuracy.estimate, (Telonics) GPS.Horizontal.Error, GPS.HDOP, (Argos) Argos.orientation, Argos.semi.minor and Argos.semi.major or Argos.location.class, etc.. To have all columns detected and not overwrite eachother's information, it is best to have only one tracking device model per file imported. Multiple deployments on a single individual can be merged afterwards.

Value

as.telemetry returns a single telemetry object or list of telemetry objects if multiple animals are identified.

Author(s)

C. H. Fleming, X. Dong, B. Kranstauber, G. Péron, and K. Safi.