Functions to import MoveBank csv files, data.frame, and Move objects, coerce them into telemetry objects, summarize them, and combine data from multiple tracking devices.

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 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 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 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 telemetry
summary(object,...)

head(x,...)

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

tail(x,...)

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

tbind(...)

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. Alternatively timeformat="auto" will attempt to infer the timestamp format with parse_date.

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.

...

telemetry objects or a list of such objects, for tbind(). Optional arguments to be fed to fread or read.csv, in the case of compressed files, for as.telemetry().

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, using tbind().

Value

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

as.telemetry will always report the smallest sampling interval, as a message, and the number repeating timestamps, as a warning. Tiny sampling intervals (and repeating timestamps) can sometimes result from misformated timestamps or an incorrect timeformat argument. However, even if geniune, they can necessitate data cleaning (outlie) or location-error modeling (vignette('error')).

Author

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

See also