siteTrans: Summarize transitions between sites for each tag

In jbrzusto/motus: fetch and use data from http://motus.org

Description

Creates a dataframe of transitions between sites; detections are ordered by detection time, then "transitions" are identified as the period between the final detection at site x (possible "departure"), and the first detection (possible "arrival") at site y (ordered chronologically). Each row contains the last detection time and lat/lon of site x, first detection time and lat/lon of site y, distance between the site pair, time between detections, rate of movement between detections, and bearing between site pairs.

Usage

siteTrans(data, latCoord = "recvDeployLat", lonCoord = "recvDeployLon")

Arguments

data	a selected table from .motus data, eg. "alltags", or a data.frame of detection data including at a minimum variables for ts, motusTagID, tagDeployID, recvDeployName, and a latitude/longitude
latCoord	a variable with numeric latitude values, defaults to recvDeployLat
lonCoord	a variable with numeric longitude values, defaults to recvDeployLon

Value

a data.frame with these columns:

• fullID: fullID of Motus registered tag

• ts.x: time of last detection of tag at site.x ("departure" time)

• lat.x: latitude of site.x

• lon.x: longitude of site.x

• site.x: first site in transition pair (the "departure" site)

• ts.y: time of first detection of tag at site.y ("arrival" time)

• lat.y: latitude of site.y

• lon.y: longitude of site.y

• site.y: second site in transition pair (the "departure" site)

• tot_ts: length of time between ts.x and ts.y (in seconds)

• dist: total straight line distance between site.x and site.y (in metres), see latLonDist function in sensorgnome package for details

• rate: overall rate of movement (tot_ts/dist), in metres/second

• bearing: bearing between first and last detection sites, see bearing function in geosphere package for more details

Author(s)

Zoe Crysler [e-mail]

Examples

You can use either a selected tbl from .motus eg. "alltags", or a data.frame, instructions to convert a .motus file to all formats are below.
sql.motus <- tagme(176, new = TRUE, update = TRUE) # download and access data from project 176 in sql format
tbl.alltags <- tbl(sql.motus, "alltags") # convert sql file "sql.motus" to a tbl called "tbl.alltags"
df.alltags <- tbl.alltags %>% collect %>% as.data.frame() ## convert the tbl "tbl.alltags" to a data.frame called "df.alltags"

View all site transitions for all detection data from tbl file tbl.alltags
transitions <- siteTrans(tbl.alltags)

View site transitions for only tag 16037 from data.frame df.alltags using gpsLat/gpsLon
transitions <- siteTrans(filter(df.alltags, motusTagID == 16037), latCoord = "gpsLat", lonCoord = "gpsLon")

jbrzusto/motus documentation built on May 18, 2019, 7:03 p.m.