siteSum: Summarize and plot detections of all tags by site

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

Description

Creates a summary of the first and last detection at a site, the length of time between first and last detection, the number of tags, and the total number of detections at a site. Plots total number of detections across all tags, and total number of tags detected at each site.

Usage

siteSum(data, units = "hours")

Arguments

data	a selected table from .motus data, eg. "alltags", or a data.frame of detection data including at a minimum variables for motusTagID, sig, recvDeployLat, recvDeployName, and ts
units	units to display time difference, defaults to "hours", options include "secs", "mins", "hours", "days", "weeks"

Value

a data.frame with these columns:

• site: site

• first_ts: time of first detection at specified site

• last_ts: time of last detection at specified site

• tot_ts: total amount of time between first and last detection at specified site, output in specified unit (defaults to "hours")

• num.tags: total number of unique tags detected at specified site

• num.det: total number of tag detections at specified site

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"

Create site summaries for all sites within detection data with time in default hours using data.frame df.alltags
site_summary <- siteSum(tbl.alltags)

Create site summaries for only select sites with time in minutes
site_summary <- siteSum(filter(df.alltags, recvDeployName %in% c("Niapiskau", "Netitishi", "Old Cur", "Washkaugou")), units = "mins")

Create site summaries for only a select species, Red Knot
site_summary <- siteSum(filter(df.alltags, speciesEN == "Red Knot"))

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