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Summarize and plot detections of all tags by site

Source : R/siteSum.R
siteSum.Rd

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.

Utilisation

siteSum(data, units = "hours")

Arguments

data

a selected table from .motus data, eg. "alltagsGPS", or a data.frame of detection data including at a minimum variables for motusTagID, sig, recvDeployLat, recvDeployLon, recvDeployName, ts, gpsLat, and gpsLon

units

units to display time difference, defaults to "hours", options include "secs", "mins", "hours", "days", "weeks"

Valeur de retour

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

Exemples

# You can use either a selected tbl from .motus eg. "alltagsGPS", or a
# data.frame, instructions to convert a .motus file to all formats are below.

# download and access data from project 176 in sql format
# usename and password are both "motus.sample"
if (FALSE) sql.motus <- tagme(176, new = TRUE, update = TRUE)

# OR use example sql file included in `motus`
sql.motus <- tagme(176, update = FALSE, 
                   dir = system.file("extdata", package = "motus"))

# convert sql file "sql.motus" to a tbl called "tbl.alltags"
library(dplyr)
tbl.alltags <- tbl(sql.motus, "alltagsGPS") 

# convert the tbl "tbl.alltags" to a data.frame called "df.alltags"
df.alltags <- tbl.alltags %>% 
  collect() %>% 
  as.data.frame() 

# 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
sub <- filter(df.alltags, recvDeployName %in% 
                c("Niapiskau", "Netitishi", "Old Cur", "Washkaugou"))
site_summary <- siteSum(sub, units = "mins")


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