README: Social connections across migration: Do Golden-crowned Sparrows (Zonotrichia atricapilla) that socialize in winter also breed together?

https://doi.org/10.7291/D1R08G

Description of the data and file structure

This collection of data includes the data and code used in the the paper titled above, published in the journal Wilson Field Ornithology. The Dryad files include field data of direct observations of the Golden-crowned sparrows recording their social interactions, GPS points from archival GPS tags, and scripts in the R programming language detailing all the analysis for the above paper. For full explanations of the study design, methods, and results, please see the publication.

The .csv files with ‘2016_flockingattributes.csv’ and ‘2016_flockingdata.csv’ are used in R code 2016_GCSPGPSFlockingnetwork.R.

The .txt files are used in the R code ‘GCSP_GPSdata.R.’

Details on each file

2016_flockingattributes.csv

A summary of the number of times each bird was seen in a flock or dominance interaction, used for filtering out any transient birds when making the flocking networks.

Variables:

Column A, No Header: The original order of the rows for reference.

Column B, ‘Bird.ID’: A unique combination of numbers specifying each bird, referred to as band numbers. This is part of the sequence of numbers on the metal band that each bird is banded with.

Column C, ‘Combos’: Abbreviation for the color bands. Each bird has a unique set of colored bands on its legs for an observer to visually identify the birds in the field.

Column D ‘times.if.flock’: How many times a bird was sighted by an observer in a flock at the field site in the 2016 season.

Column E, ‘time.in.dom’: How many times a bird was sighted by an observer in a dominance interaction at the field site in the 2016 season.

2016_flockingdata.csv

Field data for flocking records tracking which birds were seen in a particular location and time.

Variables:

Column A, ‘obs.id’: Observations of birds in the field ordered by date and time, starting with the oldest to newest.

Column B, ‘date’: Date of the observation in MM/DD/YY.

Column C, ‘time’: Time of the observation in 24 hour clock.

Column D, ‘observer’: Initials of the person doing the field observation.

Column E, ‘flock.size’: How many birds were seen in the flock, some with exact numbers and some with estimates, e.g. ‘> 2’ means more than 2 birds were seen.

Column F, ‘feeder.obs’: Noting if birds were seen at a feeding station with food placed by researchers - if ‘NA’, the observation of birds was not at a feeder, if ‘feeder,’ then they were.

Columns G-H, ‘locationX’: The location the birds were seen using a gridded map of the field site with 10m2 grid cells.

Columns O-AM, ‘ bird.idXX’: The identity of the birds seen in the flock tracked using their band numbers. Summaries of the band numbers are in 2016_flockingattributes.csv.

Column AN, ‘dup’: A row is noted as a ‘duplicate’ if the timing of the observation was too close to the previous one to count as an independent sighting of the birds in the flock.

19388_PinPoint_48485.txt

Text file of all GPS data for bird 19388. GPS points were taken on PinPoint archival GPS tags attached to the Golden-crowned Sparrows for the study. Columns are separated by tabs.

Variables:

Column A, ‘Index’: Order in which the GPS points were taken.

Column B, ‘Status’: Automated determination of if the GPS points were valid or not, based on using 3 or more satellites to determine the GPS points.

Column C, ‘Sats’: How many satellites were used to determine the GPS point.

Column D, ‘RTC-date’: Date of the point taken in YY/MM/DD.

Column E, ‘RTC-time’: Time of the point taken in 24 hr clock.

Column F, ‘FIX-date’: Date of the point taken if it was determined to be valid, in YY/MM/DD.

Column G, ‘FIX-time’: Time of the point taken if it was determined to be valid, in 24 hr clock.

Column H, ‘Delta(s)’: Not used for analysis.

Column I, ‘Latitude’: Latitude of the GPS point.

Column J, ‘Longitude: Longitude of the GPS point.

Column K, ‘Altitude’: Altitude of the GPS point taken in meters. In occasional cases where Altitude is ‘10000’ the measure is assumed to be a mis-read.

Column L, ‘HDOP’: Acronym for ‘horizontal dilution of precision,’ an estimate for accuracy of the GPS position, taking into account the number and angle of the satellites. Smaller HDOP values are better, with under 2.5 considered good, and less than 1.5 very good. However, HDOP is not as important as eRes for the type of snapshot GPS locations that were read by the PinPoint GPS tags used.

Column M, ‘eRes’: eRes, or residual error, is a measure of accuracy for the GPS location. This is influenced by factors such as the angle of the satellites used and the conditions in the atmosphere. Lower numbers are better, with under 20 considered good. However, this can only be estimated for fixes with 5 or more satellites used.

Column N, ‘Temperature(C)’: 0.0 listed for each value as this data not available for this type of GPS.

Column O, ‘Voltage(V)’: Blank - data not available for this type of GPS.

*77968_PinPoint_41720.txt *

Text file of all GPS data for bird 77968 - all columns are the same as the above text file.

81319_PinPoint_41698.txt

Text file of all GPS data for bird 81319  -all columns are the same as the above text file.

81324_PinPoint_41689.txt

Text file of all GPS data for bird 81324  - all columns are the same as the above text file.

GCSP_GPSsummary.csv

Summary measures from the GPS data and analysis and social network data analysis.

Variables:

Column A, ‘Bird_ID’: Unique number used to ID each bird from the metal band used to band them.

Column B, ‘Year’: Year which the GPS tag was put on the bird.

Column C, ‘Date_arrive’: The date when the bird arrived at the putative breeding ground from spring migration in MM/DD/YY format.

Column D, ‘Date_leave’: The date when the bird left the putative breeding ground for fall migration in MM/DD/YY format.

Column E, ‘Days_on_territory’: How many days the bird spent on the breeding ground using the arrival and leave dates.

Column F, ‘GPS_points_on_breeding’: How many GPS points were successfully taken while the bird was on the putative breeding ground.

Column G, ‘Ave_breeding-location’: The location of the breeding ground determined by the average distance of the points on the breeding ground, calculated in GCSP_GPSdata.R.

Column H, ‘Notes’: Notes about the summary

Column I, ‘Spring_start’: The date birds left on spring migration from the wintering grounds where the GPS tags were originally placed in MM/DD/YY format.

Column J,’Spring_mig_length’: The length, in days, it took the bird to migration from the wintering ground to the breeding ground.

Column K, ‘Spring_mig_distance_km’: The length of the spring migration distance in kilometers.

Column L, ‘Stop_sites’: If known, how many times the bird stopped while on migration.

Column M, ‘Fall_end’: If known, the date on which the bird returned to the wintering ground in MM/DD/YY formate.

Column N, ‘Fall_mig_length’: If known, how many days it took the bird to complete fall migration.

Column O, ‘Social_group’: which social group the bird belonged to on the wintering grounds in the 2017-2017 field season.

Column P, ‘Within_com_strength’: A social network measure called ‘Within community strength,’ measuring how strongly a bird socializes within its social group versus across other social groups.

Column Q, ‘Sex’: the sex of the bird determined by genetics.

R scripts and packages used

GCSP_GPSdata.R

- code analyzing GPS data to determine breeding locations and distances
- creating figures
- animated migration track

R Version 4.2.0

Packages used:

geosphere - v 1.4-14 
tidyverse - v 1.3.1
lubridate - v 1.8.0
cowplot - v 1.1.1

2016_GCSPGPSFlockingnetwork.R

- using the flocking attributes and flocking data to build the 2016 social network and determine the communities and within-community strength for each bird

R Version 4.2.0

Packages used:
igraph - v 1.4.0
dplyr - v 1.0.9
asnipe - v 1.1.16
readr - v 2.1.2
tidyr - v 1.2.0
ggraph - v 2.1.0
tidygraph - v 1.2.3