Data from: Weather and local density influence post-fledging survival of a migratory songbird

Metadata
Title: “Weather and local density influence post-fledging survival of a migratory songbird”
Authors: Sarah D. Mueller, Daniel J. Mennill, Stéphanie M. Doucet, Sarah L. Dobney, Hayley A. Spina, D. Ryan Norris
Journal: Journal of Avian Biology (submitted)
Year of publication: (submitted)

Study system: Savannah sparrows (Passerculus sandwichensis)
Study site: Kent Island, New Brunswick, Canada (44.58°N, 66.76°W)
Timespan: 2022-2024

Summary
The repository includes the data and R script for performing an analysis of factors influencing post-fledging survival of individual Savannah sparrows (see reference). The data come from daily monitoring of individual fledglings via radio-telemetry in addition to a long-term study of the demography and breeding biology of a population of Savannah sparrows (Passerculus sandwichensis) on Kent Island, New Brunswick, Canada (44.58°N, 66.76°W). Weather data are from an Environment and Climate Change Canada (ECCC) weather station on Grand Manan Island, NB (44.71°N, 66.80°W; https://www.climate.weather.gc.ca)

Datasets
(1) deployments.csv: contains information about each radio tag deployment on an individual Savannah sparrow fledgling (e.g. date of deployment, fate of individual at end of deployment)
(2) fledglings.csv: contains a record for all nestlings banded in the study population from 2022-2024 that fledged
(3) gm_weather.csv: contains daily weather data (precipitation and mean and min temperatures) from the Grand Manan ECCC weather station from 2022-2024
(4) nests_2022-2024: contains information about all nests found from 2022-2024
(5) survival_data.csv: contains daily records of the fates of radio-tracked nestlings and all covariates used in the survival analysis; this is the dataset used for the survival models

Variables

Variables with the same name in different files have the same interpretation and are not repeated in the description below, unless otherwise noted.

In deployments.csv:
tag = factor; unique identifier of a deployment of a tag
band_number = factor; unique aluminum band number (Canadian Wildlife Service) assigned to each individual bird
year = integer (2022-2024); study year
nest_key = factor; an alpha-numeric code assigned to the natal nest of each fledgling
tagged_age = factor; the age at which a fledgling was radio-tagged, either in the nest (N = nestling), or as a fledged juvenile (J = juvenile)
tagged_date = date (mm/dd/yy); calendar date on which the tag deployment occurred
fledge_date = date (mm/dd/yy); calendar date on which the juvenile fledged from its nest
fate = factor; the fate of the juvenile at the end of the tag deployment
died = binary; 0 = fledgling was alive or had an unknown fate at the end of the deployment, 1 = fledgling was known to be dead or was assumed dead at the end of the deployment
weight = numeric; the mass of the individual when it was banded as a nestling, in grams
age_in_d = integer; the age at which an individual was banded as a nestling, in days post-hatch (most individuals were banded on day 7 post-hatch, but a few on day 8)

In fledglings.csv:
tagged = logical; whether a fledgling was radio-tagged (TRUE) or not (FALSE)
fb_capture = logical; whether a fledgling was captured (TRUE) or not (FALSE) during standardized mist netting efforts in late Aug/early Sept

In gm_weather.csv:
date = date (mm/dd/yy): calendar date of the weather record
total_precip_mm = numeric; daily precipitation in mm
min_temp_c = numeric; minimum daily temperature in °C
mean_temp_c = numeric; mean daily temperature in °C

In nests_2022-2024:
eggs_laid = integer; number of eggs laid in the nest (clutch size)
female_id = factor; unique aluminum band number (Canadian Wildlife Service) assigned to the female parent of the nest
male_id = factor; unique aluminum band number (Canadian Wildlife Service) assigned to the male parent of the nest
found_date = date (mm/dd/yy); calendar date on which the nest was found
hatch_date = date (mm/dd/yy); calendar date on which the first egg hatched
eggs_hatched = integer; the number of eggs in the nest that hatched (brood size)
fledglings = integer; the number of young that fledged from the nest
fledge_date = date (mm/dd/yy); calendar date on which the first young fledged from the nest
fate = factor; the fate of the nest. AE = abandoned with eggs, AN = abandoned with nestlings, FL = fledged, PE = predated with eggs
clutch_number = factor; the brood number of an individual’s natal nest and whether the nest was a replacement brood and/or had uncertainty in its assignment. All codes include a brood number: second broods (coded with a “2”) are any broods attempted by a pair after they fledge one brood of young, which is the first brood (coded with a “1”). Addition of “R” indicates the brood is a replacement after losing an earlier attempt (e.g. “R1” is a replacement of a first brood). Uncertainty in assignment is indicated with an E (for “estimated,” e.g. “ERR1” is the estimated second replacement of a first brood).
x_coord = integer; easting of the nest location in UTM Zone 19N
y_coord = integer; northing of the nest location in UTM Zone 19N
fail_date = date (mm/dd/yy): calendar date on which the nest failed, if applicable
experiment = factor; nests with the experiment code “excl” received a predator exclosure; nests with “NA” had no experimental treatment
Notes = character; notes about the nest

In survival_data.csv:
time = integer; the time at which the observation occurred on a 24-hour clock (e.g., 830 means 8:30 am and 1529 means 3:29 pm)
fate_daily = factor; the fate of the fledgling on the day of observation
easting = integer; easting of the location where the fledgling was observed on the day of observation in UTM Zone 19N
northing = integer; northing of the location where the fledgling was observed on the day of observation in UTM Zone 19N
notes.tracks = character; notes about the daily observation
color = factor; color band combination of the individual, with each letter representing a color. May not uniquely identify individuals because some combinations were re-used after the individual that originally received the combination died.
fledge_date = date (mm/dd/yy); calendar date on which the juvenile fledged from its nest
fate_end = factor; the fate of the juvenile at the end of the breeding season
fate_date = date (mm/dd/yy); calendar date on which the fate occurred. For birds that died, date on which they died. For birds alive or censored at the end of their tracking period, date on which they were last observed alive.
cause_mort = factor; for birds that died, cause of mortality (predation, starvation/exposure, etc)
notes.depl = character; notes about the tag deployment record
female_age = integer; age of the female parent in years
male_age = integer; age of the male parent in years
female_age_code = factor; age of the female parent (SY = second year, a bird born last year that is breeding for the first time, ASY = after second year, a bird born > 1 year ago that has attempted to breed in previous years)
male_age_code = factor; age of the male parent (SY = second year, ASY = after second year)
age_at_fldg = integer; age of the juvenile when it fledged from its natal nest in days post-hatch
tarsus = numeric; the tarsus measurement of the juvenile on the day it was measured and banded as a nestling, in mm
date_measured = date (mm/dd/yy); calendar date on which the juvenile was measured and banded as a nestling
sex = factor; the sex of the juvenile (F = female, M = male)
days_pf = integer; age in days post-fledging (on day of fledging, days_pf = 0)
precip_3d = numeric; sum of precipitation over a 3-day window spanning the day of observation and two previous days
min_temp_3d = numeric; the minimum daily temperature over a 3-day window spanning the day of observation and two previous days
mean_temp_3d = numeric; the mean daily temperature over a 3-day window spanning the day of observation and two previous days
survived = binary; 0 = fledgling was known to be dead or was assumed dead at the end of the deployment, 1 = fledgling was alive or had an unknown fate at the end of the deployment (opposite of the variable “died”)
local_density = integer; the number of nests within a 50 m buffer of the fledgling’s natal nest that were active at the same time as the natal nest
geometry = vector; contains the easting and northing of the observation point (for use with R package sf)

Code:
pf_survival_analysis_revision_final.R
The R script provided includes all the code required to import the data and perform the statistical analyses presented in the manuscript.