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

MetadataTitle: “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 NorrisJournal: Journal of Avian Biology (submitted)Year of publication: (submitted)<br>Study system: Savannah sparrows (Passerculus sandwichensis)Study site: Kent Island, New Brunswick, Canada (44.58°N, 66.76°W)Timespan: 2022-2024<br>SummaryThe 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)<br>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<br>Variables<br>Variables with the same name in different files have the same interpretation and are not repeated in the description below, unless otherwise noted.<br>In deployments.csv:tag = factor; unique identifier of a deployment of a tagband_number = factor; unique aluminum band number (Canadian Wildlife Service) assigned to each individual birdyear = integer (2022-2024); study yearnest_key = factor; an alpha-numeric code assigned to the natal nest of each fledglingtagged_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 occurredfledge_date = date (mm/dd/yy); calendar date on which the juvenile fledged from its nestfate = factor; the fate of the juvenile at the end of the tag deploymentdied = 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 deploymentweight = numeric; the mass of the individual when it was banded as a nestling, in gramsage_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)<br>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<br>In gm_weather.csv:date = date (mm/dd/yy): calendar date of the weather recordtotal_precip_mm = numeric; daily precipitation in mmmin_temp_c = numeric; minimum daily temperature in °Cmean_temp_c = numeric; mean daily temperature in °C<br>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 nestmale_id = factor; unique aluminum band number (Canadian Wildlife Service) assigned to the male parent of the nestfound_date = date (mm/dd/yy); calendar date on which the nest was foundhatch_date = date (mm/dd/yy); calendar date on which the first egg hatchedeggs_hatched = integer; the number of eggs in the nest that hatched (brood size)fledglings = integer; the number of young that fledged from the nestfledge_date = date (mm/dd/yy); calendar date on which the first young fledged from the nestfate = factor; the fate of the nest. AE = abandoned with eggs, AN = abandoned with nestlings, FL = fledged, PE = predated with eggsclutch_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 19Ny_coord = integer; northing of the nest location in UTM Zone 19Nfail_date = date (mm/dd/yy): calendar date on which the nest failed, if applicableexperiment = factor; nests with the experiment code “excl” received a predator exclosure; nests with “NA” had no experimental treatmentNotes = character; notes about the nest<br>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 observationeasting = integer; easting of the location where the fledgling was observed on the day of observation in UTM Zone 19Nnorthing = integer; northing of the location where the fledgling was observed on the day of observation in UTM Zone 19Nnotes.tracks = character; notes about the daily observationcolor = 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 nestfate_end = factor; the fate of the juvenile at the end of the breeding seasonfate_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 recordfemale_age = integer; age of the female parent in yearsmale_age = integer; age of the male parent in yearsfemale_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 &gt; 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-hatchtarsus = numeric; the tarsus measurement of the juvenile on the day it was measured and banded as a nestling, in mmdate_measured = date (mm/dd/yy); calendar date on which the juvenile was measured and banded as a nestlingsex = 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 daysmin_temp_3d = numeric; the minimum daily temperature over a 3-day window spanning the day of observation and two previous daysmean_temp_3d = numeric; the mean daily temperature over a 3-day window spanning the day of observation and two previous dayssurvived = 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 nestgeometry = vector; contains the easting and northing of the observation point (for use with R package sf)<br><b>Code:</b>pf_survival_analysis_revision_final.RThe R script provided includes all the code required to import the data and perform the statistical analyses presented in the manuscript.