README: Least Tern Disturbance Observations and Colony Survey Data

https://doi.org/10.5061/dryad.nk98sf80m

This dataset contains multiple raw data files as .csv format, .txt files with Bayesian models written in BUGS code used to estimate Least Tern nest and chick survival, and the R script used to clean, collate, and analyze the data.

Description of the data and file structure

colony.storm.names.update.csv

This file contains beach width (m) measurements and presence or absence of dunes for each Least Tern colony in this manuscript.

ColonySurveys.zip

This file contains three .csv files with raw Least Tern colony survey data. These data were collected weekly to twice per week at all mainland colonies. The first five columns contain information about the survey: Site (site name, typically in reference to the nearest cross street that meets Highway 90), Date, Time, Species, and Survey Type (Exterior if conducted outside of the colony, Interior if surveyed by walking through the colony). Most surveys were conducted by a single observer, with counts of adults, nests, downy chicks, feathered chicks, and fledglings entered into the Adults1, Nests1, Downy1, Feath1, and Fledgeq columns. The Adults2, Nests2, etc. columns were occasionally used to enter data recorded simultaneously by a second observer, typically for training purposes. For this manuscript, only the first columns for each metric were used. The columns labeled AdultsPED, NestsPED, etc. indicate how counts were obtained: D for direct count, E for estimate, and P indicating presence but no count attempted. Chicks1 refers to counts of downy chicks (ages 1-9 days approximately), Feath1 refers to counts of feathered chicks (ages 10-20 approximately), and Fledge1 refers to counts of fledglings. The Notes column contains optional notes entered about the survey. All instances of missing data are filled with NAs; missing data were primarily the result of not recording certain information during a given visit, whether intentionally or intentionally. For example, survey time and adult counts were not consistently recorded during earlier survey years (because nest count was the primary focus in determining breeding colony size), and second-observer counts were only occasionally recorded throughout the study period.

DisturbanceDatasets.zip

This file contains five .csv files with disturbance data collected during each breeding season of this study (2017-2021). Disturbance observations were collected continuously by stewards during their work shifts at Least Tern colonies. The first six columns contain information about the work shift: Site (name of colony), Date, Start Time (beginning of the work shift or observation), End Time, Observers (observer initials), and Species (species engaged in reaction to disturbance; almost always Least Tern [LETE], a few observations of Black Skimmer [BLSK] present in data but not included in analysis). Each row represents a single instance of disturbance, with Source noted using the definitions given in the manuscript, distance (m) between the source and the edge of the colony when the terns first began to react (Distance), duration of reaction in minutes (Duration), and proportion of the colony engaged in four possible reactions: None, Alert (these two combined starting in 2020), Flush, and Defensivee.

LETE_storm_script.R

This file contains the R script used to clean, collate, and analyze all the data files used in this manuscript.

logexpos_survival_Reff.txt

This file contains the logistic exposure nest survival model written in the BUGS language to assess the effects of time period and colony size on Least Tern daily nest survival probability.

NestSurvivalData.zip

This file contains three .csv files with Least Tern nest monitoring data formatted for daily nest survival analysis. Fields include Site (colony name), Date (date of nest check), Nest.ID (unique identifier for each nest), and species (only Least Tern [LETE] used in analysis). Each row contains information from a single visit to a given nest, with a binary Status field indicating nest is still active (1) or is no longer active (0). The 2020 and 2021 files contain codes 1-8 in the Status column to indicate more specific information about nest fate; these are defined and converted to binary in the accompanying R script prior to analysis. The Chicks and Eggs are count fields indicating number of chicks and eggs present, respectively, if nest contents were observed. The Expose column contains the number of days that have elapsed since the previous visit to that nest; first visits to the nest contain NA in this field.

productivity_model_Jeffreys_priors.txt

This file contains the hierarchical chick survival model written in the BUGS language to assess the effects of time period and colony size on Least Tern chick survival probability.

storm_colonies.csv

This file contains summary information for Least Tern colonies that were impacted by tropical storms during the study period. "Site" contains the colony name, "Nests" contains the maximum number of nests observed at each colony prior to the storm (as a proxy for number of pairs in the colony), "Downy" is the maximum number of downy chicks present in the colony prior to the storm, "Renest" is a binary field indicating whether the colony re-formed after the storm, "Hatch" is the maximum proportion of nests that had hatched prior to the storm, "Year" is the calendar year, "StormWeek" is a numeric field containing the week within the year that the storm occurred, and the "5.7km bin" contains the summed colony sizes for all colonies located within 5.7 km (inclusive of focal colony) prior to the storm to represent the number of Least Tern pairs potentially available to re-form the colony post-storm, and "IncludedColonies" contains the list of colonies that were included within the 5.7 km buffer.