Code and data for: Reassessment of post-breeding migratory passage of the Critically Endangered Balearic Shearwater at the Strait of Gibraltar

R code and input data to reproduce the analyses of De la Cruz & Arroyo, Reassessment of post-breeding migratory passage of the Critically Endangered Balearic Shearwater at the Strait of Gibraltar. Daily standardised counts of Balearic Shearwaters (Puffinus mauretanicus) were conducted from the seabird observatory on Isla de Tarifa (Strait of Gibraltar, Spain) between 15 May and 15 July in 2008–2010 (period 1; Arroyo et al. 2016) and 2024–2025 (period 2). The deposit contains a single, fully commented R script that runs from the raw hourly counts to every statistical result reported in the paper, together with the two input files it requires. The script is organised in six parts: (A) import of the hourly counts and survey-effort check, restricted to the 06:00–11:00 UTC window used for the between-period comparison; (B) day-level aggregation and negative binomial generalised linear mixed models (period as a fixed effect, year as a random intercept, log-effort offset) for westbound and eastbound passage, derived net passage and its parametric bootstrap; (C) a leave-one-out sensitivity analysis assessing the robustness of the period effect to unequal survey effort among years; (D) extraction of ERA5 hourly 10 m wind components and their merge with the counts; (E) negative binomial generalised additive models used to reconstruct passage during unsampled hours within the 06:00–18:00 UTC census window, and annual totals with simulation-based 95% confidence intervals; and (F) daylight-coverage statistics and the period-level comparison of the population estimates. All random simulations use fixed seeds, so the deposited code reproduces the values reported in the manuscript exactly. Reference results from the verified run are given as comments next to the corresponding output. Requires R ≥ 4.3 and the packages dplyr, tidyr, lubridate, tibble, purrr, readr, ggplot2, patchwork, glmmTMB, DHARMa, MASS, mgcv, terra and suncalc. Contents: balearic_shearwater_gibraltar_analysis.R (full analysis), data/data_balearic.csv (hourly counts, 2008–2010 and 2024–2025), data/data.grib (ERA5 hourly wind reanalysis, Copernicus Climate Data Store), README.md, data/README.md and LICENSE.