Reproducibility data for the manuscript "Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability", it contains data and script for :
The R script 01_HDSfreq_Calibration.R of the developed approach to estimate national breeding bird population size using Hierarchical Distance Sampling (HDS) and the secondary candidate set model selection method (Morin et al., 2020)
The R script 02_pglmm_figures.R for the calibration of the Phylogenetic Generalised Mixed Model (PGLMM) used in the manuscript to compare previous population size estimates to ones modelled using 01_HDSfreq_Calibration.R, while accounting for species phylogenetic relatedness
The R script 03_results_tables.R, used to generate supplementary tables S2.1-3 and S6.1-2.
Column names are highlighted in italics.
Data description
A. BirdPhylo_Burleigh_et_al.tre
A phylogenetic tree from Burleigh et al., 2015. Phylogenetic distances are used as random effect for the PGLMM in script 02_pglmm_figures.R
B. Conservation_status.txt
A .txt file of the conservation status for France (Statut_FR) and Europe (Statut_EU) for the studied species retrieved from (UICN France et al., 2016). Only Statut_FR is used for the table S6.1.
C. FBBS_trends_20122023.txt
A .txt file containing species trend of the French Breeding Bird Survey data from 2012 to 2023.
Species names (English, French) associated with FBBS trend estimated using data collected from 2012 - 2023
Hab_specialization, determined from Julliard et al. 2006 approach
infPrec, supPerc, estimate, se, pval : Species trends over 2012-2023 period in % | lower and upper confidence intervals, mean, standard error and significance
D. PrepData_HDS.RData
A file containing .RData environment required to run 01_HDSfreq_Calibration.R script, it contains :
ATLAS12 : A dataframe with breeding status information from 2012 breeding bird atlas (used to restrict model prediction grid, in regard of 2012 known breeding locations)
ConcordTBL : A concordance table for species names (English, French and scientific notation)
EPOC_ODF : observation dataset, each line corresponds to detected individuals
UUID, Ref, ID_liste, ID, ID_place, Grid_10x10 : Columns used to identify observations, lists, sites, locations, 10x10 grids
ID_species_Biolovision, Nom_espece, english_name, scientific_name : Species ID and names
Date, Day, Month, Year, Julian_date, Obs_hour,...