README.txt file from Supplementary code and data to run SNA present in the paper 'Familiarity, dominance, sex and season shape common waxbill social networks' (Gomes et al. 2022, Behav Ecol). Generated in February 2022 by Ana Cristina R. Gomes (ana.gomes@cibio.up.pt). GENERAL INFORMATION 1. Title: Code and data from: Familiarity, dominance, sex and season shape common waxbill social networks 2. Authors: Ana Cristina R. Gomes, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal; Patrícia Beltrão, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal; Neeltje J. Boogert, Centre for Ecology and Conservation, University of Exeter, Penryn, UK; Gonçalo C. Cardoso, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal. 3. Data collection: 2017-2019 4. Funding sources: Fundação para a Ciência e a Tecnologia (PTDC/BIA-EVF/4852/2014, PTDC/BIAECO/32210/2017, DL57/2016/CP1440/CT0011, SFRH/BD/129002/2017, SFRH/BD/148392/2019), Royal Society Dorothy Hodgkin Research (DH140080). 5. Citation for this dataset: Gomes et al. (2022), Code and data from: Familiarity, dominance, sex and season shape common waxbill social networks, Dryad, Dataset 6. To replicate analyses in the paper use the file "R _ SNA_script.R". This contains the main R code to run analyses in the paper, and it calls for the other code and supplementary data files when they needed. FILE OVERVIEW 1. Description of dataset These files allow performing social network analyses to test for consistency across years and seasons of social networks and individual social traits, to test for assortment by traits, and to test for predictors of network structure, using different methods to compute the significance of the null hypothesis. 2. File List: File ‘data _ phenotypes_all.txt’ Description: Phenotypes for each individual. File ‘data R _ networks_data_objects.RDATA’ Description: R object with social networks data. File ‘R _ SNA_script.R’ in Zenodo Description: the main R file, containing all the code to replicate analyses in the paper. Throughout this file, the remaining code and data files are called for when needed. File ‘R _ DSP-BC_function’ in Zenodo Description: R code for the function to run one of the methodological procedures in the paper. METHODOLOGICAL INFORMATION Collection of phenotypic data are described in detail in Gomes et al. (2020, doi: 10.1007/s00265-020-2809-2) and Beltrão et al. (2021, doi: 10.1016/j.anbehav.2021.09.01). Proximity-based social networks of waxbills fitted with a PIT tag were calculated from RFID data recorded from antenna placed in feeders and perches. These social networks were calculated separately for 4 different two-month periods: the non-breeding season of 2017-2018, NB1; the breeding season of 2018, B1; the non-breeding season of 2018-2019, NB2; and the breeding season of 2019, B2. INFORMATION FOR: ‘data _ phenotypes_all.txt’ 1. Number of variables: 12 2. Number of cases/rows: 54 3. Variable List: phenotypic trait values per individual ID_tag: PIT tag ID sex: M, male / F, female mesocosm_enter: birds entered in mesocosm in 2016 / 2017 detour_performance: performance in detour-reaching (cylinder) task mirror_test: PC1 from PCA on movements, activity, vocalizations, and time looking at mirror in a mirror test tonic_immobility: time in seconds in tonic immobility breath_rate: breath rate (Hz) body_size: PC1 from PCA on tarsus length and head-plus-bill length RandElorat_mean: mean randomized Elo-rating across the four time periods sat_breast: red breast saturation mask_area: red mask patch size ventral_area: red breast patch size 4. Missing data: 9 missing values in variable “detour_performance” INFORMATION FOR: ‘data R _ networks_data_objects.RDATA’ 1. Number of files: 23 2. Description of files: 2.1 Files ‘network_overlap_(…)’ : 9 files 2.1.1 Social network files for each period of time; (…) refers to the period of time. 2.1.2. Number of cases: individual x individual matrix with strength of associations among individuals 2.2 Files ‘(…)_timepresent_per_ind’ : 9 files 2.2.1 Total time in RFID array of antennae per individual; (…) refers to the period of time. 2.2.2. Number of variables: 2 2.2.3. Number of cases/rows: individuals in each period of time 2.2.4: Variable List: per individual ID_tag: PIT tag ID Timepresent: total time in seconds in the RFID array of antennae 2.3 Files ‘edgelist_overlap_(…)’ : 5 files 2.3.1 The dyadic denominator of the association index (the simple ratio index) to apply in GLMQAP; (…) refers to the period of time. 2.3.2. Number of variables: 3 2.3.3. Number of cases/rows: individuals in each period of time 2.3.4: Variable List: per individual Tag: PIT tag ID of one individual of the dyad i.Tag: PIT tag ID of the other individual of the dyad totaltime: dyadic denominator of the association index (sum of total time of Tag and total time of i.Tag) INFORMATION FOR: ‘R _ SNA_script.R’ in Zenodo 1. Description: The R script is organized in the following parts 1.1 Traits, network centrality, and node permuted networks 1.2 SNA: Consistency across years and seasons 1.3 SNA: Assortment by phenotypes or familiarity 1.4 SNA: Predictors of network centrality INFORMATION FOR: ‘R _ DSP-BC_function.R’ in Zenodo 1. Description: contains the function ‘lmer.dsp_main’, adapted from the code in Franks et al. (2021, doi: 10.1111/2041-210X.13429), which allows performing the double semi-partialling permutation procedure in bias-corrected models (DSP-BC), considering general linear mixed models (i.e., includes random effects)