The data comprises summaries of field observation data required to reproduce the analyses presented in the manuscript: 
Early-life stasis in partial seasonal migration is underpinned by among-cohort variation in migratory plasticity and selective disappearance.

Study population: European shags (Gulosus aristotelis) breeding on the Isle of May National Nature Reserve (hereafter ‘IoM’), Scotland (56°11’5.40” N, 2°33’16.19 ”W).

Files are summarised below

R scripts are annotated to explain steps and definitions of all variables
Code was written and used with R version 4.3.2 and STAN v2.32.5

Description of the data and file structure

Here we include two R scripts and one STAN model script, 1 excel file with the capture-mark-recapture histories for all 11 cohorts (2010...2020), in addition to several excel files with the estimated parameters required to generate figures in the main manuscript. Below we describe the steps required to run both R scripts and explain the corresponding input and output objects.

Running R and STAN scripts

First, the R script “RunModelScript.R” is used to run the STAN file “CJS4SM.stan” using the input files “crh_allyrs.xlsx”.

The input file "crh_allyrs.xlsx" contains cohort-specific capture-recapture histories for the 11 cohorts described in the main manuscript. Each row in each file corresponds to an individual shag (denoted in the column "BirdID") ringed on IoM in the year denoted in the column "HatchYear". The 6 columns V1 … V6 are the 6 occasions detailed in the main manuscript, and the values 1-4 correspond to the state in which an individual was observed (1: resident state, 2: migrant 1 state, 3: migrant 2 state, and 4: unobserved).

This input file is then used to run each cohort individually as a separate model using the file "RunModelScript.R" with the model "CJS4SM.stan", both of which are annotated with comments describing the steps and variables needed. Each cohort is run separately by changing the variable 'cohort' to the desired year in the R script.

Running this code for each of the 11 cohorts generates 11 output files named "out2010.rds"..."out.2020.rds" and are used as input files for the second R script "DerivedParameters.R".

The R script “DerivedParameters.R” uses the STAN output objects created above to generate the derived parameters that are not coded into the STAN models. This will generate results tables for the key parameters of interest from the model and are described below.

• values20xx = the posterior means and 95% credible intervals directly estimated for each cohort model
• ep = the posterior estimates of the probability of departing from the resident state for each relevant starting occasion
• om = the posterior estimates of the probability of returning to the resident state for each relevant starting occasion
• mf = the posterior estimates of the migratory fraction for each relevant starting occasion
• nu = the posterior estimates of the repeatability for each relevant starting occasion
• di = the posterior estimates of the survival difference between migrant and resident survival for each relevant starting occasion
• phir = the posterior estimates of resident survival for each relevant starting occasion
• phim = the posterior estimates of migrant survival for each relevant starting occasion

These results are generated for each cohort and combined to create the following objects using all cohorts:

• eplxx = posterior estimates of epsilon for all relevant starting occasions, for all cohorts
• omlxx = posterior estimates of omega for all relevant starting occasions, for all cohorts
• mflxx = posterior estimates of the migratory fractions for all relevant starting occasions, for all cohorts
• nulxx = posterior estimates of the repeatability for all relevant starting occasions, for all cohorts
• di20xx = survival difference estimates for all relevant starting occasions, for all cohorts
• phirxx = posterior estimates of resident survival for all relevant starting occasions, for all cohorts
• phimxx = posterior estimates of migrant survival for all relevant starting occasions, for all cohorts

And excluding the 2012 and 2013 cohorts, which suffered substantial mortality:

• eplxx1213 = posterior estimates of epsilon for all relevant starting occasions, for cohorts 2010:2011 and 2014:2020
• omlxx1213 = posterior estimates of omega for all relevant starting occasions, for cohorts 2010:2011 and 2014:2020
• mflxx1213 = posterior estimates of the migratory fractions for all relevant starting occasions, for cohorts 2010:2011 and 2014:2020
• nulxx1213 = posterior estimates of the repeatability for all relevant starting occasions, for cohorts 2010:2011 and 2014:2020
• di20xx1213 = survival difference estimates for all relevant starting occasions, for cohorts 2010:2011 and 2014:2020
• phirxx1213 = posterior estimates of resident survival for all relevant starting occasions, for cohorts 2010:2011 and 2014:2020
• phimxx1213 = posterior estimates of migrant survival for all relevant starting occasions, for cohorts 2010:2011 and 2014:2020

Derived parameter objects

Subsequently, after combining all the above results the following derived parameters with 95% credible intervals are be estimated with the 2012 and 2013 included:

• epmfin = the grand mean of departing from the resident state (Epsilon) across all cohorts for all relevant starting occasions
• epvfin = the grand variance of departing from the resident state (Epsilon) across all cohorts for all relevant starting occasions
• ommfin = the grand mean of returning to the resident state (Omega) across all cohorts for all relevant starting occasions
• omvfin = the grand variance of returning to the resident state (Omega) across all cohorts for all relevant starting occasions
• mfmfin = the grand mean of the migratory fraction (m) across all cohorts for all relevant starting occasions
• mfvfin = the grand variance of the migratory fraction (m) across all cohorts for all relevant starting occasions
• numfin = the grand mean of the between winter repeatability (P[S]) across all cohorts for all relevant starting occasions
• nuvfin = the grand variance of the between winter repeatability (P[S]) across all cohorts for all relevant starting occasions
• dimfin = the grand mean of the survival difference (Delta[Phi]) across all cohorts for all relevant starting occasions
• divfin = the grand variance of the survival difference (Delta[Phi]) across all cohorts for all relevant starting occasions
• phirmfin = the grand mean of resident survival (Phi[R]) across all cohorts for all relevant starting occasions
• phirvfin = the grand variance of resident survival (Phi[R]) across all cohorts for all relevant starting occasions
• phimmfin = the grand mean of migrant survival (Phi[M]) across all cohorts for all relevant starting occasions
• phimvfin = the grand variance of migrant survival (Phi[M]) across all cohorts for all relevant starting occasions
• mdxx = posterior means of the migratory fraction difference (Delta[m]) for all relevant starting occasions, for all cohorts
• probom1 = posterior means of the proportions of surviving migrants becoming residents (P[MR]) for all relevant starting occasions, for all cohorts
• mfret = the grand mean of the proportions of surviving migrants becoming residents (P[MR]) across all cohorts for all relevant starting occasions
• probep1 = posterior means of the proportions of surviving migrants becoming residents (P[RM]) for all relevant starting occasions, for all cohorts
• mfdep = the grand mean of the proportions of surviving migrants becoming residents (P[RM]) across all cohorts for all relevant starting occasions
• phi_bar = posterior estimates of the mean fitness (P[A]) for all relevant starting occasions, for all cohorts
• m_sel = posterior estimates of the expected migratory fraction given no plasticity (m[sel]) for all relevant starting occasions, for all cohorts
• s_diff = posterior estimates of the expected change in the migratory fraction given no plasticity (Delta[m.sel]) for all relevant starting occasions, for all cohorts
• p_diff = posterior estimates of the expected change in the migratory fraction given no selection (Delta[m.pl]) for all relevant starting occasions, for all cohorts
• mfexsurvdiff = posterior means of the expected change in the migratory fraction given no plasticity (Delta[m.sel]) for all relevant starting occasions, for all cohorts
• mfexplasdiff = posterior means of the expected change in the migratory fraction given no selection (Delta[m.pl]) for all relevant starting occasions, for all cohorts
• prop_spdiff = posterior estimates of proportions of Delta[m.sel] and Delta[m.pl] that have the same sign for all relevant starting occasions, for all cohorts
• m_prop_spdiff = posterior means of proportions of Delta[m.sel] and Delta[m.pl] that have the same sign for all relevant starting occasions, for all cohorts
• sp_diff = posterior estimates of the absolute difference between Delta[m.pl] and Delta[m.sel] for all relevant starting occasions, for all cohorts
• msp_diff = posterior means of the absolute difference between Delta[m.pl] and Delta[m.sel] for all relevant starting occasions, for all cohorts
• mspdiff = the grand mean of the absolute difference between Delta[m.pl] and Delta[m.sel] across all cohorts for all relevant starting occasions
• covsp = the linear regression slope and intercept of the relationship between Delta[m.sel] and Delta[m.pl] for all relevant starting occasions, for all cohorts
• cor_mf = Spearman's rank correlations of the relationship between initial migratory fraction (m) and subsequent migratory fractions (m) for all relevant starting occasions, for all cohorts
• cor_ep = Spearman's rank correlations of the relationship between initial migratory fraction (m) and subsequent probabilities of departing from the resident state (Epsilon) for all relevant starting occasions, for all cohorts
• cor_om = Spearman's rank correlations of the relationship between initial migratory fraction (m) and subsequent probabilities of returning to the resident state (Omega) for all relevant starting occasions, for all cohorts
• cov11 = the linear regression slope and intercept of the relationship between initial migratory fraction (m) and subsequent probabilities of departing from the resident state (Epsilon) for all relevant starting occasions, for all cohorts
• cov21 = the linear regression slope and intercept of the relationship between initial migratory fraction (m) and subsequent probabilities of returning to the resident state (Omega) for all relevant starting occasions, for all cohorts
• cov31 = the linear regression slope and intercept of the relationship between initial migratory fraction (m) and subsequent migratory fractions (m) for all relevant starting occasions, for all cohorts

And without the 2012 and 2013 cohorts included:

• epmfin1213 = the grand mean of departing from the resident state (Epsilon) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• epvfin1213 = the grand variance of departing from the resident state (Epsilon) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• ommfin1213 = the grand mean of returning to the resident state (Omega) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• omvfin1213 = the grand variance of returning to the resident state (Omega) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• mfmfin1213 = the grand mean of the migratory fraction (m) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• mfvfin1213 = the grand variance of the migratory fraction (m) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• numfin1213 = the grand mean of the between winter repeatability (P[S]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• nuvfin1213 = the grand variance of the between winter repeatability (P[S]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• dimfin1213 = the grand mean of the survival difference (Delta[Phi]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• divfin1213 = the grand variance of the survival difference (Delta[Phi]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• phirmfin1213 = the grand mean of resident survival (Phi[R]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• phirvfin1213 = the grand variance of resident survival (Phi[R]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• phimmfin1213 = the grand mean of migrant survival (Phi[M]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• phimvfin1213 = the grand variance of migrant survival (Phi[M]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• mfret1213 = the grand mean of the proportions of surviving migrants becoming residents (P[MR]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• mfdep1213 = the grand mean of the proportions of surviving residents becoming migrants (P[RM]) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• covsp2 = the linear regression slope and intercept of the relationship between Delta[m.sel] and Delta[m.pl] across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• cor_mf = Spearman's rank correlations of the relationship between initial migratory fraction (m) and subsequent migratory fractions (m) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• cor_ep = Spearman's rank correlations of the relationship between initial migratory fraction (m) and subsequent probabilities of departing from the resident state (Epsilon) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• cor_om = Spearman's rank correlations of the relationship between initial migratory fraction (m) and subsequent probabilities of returning to the resident state (Omega) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• cov1 = the linear regression slope and intercept of the relationship between initial migratory fraction (m) and subsequent probabilities of departing from the resident state (Epsilon) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• cov2 = the linear regression slope and intercept of the relationship between initial migratory fraction (m) and subsequent probabilities of returning to the resident state (Omega) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions
• cov3 = the linear regression slope and intercept of the relationship between initial migratory fraction (m) and subsequent migratory fractions (m) across cohorts 2010:2011 and 2014:2020 for all relevant starting occasions

Excel files with estimates for figures

Finally, we have compiled several excel files with the above estimates used to generate the figures in the main manuscript. These files contain various estimates for the key and nuisance parameters estimated in the model or as derived parameters.

• "Values_Final.xlsx" provides posterior means and 95% credible intervals for the key parameters of interest (Phi[R], Phi[M], Epsilon, Omega, m, Delta[Phi], P[S], P[RM], P[MR], Delta[m], Delta[m.sel], Delta[m.pl]) for all cohorts and relevant occasions and intervals
• "epsilon_mean.xlsx" provides grand means and 95%CIs for all cohorts for all relevant intervals for the probability of departing from the resident state
• "epsilon_variance.xlsx" provides grand variances and 95%CIs for all cohorts for all relevant intervals for the probability of departing from the resident state
• "omega_mean.xlsx" provides grand means and 95%CIs for all cohorts for all relevant intervals for the probability of returning to the resident state
• "omega_variance.xlsx" provides grand variances and 95%CIs for all cohorts for all relevant intervals for the probability of returning to the resident state
• "mf_mean.xlsx" provides grand means and 95%CIs for all cohorts for all relevant occasions for the migratory fraction
• "mf_variance.xlsx" provides grand variances and 95%CIs for all cohorts for all relevant occasions for the migratory fraction
• "repeat_mean.xlsx" provides grand means and 95%CIs for all cohorts for all relevant intervals for the between winter repeatability
• "repeat_variance.xlsx" provides grand variances and 95%CIs for all cohorts for all relevant intervals for the between winter repeatability
• “d_mean.xlsx” provides grand means and 95%CIs for all cohorts for all relevant intervals for the survival differences between migrants and residents
• “d_variance.xlsx” provides grand variances and 95%CIs for all cohorts for all relevant intervals for the survival differences between migrants and residents
• “phir_mean.xlsx” provides grand means and 95%CIs for all cohorts for all relevant intervals for the probability surviving as a resident
• “phir_variance.xlsx” provides grand variances and 95%CIs for all cohorts for all relevant intervals for the probability surviving as a resident
• “phim_mean.xlsx” provides grand means and 95%CIs for all cohorts for all relevant intervals for the probability surviving as a migrant
• “phim_variance.xlsx” provides grand variances and 95%CIs for all cohorts for all relevant intervals for the probability surviving as a migrant
• "Detection_Estimates.xlsx" provides posterior means and 95% credible intervals for the detection parameters pR, pM1, and pM2 that correspond to detection in the resident, intensively surveyed migrant, and non-intensively surveyed migrant states for all cohorts for the focal occasions 2:5
• "Nuisance_Parameters.xlsx" provides posterior means and 95% credible intervals for the nuisance parameters delta and gamma (where delta represents the probability that an individual transitions to the M1 state condtional on departing the resident state, and gamma represents the probability of switching between either migrant state conditional on remaining migant) for all cohorts and focal intervals

Code/Software

See above for summary of the R script and STAN files linked to each set of data files.