rmcelreath/wythamewa

Wytham Woods Parus social learning analysis

wythamewa

This package contains models and data to replicate the payoff and frequency dependent social learning analysis of the Aplin, Sheldon, McElreath 2017, "Conformity does not perpetuate suboptimal traditions in a wild population of songbirds" (doi: 10.1073/pnas.1621067114).

This package requires rstan (http://mc-stan.org/) and rethinking (https://github.com/rmcelreath/rethinking) to fit the statistical models.

See ?wythamewa for a quick start guide to replicating the analysis and figures in the paper. Full scripts to reproduce the figures are found in the various help pages accessible from there.

The full model can be replicated with the following code:

lms <- list(
    "mu[1] + a_bird[bird[i],1] + b_age[1]*age[i]",
    "mu[2] + a_bird[bird[i],2] + b_age[2]*age[i]",
    "mu[3] + a_bird[bird[i],3] + b_age[3]*age[i]",
    "mu[4] + a_bird[bird[i],4] + b_age[4]*age[i]"
    )
links <- c("logit", "logit", "log", "logit", "")
prior <- "
    mu ~ normal(0,1);
    diff_hi ~ cauchy(0,1);
    b_age ~ normal(0,1);
    to_vector(z_bird) ~ normal(0,1);
    L_Rho_bird ~ lkj_corr_cholesky(3);
    sigma_bird ~ exponential(2);"
mod1 <- ewa_def( model=lms , prior=prior , link=links )
set.seed(1)
m <- ewa_fit( mod1 , warmup=500 , iter=1000 , chains=3 , cores=3 ,
    control=list( adapt_delta=0.99 , max_treedepth=12 ) )