From 92cf94fb3cbd25d671672a3c6e885b241ff89891 Mon Sep 17 00:00:00 2001 From: Nick Croucher Date: Mon, 2 Aug 2021 06:32:55 +0100 Subject: [PATCH] Change sampling to avoid divergent transitions --- examples/s-pneumoniae-strain-invasiveness-adults.Rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/examples/s-pneumoniae-strain-invasiveness-adults.Rmd b/examples/s-pneumoniae-strain-invasiveness-adults.Rmd index c799ca5..91224ca 100644 --- a/examples/s-pneumoniae-strain-invasiveness-adults.Rmd +++ b/examples/s-pneumoniae-strain-invasiveness-adults.Rmd @@ -123,7 +123,7 @@ full_strain_and_serotype_specific_poisson_fit <- rhat_plot <- plot(full_strain_and_serotype_specific_poisson_fit, plotfun = "rhat", binwidth = 0.00005) -trace_plot <- rstan::traceplot(full_strain_and_serotype_specific_poisson_fit, pars = "lp__") +trace_plot <- rstan::traceplot(full_strain_and_serotype_specific_poisson_fit, pars = "lp__") + theme(axis.text.x = element_text(angle = 90)) (full_strain_and_serotype_validation_plot <- cowplot::plot_grid(plotlist = list(rhat_plot,trace_plot), @@ -298,13 +298,13 @@ best_fitting_output %<>% combined_heterogeneity_plot <- cowplot::plot_grid(plotlist = list(strain_invasiveness_plot, serotype_invasiveness_plot), ncol = 1, nrow = 2, - rel_heights = c(0.33, 1), + rel_heights = c(0.5, 1), labels = "AUTO") ggsave(combined_heterogeneity_plot, file = "mixed_within_strain_invasiveness_variation_plot.png", - width = 8, - height = 12 + width = 12, + height = 17.5 ) ```