Worked examples

Each of the following notebooks walks through an analysis of simulated data.

Please submit feedback or comments as an issue or on gitter.

• PEM survival model: unstructuredhazard
  • The model
  • Stan code for the model
  • Simulate survival data
  • Explore simulated data
  • Transform to long or per-timepoint form
  • Fit stan model
  • Superficial review of convergence
  • Plot posterior estimates of parameters
  • Posterior predictive checking
  • Building up the plot semi-manually, for more customization
  • Use plotly to summarize posterior predicted values
• PEM survival model: gammahazard
• PEM survival model: randomwalkhazard
• PEM survival model: time-dependenteffects
  • superficial check of convergence
  • summarize coefficient estimates
  • posterior-predictive checks
  • summarize time-varying effect of sex on survival
  • accessing lower-level functions for plotting effects over time
• User-supplied PEM survival model with gammahazard
  • Simulate survival data
  • Explore simulated data
  • model1: original spec
  • model2: alternate version of surv_gamma_lpdf
  • model3: use log_mix inside surv_gamma_lpdf
  • model4: vectorize surv_gamma_lpdf
  • compare coefficient estimates for each model spec