Package index • biPOD

Fit data

Functions to initialize data and fit them.

init(): Create a biPOD Object

fit_breakpoints(): Identify and Fit Optimal Breakpoints in Population Growth Data

fit(): Fit a Growth Model to a Bipod Object

fit_two_pop_model(): Fit a Two-Population Growth Model to a bipod Object

Plot data

Function to visualize data and results.

plot_bayes_factor(): Plot Bayes Factor Over Input Data

plot_breakpoints_posterior(): Plot Posterior Distributions of Inferred Breakpoints

plot_elbo(): Plot the Logarithm of the ELBO and Delta ELBO Mean

plot_fit(): Visualize Model Fit with Input Data

plot_input(): Plot Population Counts Over Time

plot_mixture_model_omega(): Plot Omega Values from Mixture Model Fit

plot_normalized_growth_rate_posteriors(): Visualize Normalized Growth Rate Posterior Distributions

plot_posterior(): Plot Posterior Density for a Specific Parameter

plot_posteriors(): Plot Posterior Densities for Multiple Parameters

plot_report(): Generate a Comprehensive Model Analysis Report

plot_t0_posterior(): Visualize t0 Parameter Posterior Distribution

plot_traces(): Plot Traces of Specified Parameters from a Fitted Stan Model

plot_two_pop_fit(): Plot the Fit Over the Input Data for Two Populations

biPOD_ppc_dens_overlay(): Overlay Posterior Predictive Density

biPOD_ppc_intervals(): Posterior Predictive Intervals Plot

biPOD_ppc_ribbon(): Posterior Predictive Ribbon Plot

print(<bipod>): Print Method for Class 'bipod'

Simulate data

Function to produce synthetic data.

sim_stochastic_exponential(): Simulate a Stochastic Birth-Death Process (Exponential Growth)

sim_stochastic_logistic(): Simulate Population Growth with Stochastic Logistic Dynamics

Data

Example dataset to perform analysis.

xenografts: Xenografts Mouse Model Dataset