Function reference • BayesPharma

All functions

BayesPharma BayesPharma-package: BayesPharma: Tools for Bayesian Analysis of Non-Linear Pharmacology Models

MuSyC_formula(): Create a Formula for the MuSyC Synergy Model

MuSyC_genquant(): Stan Code for the MuSyC Generated Quantities

MuSyC_hi_to_si(): Convert Exponent to Slope Parameterization for Drug i in MuSyC Model

MuSyC_init(): Create Initial Parameter Values for the MuSyC Model

MuSyC_model(): Fit a MuSyC Synergy Model

MuSyC_prior(): Create a Prior for the MuSyC Synergy Model

MuSyC_robust(): Generate MuSyC Ed Scores Using a Robust Functional Form

MuSyC_si_to_hi(): Convert From Slope to Exponent Parameterization for Drug i in the MuSyC Model

MuSyC_stanvar(): Stan Code for the MuSyC Function.

Pnear(): Compute the Pnear Quality Metric for a RMSD Funnel

basic_stats(): Give Basic Statistical Information About the Model Results

bpfit-class bpfit: Class bpfit of Models Fit with the BayesPharma Package

calculate_log_dose(): Add a Log(dose) (in base 10) Column to the Input data.frame

cli_init_output_path(): Helper function to initialize output for the BayesPharma CLI

cli_load_bivariate_formula(): Helper function to load sigmoid formula the BayesPharma CLI

cli_load_data(): Helper function to load data for the BayesPharma CLI

cli_load_init(): Helper function to load init the BayesPharma CLI

cli_load_model_fn(): Helper function to load model function the BayesPharma CLI

cli_load_prior(): Helper function to load prior the BayesPharma CLI

cli_load_univariate_formula(): Helper function to load a univariate formula for the BayesPharma CLI

cli_parse_options(): Helper function to parse command line arguments for the BayesPharma CLI

constant_formula(): Formula for a Curve with a Constant Response

drc_model(): Wrapper for DRC Dose Response Models

eval_init(): Evaluate an init

eval_init_one_param(): Helper function for eval_init_one_param

expect_gg(): Check if an Object is a ggplot2 Plot

fit_model_cli(): Fit model using command line arguments

get_response_units(): Get the Response Variable Units from a BayesPharma Model

get_response_variable(): Get the Response Variable from a BayesPharma Model

get_treatment_units(): Get the Treatment Variable Units from a BayesPharma Model

get_treatment_variable(): Get the Treatment Variable from a BayesPharma Model

growth_richards(): Richards growth function

growth_richards_formula(): Create a Formula for the Richards Growth Model

growth_richards_init(): Create Initialization for the Richards Growth Model

growth_richards_model(): Run Bayesian Richards Growth Model

growth_richards_prior(): Create a Prior for the Richards Growth Model

growth_richards_stanvar(): Stan Code for the Richards Growth Function.

growth_sigmoid(): Sigmoid growth function

growth_sigmoid_formula(): Create a Formula for the Sigmoid Growth Model

growth_sigmoid_init(): Create Initialization for the Sigmoid Growth Model

growth_sigmoid_model(): Run the Bayesian Sigmoid Growth Model

growth_sigmoid_prior(): Create a Prior for the Sigmoid Growth Model

growth_sigmoid_stanvar(): Stan Code for the Growth Richards Function.

kor_antag: Dose Response Measurements of Four Different Kappa Opioid Receptor Antagonists

michaelis_menten(): Generate Data from the Michaelis Menten Enzyme Kinetics

michaelis_menten_formula(): Define a Formula for the Michaelis Menten Enzyme Kinetics Model

michaelis_menten_genquant(): Stan Code for the Michaelis Menten Model Generated Quantities

michaelis_menten_init(): Initialize Parameter Values for the Michaelis Menten Enzyme Kinetic Model

michaelis_menten_model(): Model for the Michaelis Menten Enzyme Kinetics Model

michaelis_menten_prior(): Create a Prior for the Michaelis Menten Enzyme Kinetics Model

michaelis_menten_stanvar(): Stan Code for the Michaelis Menten Kinetics Model

plot_density_distribution(): Plot Density Distribution of Model Parameters

plot_drc(): Create Plot of a DRC Model

plot_posterior_density(): Plot Posterior Density Distributions of modeled parameters

plot_posterior_draws(): Plot of Posterior Model Fit Draws

plot_pp_check(): Perform Posterior Predictive Check

plot_prior_posterior_densities(): Plot Prior and Posterior Marginal Distributions

plot_sigmoid_functional_form(): Plot the Sigmoid Functional Form with Labeled Parameters

plot_synergy_checkerboard(): Plot Synergy Checkerboard

prepare_init(): Helper Function to Prepare an Init for a brms Model

prepare_prior(): Helper Function to Prepare a Prior for a brms Model

rstan_default_init(): Helper Function to Create the Default rstan scalar init

sigmoid(): Sigmoid Function

sigmoid_agonist_formula(): Create an Agonist Sigmoid Formula for the Sigmoid Model

sigmoid_agonist_init(): Initialize Parameter Values for an Agonist Sigmoid Model

sigmoid_agonist_prior(): Create a Prior an Agonist Sigmoid Model

sigmoid_antagonist_formula(): Create a Formula for the Sigmoid Antagonist Model

sigmoid_antagonist_init(): Initialize Parameter Values for an Antagonist Sigmoid Model

sigmoid_antagonist_prior(): Create a Prior an Antagonist Sigmoid Model

sigmoid_hill_to_slope(): Convert Hill to Slope Parameters a the Sigmoid Functional Form

sigmoid_model(): Fit a Bayesian Sigmoid Model

sigmoid_slope_to_hill(): Convert Slope to Hill Parameters a the Sigmoid Functional Form

sigmoid_stanvar(): Stan Code for the Sigmoid Model.

tQ_formula(): Define a Formula for the Total QSSA (tQ) Enzyme Kinetics Model

tQ_genquant(): Stan Code for the tQ Model Generated Quantities

tQ_init(): Initialize Parameter Values for the tQ Enzyme Kinetic Model

tQ_model(): Model for the tQ Enzyme Kinetics Model

tQ_model_generate(): Generate Data from the Total QSSA (tQ) Model for Enzyme Kinetics

tQ_prior(): Create a Prior for the tQ Enzyme Kinetics Model

tQ_stanvar(): Stan Code for the tQ Enzyme Kinetics Model