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stanette (version 2.21.4)

R Interface to Stan

Description

Expansion and additions to 'rstan' to facilitate pharmacokinetics (PK) and pharmacodynamics (PD) modeling with 'rstan'. A PKPD model often is specified via a set of ordinary differential equations(ODEs) and requires flexible and different routes of drug administrations. These features make PKPD modeling with plain 'rstan' challenging and tedious to code. 'stanette' provides a powerful Stan-compatible ODE solver ('LSODA') and mechanism/utilities that make easy specification of flexible dosing records.

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Version

Install

install.packages('stanette')

Monthly Downloads

11

Version

2.21.4

License

GPL (>= 3)

Homepage

https://mc-stan.org/rstan/

Maintainer

Wenping Wang

Last Published

May 11th, 2022

Functions in stanette (2.21.4)

simulated theophylline data

simulated theophylline data

Creation of a PMXStanModel object

simulated theophylline data

Convergence and efficiency diagnostics for Markov Chains

Simulation Based Calibration (sbc)

Defunct function to set the compiler optimization level

Pointwise comparison between observed data vs. predicted medians.

RStan --- the R interface to Stan

Create an mcmc.list from a stanfit object

Created named lists

Set and read options used in RStan

Generation of a PMXStanFit object

ggplot2 for RStan

Construct a Stan model

Extract samples from a fitted Stan model

Overall goodness-of-fit plots.

idv.obs.pred.vs.time

Comparison of the time profiles of observations with the predictions for each individual.

Pointwise comparison between residuals vs. predicted medians.

instant.stan.extension

generate a customized NUTS-compatible ODE solver

Look up the Stan function that corresponds to a R function or name.

check_hmc_diagnostics

Check HMC diagnostics after sampling

Generation of trace plots of the samples

Diagnostics for a fitted Bayesian model

log_prob-methods

log_prob and grad_log_prob functions

rstan-plotting-functions

RStan Plotting Functions

expose_stan_functions

Expose user-defined Stan functions to R for testing and simulation

extract_sparse_parts

Extract the compressed representation of a sparse matrix

Diagnostic plots

RStan Diagnostic plots

prepareInputData

Transformation of a NONMEM-readable dataset to a Stan-readable list

Compilation of Stan code

Dump the data for a Stan model to R dump file in the limited format that Stan can read.

Obtain the version of Stan

loo_moment_match.stanfit

Moment matching for efficient approximate leave-one-out cross-validation (LOO)

Markov chain traceplots

rstan_gg_options

Set default appearance options

Merge a list of stanfit objects into one

Create a matrix of output plots from a stanfit object

summary-methods

Summary method for stanfit objects

Fit a model with Stan

Print a summary for a fitted model represented by a stanfit object

Compute summaries of MCMC draws and monitor convergence

Internal Functions and Methods

Obtain the full path of file Makeconf

Approximate leave-one-out cross-validation

Plots for stanfit objects

Create array, matrix, or data.frame objects from samples in a stanfit object

Read data in an R dump file to a list

stanmodel-class

Class representing model compiled from C++

Translate Stan model specification to C++ code

Draw samples from a Stan model

Run Stan's variational algorithm for approximate posterior sampling

Class stanfit: fitted Stan model

Read CSV files of samples generated by (R)Stan into a stanfit object

Draw samples of generated quantities from a Stan model

Demonstrate examples included in Stan

Obtain a point estimate by maximizing the joint posterior

Replication of an existing PMXStanModel object