gen_quantile_interval: Generate a Poisson-quantile-based prediction interval for...

In statdivlab/paramedic: Predicting Absolute and Relative Abundance by Modeling Efficiency to Derive Intervals and Concentrations

Generate a Poisson-quantile-based prediction interval for qPCR

Description

Return a Poisson-quantile-based prediction interval for qPCR values given Markov Chain Monte Carlo samples for the estimated concentrations.

Usage

gen_quantile_interval(
  mu_quantiles,
  mu_samps,
  alpha = 0.05,
  type = "credible_quantiles",
  div_num = 1
)

Arguments

mu_quantiles	the (alpha/2, 1 - alpha/2) quantiles from the MCMC sampling distribution for the true absolute concentration \mu; only supply if type = "credible_quantiles" (a matrix of dimension N (the sample size) x q (the number of taxa) by 2).
mu_samps	the estimated concentrations [an array with dimension (number of MCMC samples) by N by q]; only supply if type = "sample_quantiles".
alpha	the desired level (defaults to 0.05, corresponding to an interval using the 2.5% and 97.5% quantiles)
type	the type of intervals desired, either "credible_quantiles" or "sample_quantiles" (please see Details for more information on the difference between these two types).
div_num	the number to multiply by.

Value

A (1 - \alpha)x100% Poisson-quantile-based prediction interval for each qPCR

Examples

# load the package, read in example data
library("paramedic")
data(example_16S_data)
data(example_qPCR_data)

# run paramedic (with an extremely small number of iterations, for illustration only)
# on only the first 10 taxa
mod <- run_paramedic(W = example_16S_data[, 1:10], V = example_qPCR_data,
n_iter = 30, n_burnin = 25, 
n_chains = 1, stan_seed = 4747)
# get model summary
mod_summ <- rstan::summary(mod, probs = c(0.025, 0.975))$summary
# get samples
mod_samps <- rstan::extract(mod$stan_fit)
# extract relevant summaries
summs <- extract_posterior_summaries(stan_mod = mod_summ, stan_samps = mod_samps, 
taxa_of_interest = 1:3,
mult_num = 1, level = 0.95, interval_type = "quantile")

statdivlab/paramedic documentation built on May 3, 2024, 7:08 p.m.