# Predicting Ploidal Level from Sequence Data

## Documentation for package ‘nQuack’ version 1.0.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

alphabetacalc | Calculate Alpha and Beta from Mean and Variance
alphabetacalctau | Calculate Alpha and Beta from Mean, Tau, and Error rate.
alphabetacalctauvec | Vector-based - Calculate Alpha and Beta from Mean, Tau, and Error rate.
alphabetacalcvec | Vector-based - Calculate Alpha and Beta from Mean and Variance
Bclean | Remove Noise with the Beta Distribution
bestquack | Model Selection - Expectation Maximization - Optimal Distribution and Type
denoise_data | Denoise Data
emstepB | Expectation maximization - Beta Distribution
emstepB3 | Expectation maximization - Beta + Beta + Beta Distribution
emstepBB | Expectation maximization - Beta-Binomial Distribution
emstepBBU | Expectation maximization - Beta-Binomial and Uniform Distributions
emstepBU | Expectation maximization - Beta and Uniform Distributions
emstepN | Expectation maximization - Normal Distribution
emstepNA | Expectation maximization - Normal Distribution
emstepNU | Expectation maximization - Normal and Uniform Distribution
emstepNUA | Expectation maximization - Normal Distribution
estepB3 | E-Step for Expectation Maximization - Beta + Beta + Beta Distribution
muvarcalcvec | Variance calculation from Mean, Tau, and Sequencing Error
nQuire_reformat | Data Preparation - Use nQuire's Data
prepare_data | Prepare Data - Step 1
process_data | Process Data - Step 2
process_nquire | Use nQuire's Data
process_rcpp | Data Preparation - Matrix Filtering
quackBeta | Model Selection - Expectation Maximization - Beta Mixture
quackBetaBinom | Model Selection - Expectation Maximization - Beta-Binomial Mixture
quackit | Model Selection - Based on BIC or Log-Likelihood
quackNboots | Bootstrapping - Expectation Maximization - Optimal Distribution and Type
quackNormal | Model Selection - Expectation Maximization - Normal Mixture
quackNormalNQ | Model Selection - Expectation Maximization - Normal Mixture (nQuire)
resample_xm | Calculate Alpha and Beta from Mean and Variance
setconvert | Calculate Variance from Mean, Tau, and Sequencing Error
SetupBasicExample | Setup Basic Example
sim.ind.BB | Simulate Allele Counts for Single Individual - Beta-Binomial Distribution
sim.ind.BB.tau | Simulate Allele Counts for Single Individual - Beta-Binomial Distribution with Overdispersion and Error
sim.ind.simple | Simulate Allele Counts for Single Individual - Simple Approach