Package index • nQuack

Preparing Data

Prepare your data for ploidal estimation with nQuack.

Simulate data for a given ploidal level.

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

Wrapper functions to run model selection for diploids, triploids, tetraploids, pentaploids, and hexaploids.

quackNormal(): Model Selection - Expectation Maximization - Normal Mixture
quackNormalNQ(): Model Selection - Expectation Maximization - Normal Mixture (nQuire)
quackBeta(): Model Selection - Expectation Maximization - Beta Mixture
quackBetaBinom(): Model Selection - Expectation Maximization - Beta-Binomial Mixture

Wrapper functions for model selection, running specific sets of mixture models, and bootstrap replication.

quackit(): Model Selection - Based on BIC or Log-Likelihood
bestquack(): Model Selection - Expectation Maximization - Optimal Distribution and Type
quackNboots(): Bootstrapping - Expectation Maximization - Optimal Distribution and Type

Functions used within our mixture models

emstepN(): Expectation maximization - Normal Distribution
emstepNU(): Expectation maximization - Normal and Uniform Distribution
emstepNA(): Expectation maximization - Normal Distribution
emstepNUA(): Expectation maximization - Normal Distribution
emstepB(): Expectation maximization - Beta Distribution
emstepBU(): Expectation maximization - Beta and Uniform Distributions
emstepBB(): Expectation maximization - Beta-Binomial Distribution
emstepBBU(): Expectation maximization - Beta-Binomial and Uniform Distributions
estepB3(): E-Step for Expectation Maximization - Beta + Beta + Beta Distribution
emstepB3(): Expectation maximization - Beta + Beta + Beta Distribution

Everything else.

SetupBasicExample(): Setup Basic Example
alphabetacalc(): Calculate Alpha and Beta from Mean and Variance
alphabetacalctau(): Calculate Alpha and Beta from Mean, Tau, and Error rate.
alphabetacalcvec(): Vector-based - Calculate Alpha and Beta from Mean and Variance
alphabetacalctauvec(): Vector-based - Calculate Alpha and Beta from Mean, Tau, and Error rate.
muvarcalcvec(): Variance calculation from Mean, Tau, and Sequencing Error
process_rcpp(): Data Preparation - Matrix Filtering
nQuire_reformat(): Data Preparation - Use nQuire's Data
setconvert(): Calculate Variance from Mean, Tau, and Sequencing Error
resample_xm(): Calculate Alpha and Beta from Mean and Variance