_pkgdown.yml

url: http://mlgaynor.com/nQuack/
template:
  bootstrap: 5
  params:
    ganalytics: G-YWYQ5CX5NC
reference:
- title: Preparing Data
  desc: |
    Prepare your data for ploidal estimation with nQuack.
  contents:
  - prepare_data
  - process_data
  - process_nquire
  - denoise_data
  - Bclean
- title: Simulating data
  desc: |
    Simulate data for a given ploidal level.
  contents:
  - sim.ind.BB
  - sim.ind.BB.tau
  - sim.ind.simple
- title: Basic Mixture Models
  desc: |
    Wrapper functions to run model selection for diploids, triploids, tetraploids, pentaploids, and hexaploids.
  contents:
  - quackNormal
  - quackNormalNQ
  - quackBeta
  - quackBetaBinom
- title: More on Mixture Models
  desc: |
    Wrapper functions for model selection, running specific sets of mixture models, and bootstrap replication.
  contents:
  - quackit
  - bestquack
  - quackNboots
- title: Expectation Maximization Base Functions
  desc: |
    Functions used within our mixture models
  contents:
  - emstepN
  - emstepNU
  - emstepNA
  - emstepNUA
  - emstepB
  - emstepBU
  - emstepBB
  - emstepBBU
  - estepB3
  - emstepB3
- title: Helper functions
  desc: |
    Everything else.
  contents:
  - alphabetacalc
  - alphabetacalctau
  - alphabetacalcvec
  - alphabetacalctauvec
  - muvarcalcvec
  - process_rcpp
  - nQuire_reformat
  - muvarcalcvec
  - setconvert
  - resample_xm
articles:
- title: nQuack
  navbar: ~
  contents:
  - BasicExample
  - DataPreparation
  - ModelOptions
  - SimulateData
  - Outliers
  - SimulateData
navbar:
  structure:
    left:
    - reference
    - articles
    right: search