_pkgdown.yml

url: https://jsilve24.github.io/fido/

home:
  title: Bayesian Multiniomial Logisic Normal Models (really fast)

authors:
  Justin Silverman:
    href: https://www.justin-silverman.com/
  Michelle Nixon:
  Kimberly Roche:

template:
  bootstrap: 5

development:
  mode: auto

articles:
- title: Models
  navbar: ~
  contents:
  - introduction-to-fido
  - non-linear-models
  - orthus

- title: Examples
  contents:
  - mitigating-pcrbias

- title: Advanced Details
  contents:
  - picking_priors

reference:
- title: Model functions
  desc:  Functions for fitting the main models
  contents:
  - pibble
  - refit
  - basset
  - orthus

- title: Model checking
  contents:
  - starts_with("plot")
  - starts_with("ppc")

- title: Useful functions for determining model fit
  contents:
  - starts_with("plot")
  - starts_with("ppc")
  - starts_with("r2")
  - starts_with("sample_prior")
  - summarise_posterior

- title: Transformation functions
  contents:
  - starts_with("to")

- title: Helper functions
  contents:
  - starts_with("alr")
  - starts_with("as.")
  - check_dims
  - starts_with("clr")
  - starts_with("coef")
  - conjugateLinearModel
  - convert_orthus_covariance
  - create_default_ilr_base
  - gather_array
  - kernels
  - lambda_to_iqlr
  - starts_with("loglik")
  - lmvgamma
  - lmvgamma_deriv
  - starts_with("miniclo")
  - mongrel-deprecated
  - starts_with("name")
  - starts_with("ncategories")
  - starts_with("optim")
  - orthusfit
  - orthus_lr_transforms
  - orthus_tidy_samples
  - pibblefit
  - starts_with("predict")
  - starts_with("print")
  - pibble_tidy_samples
  - random_pibble_init
  - starts_with("req")
  - store_coord
  - starts_with("summary")
  - starts_with("uncollapse")
  - starts_with("verify")

- title: Data sets and data simulators
  contents:
  - fido_package
  - mallard
  - mallard_family
  - metadata
  - orthus_sim
  - pcrbias_mock
  - pibble_sim
  - RISK_CCFA
  - RISK_CCFA_otu
  - RISK_CCFA_sam
  - RISK_CCFA_tax
  - 'Y'