_pkgdown.yml

navbar:
  left:
  - text: Tutorial
    href: articles/tutorial.html
  - text: New World Monkeys
    href: articles/monkeys.html
  - text: Reference
    href: reference/index.html

reference:
  - title: "PhyloEM"
    desc: "Functions for the inference of shifts."
    contents: 
      - PhyloEM
      - find_grid_alpha
      - estimateEM
  - title: "PhyloEM Handling Functions"
    desc: "Functions to handle objects of class `PhyloEM`."
    contents: 
      - plot.PhyloEM
      - params_process.PhyloEM
      - imputed_traits
      - imputed_traits.PhyloEM
      - model_selection.PhyloEM
      - residuals.PhyloEM
      - enlight
      - enlight.PhyloEM
      - log_likelihood.PhyloEM 
      - find_rotation
      - merge_rotations
      - get_criterion
      - plot_criterion
  - title: "Parameters and Simulations"
    desc: >
      Functions to simulate various processes on the tree, and deal with their parameters.
    contents: 
      - simul_process
      - simul_process.params_process
      - simul_process.PhyloEM
      - params_BM
      - params_OU
      - params_process
      - params_process.character
      - plot.params_process
      - extract.simul_process
      - log_likelihood
      - log_likelihood.params_process
  - title: "Identifiability"
    desc: >
      Functions to deal with the non-identifiability of shifts allocations.
    contents: 
      - equivalent_shifts
      - extract.equivalent_shifts
      - plot.equivalent_shifts
  - title: "Parsimony and Enumeration"
    desc: >
      Functions to compute parsimony scores, and enumerate all equivalent solutions
      to a given clustering of the tips.
    contents: 
      - enumerate_parsimony
      - extract.enumerate_parsimony
      - plot.enumerate_parsimony
      - partitionsNumber
      - extract.partitionsNumber
      - parsimonyNumber
      - extract.parsimonyNumber
      - parsimonyCost
      - extract.parsimonyCost
  - title: "Shifts vs Regimes"
    desc: >
      Functions to switch between representations using shifts positions, and
      representations using regimes allocations.
    contents: 
      - shifts_to_simmap
      - allocate_regimes_from_shifts
      - allocate_shifts_from_regimes
      - check_parsimony
      - clusters_from_shifts
      - compute_betas_from_shifts
      - compute_shifts_from_betas
      - node_optimal_values
      - correspondenceEdges
      - enumerate_tips_under_edges
  - title: "Tree Matrices"
    desc: "Functions for computing several matrices associated with a tree."
    contents:
      - compute_dist_phy
      - compute_times_ca
      - incidence.matrix
      - incidence.matrix.full
      - shifts.list_to_matrix
      - shifts.matrix_to_list
  - title: "OU Helper Functions"
    desc: "Miscellaneous functions to deal with the OU process"
    contents:
      - compute_stationary_variance
      - transform_branch_length
      - extract
  - title: "Dataset"
    desc: "New World Monkeys dataset"
    contents:
      - monkeys