_pkgdown.yml

template:
  bootstrap: 5
  bootswatch: flatly
url: https://lebeerlab.github.io/tidytacos/
articles:
  - title: "Tutorials"
    contents: 
    - getting-started
    - stacked-barplot
    - network-analysis     
    - data-processing
reference:
  - title: "Tidytacos"
    desc: >
      Package overview
    contents:
      - tidytacos-package
      - tidytacos
  - title: "File handling"
    desc: >
      Functions for loading in or creating tidytaco objects or converting to another datatype. 
    contents:
      - read_tidytacos
      - write_tidytacos
      - merge_tidytacos
      - create_tidytacos
      - add_metadata
      - starts_with("from_")
      - as_phyloseq
      - starts_with("to_")
  - title: "Table manipulation"
    desc: >
      Functions for manipulation of the three distinct tables using tidy-related functions.
    contents:
      - samples
      - taxa
      - counts
      - starts_with("select_")
      - starts_with("mutate_")
      - filter_counts
      - filter_samples
      - filter_taxa
      - starts_with("aggregate")
      - everything
  - title: "Relative abundance, prevalence and other count computations"
    desc: >
      Functions for transforming the count table to different matrix representations or pairwise comparison.
    contents:
      - counts_matrix
      - rel_abundance_matrix
      - add_rel_abundance
      - add_mean_rel_abundance
      - mean_rel_abundances
      - add_absolute_abundance
      - add_spike_ratio
      - add_density
      - add_logratio
      - add_clr_abundance
      - add_jervis_bardy
      - prevalences
      - add_prevalence
      - counts_tidy
      - starts_with("add_total")
      
  - title: "Plotting"
    desc: >
      Functions for various plots that can be made with the data in a tidytacos object.
    contents:
      - starts_with("tacoplot")
  - title: "Statistical tests"
    desc: >
      Functions for various statistical tests that can be performed on a tidytacos object.
    contents:
      - starts_with("perform")
      - add_codifab
  - title: "Taxonomy related functions"
    desc: >
      Functions to manipulate taxonomy names.
    contents:
      - rank_names
      - set_rank_names
      - starts_with("add_taxon_")
      - add_eigentaxa
      
  - title: "Diversity analysis"
    desc: >
      Functions to add various diversity metrics to the tidytacos object.
    contents:
      - add_alpha
      - add_alphas
      - betas
      - add_ord
      - add_copca
      - add_tree
      - calculate_unifrac_distances

  - title: "Clustering"
    desc: >
      Functions to cluster the sample and taxa table.
    contents:
      - cluster_samples
      - cluster_taxa
      - add_sample_clustered
  - title: "Network analysis"
    desc: >
      Functions to perform network inference, clustering and filtering the resulting clusters.
    contents:
      - network
      - filter_network
      - cluster_network
  - title: "Datasets"
    desc: >
      Test datasets used as examples.
    contents:
      - urt
      - leaf
  - title: "Miscellaneous"
    desc: >
      Functions to tidy up the three tables or convert to other data structures.
    contents:
      - trim_asvs
      - classify_taxa
      - reset_ids
      - starts_with("change_id_")
      - remove_empty_samples
      - tidy_count_to_matrix
      - rarefy
      - test_taco
      - taxonlist_per_condition
      - tacosum