_pkgdown.yml

reference:
  - title: "Data import"
    desc: >
      Functions for importing external data and converting other R object
      as phyloseq or reverse converting
    contents:
      - starts_with("import")
      - phyloseq2DESeq2
      - phyloseq2edgeR
      - phyloseq2metagenomeSeq
      - otu_table2metagenomeSeq
  - title: Miscellaneous
    desc: >
      Functions to manipulate object
    contents:
      - aggregate_taxa
      - summarize_taxa
      - subset_marker
  - title: "Data Processing"
    desc: >
      Functions to precess data before test
    contents:
      - abundances
      - transform_abundances
      - trim_prevalence
      - filter_abundance
      - impute_abundance
      - starts_with("norm")
      - scale_variables
  - title: "Example data"
    contents:
      starts_with("data")
  - title: "Community Analysis"
    desc: >
      Functions to investigate association between variables and microbiota community
    contents:
      - run_betadisper
      - run_ANOSIM
      - run_distance
      - run_MANTEL
      - run_MRPP
      - run_PERMANOVA
      - run_ord
      - get_alphaindex
  - title: "Differential analysis"
    desc: Functions for identifying the microbiome markers
    contents:
      - run_aldex
      - run_ancom
      - run_ancombc
      - run_deseq2
      - run_edger
      - run_lefse
      - run_limma_voom
      - run_metagenomeseq
      - run_simple_stat
      - run_sl
      - run_test_multiple_groups
      - run_test_two_groups
      - run_marker
      - postHocTest
      - run_metabolomeDA
  - title: "Microbiome marker"
    desc: S4 class and methods for microbiomeMarker
    contents:
      - microbiomeMarker
      - starts_with("microbiomeMarker-class")
      - marker_table-class
      - marker_table
      - marker_table<-
      - assign-otu_table
      - abundances
      - nmarker
      - starts_with("postHocTest-class")
      - "["
  - title: "Statistical tookits"
    desc: >
      Functions to do statistical test
    contents:
      - calculate_median_abundance
      - calculate_mean_abundance
      - calculate_MeanRank_abundance
      - calculate_geometricmean_abundance
      - calculate_occurrence_taxa
      - run_OddRatio
      - run_CI
      - run_group.CI
      - run_STDERR
      - run_group.STDERR
      - run_summarySE
      - insertRow
      - insertCol
  - title: "Additional tookits"
    desc: >
      Additional Functions
    contents:
      - default_color
      - check_sample_names
      - get_GUniFrac
      - get_eigValue
      - confounder
  - title: "Functions to visualization"
    desc: >
      visualization Functions
    contents:
      - plot_ord
      - plot_volcano