_pkgdown.yml

---
url: https://insightsengineering.github.io/tern

template:
  package: nesttemplate

navbar:
  structure:
    left: [intro, reference, articles, tutorials, news, reports]
    right: [search, github]
  components:
    reports:
      text: Reports
      menu:
        - text: Coverage report
          href: coverage-report/
        - text: Unit test report
          href: unit-test-report/
    github:
      icon: fa-github
      href: https://github.com/insightsengineering/tern

reference:
  - title: Overview Pages
    contents:
      - tern-package
      - analyze_functions
      - analyze_colvars_functions
      - summarize_functions
      - formatting_functions

  - title: Control Functions
    desc: These functions capture options in lists and take care of defaults
          (and checks where applicable). They avoid cluttering of function
          signatures with long lists of single arguments.
    contents:
      - starts_with("control_")

  - title: Analysis Functions
    desc: |
          Analyze functions with their corresponding statistics functions and
          formatted analysis functions.

          - **Analyze functions** are used in combination with `rtables`
            layout functions in the pipeline which creates the table.

          - **Statistics functions** (denoted by `s_` prefix) compute the
            numbers that are tabulated later. In order to separate computation
            from formatting, they do not take care of `rcell` type formatting
            themselves.

          - **Formatted analysis functions** (denoted by `a_` prefix) have the
            same arguments as the corresponding statistics functions, and can
            be further customized by calling `rtables::make_afun()` on them.
            They are used as `afun` in `rtables::analyze()`.

    contents:
      - starts_with("analyze_", internal = TRUE)
      - compare_vars
      - starts_with("count_", internal = TRUE)
      - starts_with("estimate_", internal = TRUE)
      - starts_with("summarize_", internal = TRUE)
      - starts_with("surv_", internal = TRUE)
      - starts_with("tabulate_", internal = TRUE)
      - test_proportion_diff
      - -analyze_colvars_functions
      - -analyze_functions
      - -estimate_coef
      - -summarize_functions

  - title: Analysis Helper Functions
    desc: These functions are useful in defining an analysis.
    contents:
      - default_stats_formats_labels
      - starts_with("h_")
      - imputation_rule
      - labels_use_control
      - starts_with("or_")
      - starts_with("prop_")
      - -starts_with("h_col_")
      - -h_content_first_row
      - -h_data_plot
      - -h_g_ipp
      - -starts_with("h_grob_")
      - -starts_with("h_row_")
      - -h_xticks
      - -prop_diff

  - title: Model-Specific Functions
    desc: These functions help with fitting or extracting results from specific
          models.
    contents:
      - estimate_coef
      - starts_with("extract_")
      - starts_with("fit_")
      - get_smooths
      - starts_with("logistic_")
      - starts_with("tidy.")
      - univariate

  - title: Graphs
    desc: These function create graphical type output.
    contents:
      - starts_with("g_")

  - title: rtables Helper Functions
    desc: These functions help to work with the `rtables` package and may be
          moved there later.
    contents:
      - add_riskdiff
      - add_rowcounts
      - append_varlabels
      - default_na_str
      - set_default_na_str
      - starts_with("as.rtable")
      - starts_with("combine_")
      - starts_with("h_col_")
      - h_content_first_row
      - starts_with("h_row_")
      - is_leaf_table
      - rtable2gg
      - split_cols_by_groups
      - to_string_matrix
      - groups_list_to_df
      - utils_split_funs

  - title: rtables Formatting Functions
    desc: These functions provide customized formatting rules to work with the
          `rtables` package.
    contents:
      - starts_with("format_")

  - title: rtables Scoring Functions
    desc: These functions can help with table sorting.
    contents:
      - starts_with("score_")

  - title: rtables Pruning Functions
    desc: These functions and classes help with flexible pruning of tables.
    contents:
      - CombinationFunction
      - has_count_in_any_col
      - starts_with("has_fraction")
      - starts_with("keep_")

  - title: Graph Helper Functions
    desc: These functions are useful to modify graphs.
    contents:
      - starts_with("decorate_")
      - h_g_ipp
      - matches(".*grob.*")
      - h_xticks
      - forest_viewport

  - title: Data Helper Functions
    desc: These functions are used by other functions to derive data.
    contents:
      - aesi_label
      - as_factor_keep_attributes
      - bins_percent_labels
      - combine_levels
      - cut_quantile_bins
      - day2month
      - df_explicit_na
      - starts_with("d_")
      - explicit_na
      - starts_with("fct_")
      - starts_with("f_")
      - h_data_plot
      - month2day
      - reapply_varlabels
      - sas_na
      - starts_with("stat_")
      - strata_normal_quantile
      - to_n
      - update_weights_strat_wilson

  - title: Assertion Functions
    desc: These functions supplement those in the `checkmate` package.
    contents:
      - assertions

  - title: Data
    desc: Data included in the package.
    contents:
      - starts_with("ex_")

  - title: Deprecated Functions
    desc: Functions that are currently deprecated within `tern`.
    contents:
      - starts_with("create_")
      - summarize_vars
      - summary_custom