_pkgdown.yml

url: https://go-bayes.github.io/margot/

template:
  bootstrap: 5
  bslib:
    # set the base font family using a Google Font
    base_font: {google: "Fira Code"}
    # set the font for headings
    heading_font: {google: "Fira Sans"}
    # set the font for code elements
    code_font: {google: "Fira Code"}

    # adjust the overall font size scale
    font_scale: 0.75  # makes the font smaller; 1 is the default size
    bg: "#ffffff"      # white background
    fg: "#333333"      # dark gray font color for better readability
    primary: "#007bff" # primary blue theme color for links, buttons, etc.
    secondary: "#6c757d" # secondary color (used for muted text, etc.)
    # Additional color settings for a cohesive blue theme
    info: "#17a2b8"    # info color (light blue)
    success: "#28a745" # success color (green)
    warning: "#ffc107" # warning color (yellow)
    danger: "#dc3545"  # danger color (red)
    light: "#f8f9fa"   # light color for contrasts
    dark: "#343a40"    # dark color for contrasts


authors:
  Joseph A Bulbulia:
    href: https://github.com/go-bayes

development:
  version_label: default
  version_tooltip: "Version"

vignette_engine: quarto

reference:
  - title: "Simulate"
    contents:
      - run_simulations
      - simulate_ate_data_with_weights

  - title: "Describe Longitudinal Data"
    contents:
    - margot_count_dyads
    - margot_count_ids
    - margot_plot_boxplot
    - margot_plot_boxplot_covariate
    - margot_plot_discontinuity
    - margot_plot_histogram
    - margot_plot_response_timeline
    - margot_plot_slope
    - margot_plot_slope_covariate
    - margot_plot_slope_covariate_batch
    - margot_plot_slope_covariate_combo
    - margot_summary_panel

  - title: "Check assumptions"
    contents:
    - create_transition_matrix
    - match_mi_general
    - margot_make_tables
    - margot_plot_categorical
    - margot_plot_individual_responses
    - margot_plot_shift
    - margot_propensity_model_and_plots
    - margot_summary_tables
    - transition_table

  - title: "Prepare data for models"
    contents:
    - create_ordered_variable
    - impute_and_combine
    - margot_adjust_weights
    - margot_amelia_to_mice
    - margot_censor
    - margot_compute_gender_weights_by_wave
    - margot_filter
    - margot_impute_carry_forward
    - margot_log_transform_vars
    - margot_process_binary_vars
    - margot_process_longitudinal_data
    - margot_process_longitudinal_data_wider
    - margot_wide
    - margot_wide_impute_baseline
    - margot_wide_machine

  - title: "Treatment effect estimation"
    contents:
    - causal_contrast_engine
    - causal_contrast_marginal
    - double_robust_marginal
    - margot_causal_forest
    - margot_lmtp
    - margot_multi_arm_causal_forest

  - title: "Interpret and Report Results"
    contents:
    - margot_compare_groups
    - margot_omnibus_hetero_test
    - margot_interpret_marginal
    - margot_interpret_policy_tree
    - margot_interpret_policy_batch
    - margot_interpret_qini
    - margot_lmtp_evalue
    - margot_lmtp_tab
    - margot_model_evalue
    - margot_model_tab
    - margot_policy
    - margot_subset_model
    - margot_summary_cate_difference_gain

  - title: "Visualise Causal Effect Estimates"
    contents:
    - margot_plot
    - margot_plot_batch_rate
    - margot_plot_decision_tree
    - margot_plot_multi_arm
    - margot_plot_policy_combo
    - margot_plot_policy_tree
    - margot_plot_qini
    - margot_plot_rate

  - title: "Utility functions"
    contents:
    - back_transform_logmean
    - back_transform_zscore
    - construct_formula
    - here_read
    - here_save
    - here_read_qs
    - here_save_qs
    - lmtp_evalue_tab
    - margot_log_transform_vars
    - margot_plot_create_options
    - margot_plot_exposure
    - margot_process_binary_vars
    - margot_prop_missing
    - margot_save_png
    - margot_size
    - prepare_panel_data
    - pretty_number
    - read_multiple_images
    - remove_numeric_attributes
    - regress_with_covariates
    - select_and_rename_cols
    - transform_table_rownames


  - title: "Simulated data"
    contents:
    - df_nz

  - title: "Deprecated Functions"
    contents:
    - coloured_histogram
    - coloured_histogram_sd
    - coloured_histogram_shift
    - coloured_histogram_quantiles
    - margot_plot_hist