_pkgdown.yml

url: https://egouldo.github.io/ManyEcoEvo/
development:
  mode: auto
template:
  bootstrap: 5
reference:
- title: Unprocessed data cleaning and checking
  desc: |
    Functions for cleaning and QA checking unprocessed analyst data
- subtitle: Miscellaneous cleaning functions
  contents:
  - rm_inf_na
  - anonymise_teams
  - clean_response_transformation
  - assign_transformation_type
- subtitle: Tidying analyst out-of-sample predictions
  desc: ~
  contents:
  - augment_prediction_data
  - preprocess_prediction_files
  - preprocess_updated_prediction_files
  - read_submission_data
  - starts_with("validate_predictions")
- title: Data Processing for Meta-analysis and Modelling
  desc: |
    Calculating and standardising variables for meta-analysis and modelling
- subtitle: Back-transforming / standardising analyst estimates
  contents:
  - ends_with("_back")
  - starts_with("back")
  - conversion
  - conversion_2
  - convert_predictions
  - est_to_zr
  - Z_VZ_preds
  - pred_to_Z
  - standardise_response
- subtitle: Excluding Data from Meta-analysis
  contents:
  - apply_VZ_exclusions
  - starts_with("exclude_")
  - starts_with("subset_fns")
- subtitle: Transforming and standardising meta-analysis variables
  desc: |
    Functions for computing and standardising response and predictor 
    variables for meta-analysis.
  contents:
  - box_cox_transform
  - variance_box_cox
  - folded_params
  - starts_with("log_transform")
  - calculate_deviation_score
  - calculate_sorensen_diversity_index
  - apply_sorensen_calc
- title: Process and create datasets for analysis
  desc: |
    Functions for creating datasets ready for meta-analysis and modelling
  contents:
  - make_param_table
  - compute_MA_inputs
  - compute_metaanalysis_inputs
  - get_diversity_data
  - starts_with("prepare_")
  - split_yi_subsets
  - rename_prediction_cols
- title: Model Fitting & Meta-analysis
  desc: |
    Functions for fitting meta-analysis and other models described in *Gould
    et al. (2023)*
  contents: starts_with("fit_")
- title: Extracting Analysis Outputs & Visualisation
  desc: |
    Functions for extracting model outputs, and visualising analysis results
- subtitle: Extracting meta-analysis outputs
  contents:
  - i2_ml
  - calc_I2_ml
  - apportion_heterogeneity_ml
- subtitle: Plotting
  contents:
  - gg_forest
  - contains("plot_")
- subtitle: Model Checking and Comparison
  contents:
  - compare_ml_MA
  - get_MA_fit_stats
  - run_model_checks
- subtitle: Summarising Analysis Features
  desc: |
    Functions for summarising qualitative and quantitative features of analyses, 
    including model specification and variable selection, analyst conclusions and 
    modelling approaches.
  contents:
  - starts_with("summarise")
  - starts_with("count")
  - calc_analyses_per_team
  - calc_summary_stats_binary
  - calc_summary_stats_numeric
  - calc_teams_per_dataset
  - calculate_variable_counts
- title: 'Scaling Up: Working with data subsets or multiple datasets'
  desc: |
    Functions for working with multiple datasets or data subsets within a 
    tidyverse list-column framework.
- subtitle: Wrapper Functions
  desc: ''
  contents:
  - compute_metaanalysis_inputs
  - meta_analyse_datasets
  - make_viz
- subtitle: Generate data subsets of full ManyEcoEvo or ManyAnalyst dataset
  desc: ''
  contents: starts_with("generate_")
- title: Utility Functions
  desc: Miscelaneous utility functions
  contents:
  - capwords
  - named_group_split
  - "%nin%"