├── .Rbuildignore ├── .github ├── .gitignore ├── pull_request_template.md └── workflows │ ├── R-CMD-check.yaml │ └── pkgdown.yaml ├── .gitignore ├── CONTRIBUTING-DATA.md ├── DESCRIPTION ├── LICENSE ├── LICENSE-CC0 ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── assertions.R ├── assign_qa_score.R ├── data.R ├── epireview-package.R ├── fig_utils.R ├── filter_cols.R ├── filter_df_for_metamean.R ├── filter_df_for_metaprop.R ├── forest_plot.R ├── forest_plot_delay.R ├── forest_plot_other.R ├── forest_plot_r.R ├── get_key_columns.R ├── get_parameter.R ├── load_epidata.R ├── load_epidata_raw.R ├── make_unique_id.R ├── mark_multiple_estimates.R ├── pretty_article_label.R ├── reorder_studies.R └── utils.R ├── README.md ├── _pkgdown.yml ├── epireview.Rproj ├── inst ├── CITATION └── extdata │ ├── ebola_articles.csv │ ├── ebola_models.csv │ ├── ebola_parameters.csv │ ├── lassa_articles.csv │ ├── lassa_models.csv │ ├── lassa_outbreaks.csv │ ├── lassa_parameters.csv │ ├── marburg_article.csv │ ├── marburg_dropdown_models.csv │ ├── marburg_dropdown_outbreaks.csv │ ├── marburg_dropdown_parameters.csv │ ├── marburg_model.csv │ ├── marburg_outbreak.csv │ ├── marburg_parameter.csv │ ├── param_name.csv │ ├── sars_articles.csv │ ├── sars_models.csv │ ├── sars_parameters.csv │ ├── zika_articles.csv │ ├── zika_excluded_papers.csv │ ├── zika_models.csv │ ├── zika_outbreaks.csv │ ├── zika_parameters.csv │ └── zika_systematic_reviews.xlsx ├── man ├── article_column_type.Rd ├── assign_qa_score.Rd ├── attack_double_growth_key_columns.Rd ├── cfr_key_columns.Rd ├── check_column_types.Rd ├── check_df_for_meta.Rd ├── check_ulim.Rd ├── color_palette.Rd ├── country_palette.Rd ├── custom_palette.Rd ├── delay_key_columns.Rd ├── delays_to_days.Rd ├── epireview-package.Rd ├── epireview_read_file.Rd ├── figures │ ├── hex-epireview.png │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-soft-deprecated.svg │ └── lifecycle-stable.svg ├── filter_cols.Rd ├── filter_df_for_metamean.Rd ├── filter_df_for_metaprop.Rd ├── forest_plot.Rd ├── forest_plot_delay_int.Rd ├── forest_plot_doubling_time.Rd ├── forest_plot_incubation_period.Rd ├── forest_plot_infectious_period.Rd ├── forest_plot_r0.Rd ├── forest_plot_rt.Rd ├── forest_plot_serial_interval.Rd ├── genomic_key_columns.Rd ├── get_key_columns.Rd ├── get_parameter.Rd ├── get_specific.Rd ├── invert_inverse_params.Rd ├── key_columns.Rd ├── load_epidata.Rd ├── load_epidata_raw.Rd ├── make_unique_id.Rd ├── marburg_article.Rd ├── marburg_dropdown_models.Rd ├── marburg_dropdown_outbreaks.Rd ├── marburg_dropdown_parameters.Rd ├── marburg_model.Rd ├── marburg_outbreak.Rd ├── marburg_parameter.Rd ├── mark_multiple_estimates.Rd ├── model_column_type.Rd ├── outbreak_column_type.Rd ├── overdispersion_contribution_key_columns.Rd ├── param_pm_uncertainty.Rd ├── parameter_column_type.Rd ├── parameter_palette.Rd ├── pretty_article_label.Rd ├── priority_pathogens.Rd ├── qa_questions.Rd ├── reorder_studies.Rd ├── reparam_gamma.Rd ├── reproduction_number_key_columns.Rd ├── risk_factors_key_columns.Rd ├── sero_key_columns.Rd ├── shape_palette.Rd ├── short_parameter_type.Rd ├── theme_epireview.Rd ├── update_article_info.Rd └── value_type_palette.Rd ├── miscellaneous_files ├── DIDE Priority Pathogens - BLANK.accdb └── add-new-pathogen.md ├── tests ├── testthat.R └── testthat │ ├── test-add-qa.R │ ├── test-filter_df_for_metamean.R │ ├── test-filter_df_for_metaprop.R │ ├── test-get_key_columns.R │ ├── test_add_unique_labels.R │ ├── test_assertions.R │ ├── test_check_column_types.R │ ├── test_data_load_and_prep.R │ ├── test_doi_included.R │ ├── test_get_parameter.R │ ├── test_make_unique_id.R │ ├── test_prep_data_forest_plots.R │ ├── test_reorder_studies.R │ ├── test_short_parameter_type.R │ ├── test_utils.R │ └── testdata │ └── offending_dataset.csv └── vignettes ├── .gitignore 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