Origin | Aim | Funding | Contributers

Introduction | Purpose of this guide | Who this guide is for | Outbreak report contents | Instructions | Structure of the outbreak report Rmd | How to produce the report | Requirements for report generation | Detailed guide | YAML | Set up and load data | setup chunk | definitions chunk | set_plot_defaults chunk | Import data | read_population_data chunk | read_data chunk | browse_data chunk | Clean linelist data | standardise_dates chunk | create_age_group chunk | standardise_values chunk | create_vars chunk | duplicates chunk | remove_unused_data chunk | save_cleaned_data chunk | Analysis | Recommendations text | Summary text | epicurve chunk | Age and sex distribution | Combined count, attack rate, and case fatality ratio tables | Other case characteristics | Geographic distribution - tables | Geographic distribution - maps | Geographic detail

Introduction | Purpose of this guide | Who this guide is for | Outbreak report contents | Instructions | Structure of the outbreak report Rmd | How to produce the report | Requirements for report generation | Detailed guide | YAML | Set up and load data | setup chunk | definitions chunk | set_plot_defaults chunk | Import data | read_population_data chunk | read_data chunk | browse_data chunk | Clean linelist data | standardise_dates chunk | create_age_group chunk | standardise_values chunk | create_vars chunk | duplicates chunk | remove_unused_data chunk | save_cleaned_data chunk | Analysis | Recommendations text | Summary text | epicurve chunk | Age and sex distribution | Severity | Combined count, attack rate, and case fatality ratio tables | Vaccination, laboratory results, and outcomes | Geographic distribution - tables | Geographic distribution - maps | Geographic detail

Introduction | Purpose of this guide | Who this guide is for | Outbreak report contents | Instructions | Structure of the outbreak report Rmd | How to produce the report | Requirements for report generation | Detailed guide | YAML | Set up and load data | setup chunk | definitions chunk | set_plot_defaults chunk | Import data | read_population_data chunk | read_data chunk | browse_data chunk | Clean linelist data | standardise_dates chunk | create_age_group chunk | standardise_values chunk | create_vars chunk | duplicates chunk | remove_unused_data chunk | save_cleaned_data chunk | Analysis | Recommendations text | Summary text | epicurve chunk | Age and sex distribution | Symptoms, underlying conditions, and treatment | Combined count, attack rate, and case fatality ratio tables | Vaccination, laboratory results, and outcomes | Geographic distribution - tables | Geographic distribution - maps | Geographic detail

Introduction | Purpose of this guide | Who this guide is for | Outbreak report contents | Instructions | Structure of the outbreak report Rmd | How to produce the report | Requirements for report generation | Detailed guide | YAML | Set up and load data | setup chunk | definitions chunk | set_plot_defaults chunk | Import data | read_population_data chunk | read_data chunk | browse_data chunk | Clean linelist data | standardise_dates chunk | create_age_group chunk | standardise_values chunk | create_vars chunk | duplicates chunk | remove_unused_data chunk | save_cleaned_data chunk | Analysis | Recommendations text | Summary text | epicurve chunk | Age and sex distribution | Combined count, attack rate, and case fatality ratio tables | Other characteristics and outcomes chunks | Geographic distribution - tables | Geographic distribution - maps | Geographic detail

Introduction | Purpose of this guide | Who this guide is for | Outbreak report contents | Instructions | Structure of the outbreak report Rmd | How to produce the report | Requirements for report generation | Detailed guide | YAML | Set up and load data | setup chunk | definitions chunk | set_plot_defaults chunk | Import data | read_population_data chunk | read_data chunk | browse_data chunk | Clean linelist data | standardise_dates chunk | create_age_group chunk | standardise_values chunk | create_vars chunk | duplicates chunk | remove_unused_data chunk | save_cleaned_data chunk | Analysis | Recommendations text | Summary text | epicurve chunk | Age and sex distribution | Symptoms and malnutrition | Combined count, attack rate, and case fatality ratio tables | Vaccination, laboratory results, and outcomes | Geographic distribution - tables | Geographic distribution - maps | Geographic detail

Introduction | Purpose of this guide | Who this guide is for | Instructions | Structure of the recoding Rmd | How to use the recording Rmd | Requirements for this Rmd | Detailed guide | Set up and loading data | setup chunk | Import and inspect data | Understand your expected data format | clean_column_names chunk | standardise_capitalisation chunk | browse_data chunk | recode_factor_vars chunk | recode_numeric_vars chunk | save_recoded_data chunk

Acute Jaundice Syndrome (AJS) | Variables in the intersectional dictionary | Option codes in the intersectional dictionary | Variables in the OCA dictionary | Option codes in the OCA dictionary | Cholera | Measles | Meningitis | Diphtheria | Exploring the dictionaries

Retrospective mortality and access to care ("mortality") | Variables in the dictionary | Option codes | Malnutrition ("nutrition") | Vaccination Coverage ("vaccination_long" or "Vaccination_short") | Exploring the dictionaries