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

Raw data | Construction | sequence2gtypes - Convert DNA sequences | Conversions from other packages. | Accessor functions | Subsetting/Indexing | Summary | Stratifying samples | Exporting

Installation | How to install the current version of ade4? | How to install the development version of ade4? | How do I know which ade4 version I'm using? | Graphics | What is adegraphics? | How to load adegraphics? | How to interpret ellipses plotted by s.class function? | Simple Analysis | How to obtain coordinates for individuals? | How to obtain coordinates for variables? | What are the $l1 and $c1 elements of a dudi ?

Example data: simulated Ebola outbreak | The plot.incidence function | Default behaviour | Changing colors | The default palette | Using different palettes | Specifying colors manually | Example 1: changing a single color | Example 2: changing several colors (note that naming colors is optional) | Example 3: using color to highlight specific groups | Useful ggplot2 tweaks | Changing dates on the x-axis | Changing date format | Changing the grid | Handling non-ISO weeks | Labelling every bin | Changing the legend | Applying the style of European Programme for Intervention Epidemiology Training (EPIET) | Display individual cases

Installing the package | What does it do? | Worked example: simulated Ebola outbreak | Loading the data | Computing and plotting incidence | Handling incidence objects | Modelling incidence

Introduction | Format required by most functions in Hierfstat | Importing data files | Importing FSTAT data files | Importing from adegenet: genind objects | Allelic dosages | Importing from adegenet: genlight objects | importing VCF files | Data generated by external genetic data simulators | Importing from Quantinemo | Importing from ms

Introduction | Loading data | Descriptive statistics | Population statistics | Hierarchical analyses | Testing | Genetic distances | Population Principal coordinate analysis | Population specific $F_{ST}$s | Individual statistics | Individual PCA | kinships, GRM and individual inbreeding coefficients | Simulating genetic data | Exporting to other programs | Miscellaneous | Sex-biased dispersal

Use Cases | Workflow | Examples | Markdown | R Markdown | Inserting new Markdown elements | Background / pre-requisites | Loss of Markdown style | General principles and solution | The special case of tables | LaTeX equations

Use Cases | Workflow | Examples | Markdown | R Markdown | Inserting new Markdown elements | Background / pre-requisites | Loss of Markdown style | General principles and solution | The special case of tables | LaTeX equations

Introduction | Converting dates to weeks | How does it work? | The aweek class | Best practices | Weekly aggregation | Factors | Weeks to weeks | Combining aweek objects | Dates can be appended to aweek objects | Add characters with caution | Working with weeks in data frames | weeks as numbers | weeks as characters | Converting weeks to dates

Introduction | Converting dates to weeks | How does it work? | The aweek class | Best practices | Weekly aggregation | Factors | Weeks to weeks | Combining aweek objects | Dates can be appended to aweek objects | Add characters with caution | Working with weeks in data frames | weeks as numbers | weeks as characters | Converting weeks to dates

Exporting results | Importing pre-computed incidence

Structure of an incidence object. | $dates | $counts | $timespan | $interval | $n | $weeks

Structure of an incidence_fit object | Building an incidence_fit object from scratch | Step 1: create the model | Step 2: creation of the $info list: | Step 3: combine lists and create object | Structure of an incidence_fit_list object | Example: A tale of two fits | Example: Nested incidence_fit

What the repvar package does | How it works | Functions in this package | Quickstart | Detailed Example: Monilinia fructicola