This type wraps a ReportPlot into an AbstractSection struct. Thus the only field is a report plot. Its mainly used to add plots to reports. You can look up the aviailable default report styles to get an idea how that might look like.

You can either pass an instance of a SimulationPlot to the constructor like:

PlotSection(TickCases())

or pass the SimulationPlot type as a Symbol like:

PlotSection(:TickCases)

The gemsplot() function contains a comprehensive list on the available plot types.

GEMS.Report — Type

Supertype for all simulation reports

GEMS.ReportPlot — Type

Supertype for all plots that go into reports

GEMS.Section — Type

Section(title::String = "", content::String = "", subsections::Vector{AbstractSection} = [])
Section(rd::ResultData, type::Symbol)
Section(rd::BatchData, type::Symbol)

A type for Report Sections. All reports consist of (nested) sections. A report section will be parsed into a markdown section (indicated by "#"s) during report generation. Each section must have a title and content. It can have an arbitrary number of subsections.

Example

This code creates two sections. The first one having a title and some content. The second section contains the first secion as a subsection.

sec_1 = Section(
    title = "My Section Title",
    content = "Great section contents"
)

sec_2 = Section(
    title = "My Second Section
    subsections = [sec_1]
)

Defaut Sections

There are a number of default sections that you can simply plug into your report by calling the Section() constructor and pass a ResultData or BatchData object and a Symbol qualifying the type of section you'd like to get:

# run simulation
sim = Simulation()
run!(sim)
rd = ResultData(sim)

overview_section = Section(rd, :Overview)

Default Sections for Single Simulation Reports

Input must be ResultData.

Type	Title	Content
`:Debug`	Debug Information	Contains `:Memory`, `:Processor`,`:Repo`, and `:System` section.
`:General`	General	Geeral simulation info; tick unit, start conditions, and others.
`:InputFiles`	Input Files	Config- and population file paths.
`:Interventions`	Interventions	Triggers, strategies, and measures.
`:Memory`	Memory	Available and used system memory.
`:Model`	Model Configuration	Contains `:InputFiles`, `:Interventions`, `:General`, `:Pathogens`, and `:Settings`
`:Observations`	Observations	Summary of observed progression, detection rate, dark figure, and others.
`:Overview`	Overview	Simulation summmary with initial infections, total attack rate, and others.
`:Pathogens`	Pathogens	Pathogen configuration with one subsection per pathogen.
`:Processor`	Processor	Processor model, cores, and others.
`:Repo`	Repository	Current repo-, branch- and commit-ID.
`:Settings`	Settings	Number of settings per type and min, max, average number of individuals.
`:System`	System Information	Julia config, number of threads, and others.

Default Sections for Batch Reports

Input must be BatchData.

Type	Title	Content
`:Allocations`	Allocations	Summary statistics on memory usage across simulation runs in `BatchData` object.
`:Debug`	Debug Information	Contains `:Memory`, `:Processor`,`:Repo`, and `:System` section.
`:General`	Genera	Geeral simulation info; tick unit, start conditions, and others.
`:Memory`	Memory	Available and used system memory.
`:Overview`	Overview	Summary statistics on total infections, attack rates, and others.
`:Processor`	Processor	Processor model, cores, and others.
`:Repo`	Repository	Current repo-, branch- and commit-ID.
`:Resouces`	Resources	Contains `:Runtime` and `:Allocations` sections.
`:Runtime`	Runtime	Summary statistics on runtime across simulation runs in `BatchData` object.
`:Settings`	Settings	Number of settings per type and min, max, average number of individuals.
`:System`	System Information	Julia config, number of threads, and others.

GEMS.SimulationReport — Type

SimulationReport <: Report

A Type for generating a single-run simulation report.

Fields

Result Data

rd::ResultData: Result data object used to generate this report

Meta Information

title::String: Report title
subtitle::String: Report subtitle
author::String: Report authors
date::String: Simulation execution date (post processing)
abstract::String: Report abstract

Configuration

glossary::Bool: flag to add or remove glossary with term definitions
dpi::Int64: dots per inch for report plots (default: 300)
fontfamily::String: font family for report (default: Times New)

Functions

GEMS.abstract — Function

abstract(report::Report)

Returns the abstract of a Report.

GEMS.abstract! — Function

abstract!(report::Report, abstract::String)

setss the abstract of a Report.

GEMS.addsection! — Function

addsection!(section::Section, subsection::AbstractSection)

Adds a subsection to a provided section.

addsection!(section::Section, subsections::Vector)

Adds multiple subsection to a provided section.

addsection!(report::Report, section::AbstractSection)

Adds a Section to a Report. It can either be a regular section or a plot section.

GEMS.addtimer! — Function

addtimer!(rep::SimulationReport, to::TimerOutput)

Generates a Section from the consolue output of a TimerOutput object and adds it to a SimulationReport.

GEMS.author! — Function

author!(report::Report, author::String)

Sets the author of a Report.

GEMS.author — Function

author(report::Report)

Returns the author of a Report.

GEMS.buildreport — Function

buildreport(data::Union{ResultData,BatchData}, style::String = "")

Initializes and configures a simulation report with the tile, abstract, sections etc. provided in config. If config is an empty dictionary all available standard sections, plots, and the glossary etc. will be used. It returns a full SimulationReport object which can then be generated using the generate() function.

GEMS.content! — Function

content!(section::Section, content::String)

Sets a section's content.

GEMS.content — Function

content(section::Section)

Returns a section's content.

GEMS.date! — Function

date!(report::Report, date::String)

Sets the date of a Report.

GEMS.date — Function

date(report::Report)

Returns the date of a Report.

GEMS.description! — Method

description!(plot::ReportPlot, description::String)

Setter for report plot description.

GEMS.description — Method

description(plot::ReportPlot)

Return description from report plot object.

GEMS.dpi — Function

dpi(report)

Returns dpi (dots per inch) from a report object. dpi conditions the resolution of images generated for the report.

GEMS.dpi! — Method

dpi!(report, dpi)

Setter for report dpi (dot per inch) for images.

GEMS.escape_markdown — Method

escape_markdown(str::String)

Replaces markdown controls (e.g. "_" or "*") with their escaped version.

GEMS.filename! — Method

filename!(plot::ReportPlot, filename::String)

Setter for report plot filename.

GEMS.filename — Method

filename(plot::ReportPlot)

Return filename from report plot object.

GEMS.fontfamily! — Function

fontfamily!(report, fontfamily)

Setter for report fontfamily.

GEMS.fontfamily — Function

fontfamily(report)

Returns font family config from a report object.

GEMS.generate — Method

generate(report::Report, directory::AbstractString)

Generates markdown string from a Report object including its nested subsections. The report will be stored as PDF, HTML, and MD in the provided directory. Images are generated and stored in an "/img" subfolder.

GEMS.glossary! — Function

glossary!(report::Report, glossary::Bool)

Sets the glossary flag of a Report. If true, the glossary will be copied into the report upon generation.

GEMS.glossary — Function

glossary(report::Report)

Returns the glossary flag of a Report.

GEMS.markdown — Function

markdown(infFrac::InfectedFraction)