_pkgdown.yml

authors:
  Alejandro Reyes:
    href: http://alejandroreyes.org
  Patrick Kimes:
    href: https://www.pkimes.com

development:
  version_label: "info"
  version_tooltip: "Bioc Devel"

navbar:
  structure:
    left:
    - home
    - intro
    - reference
    - vignettes
    right:
    - news
    - search
    - github
  components:
    intro: 
      text: Quick Start
      href: articles/SummarizedBenchmark-Introduction.html
    articles: ~
    vignettes:
      text: Articles
      menu:
      - text: General
      - text: Introduction
        href: articles/SummarizedBenchmark-Introduction.html
      - text: Class Details
        href: articles/SummarizedBenchmark-ClassDetails.html
      - text: Full Case Study
        href: articles/SummarizedBenchmark-FullCaseStudy.html
      - text: --------
      - text: Features
      - text: Error Handling
        href: articles/Feature-ErrorHandling.html
      - text: Iterative Benchmarking
        href: articles/Feature-Iterative.html
      - text: Parallelization
        href: articles/Feature-Parallel.html
      - text: --------
      - text: More Case Studies
      - text: scRNA-seq Simulation
        href: articles/CaseStudy-SingleCellSimulation.html
      - text: RNA-seq Quantification
        href: articles/CaseStudy-RNAseqQuantification.html

toc:
  depth: 1

reference:
- title: Creating Objects
  desc: >
    Several classes are defined in the package, most importantly, the [BenchDesign](BenchDesign-class.html) and
    [SummarizedBenchmark](SummarizedBenchmark-class.html) classes for encapsulating the benchmark design and
    benchmark results, repectively. The following set of functions can be used to create new instances of
    each class. For more details, see [class definitions](#section-class-definitions) below.
  contents:
  - '`BenchDesign`'
  - '`BDMethod`'
  - '`BDMethodList`'
  - '`BDData`'
  - '`SummarizedBenchmark`'
- title: Executing Benchmarks
  desc: >
    Benchmark experiments can be executed from either BenchDesign or SummarizedBenchmark objects using the following
    set of functions.
  contents:
  - '`buildBench`'
  - '`updateBench`'
- title: BenchDesign Methods
  desc: >
    Methods and data for benchmark experiments are stored in [BenchDesign](BenchDesign-class.html) objects.
    The following functions are available for working with these objects to add, remove, or modify methods
    in the design, as well as to compare the methods and data contained in these objects.
  contents:
  - '`addMethod`'
  - '`dropMethod`'
  - '`expandMethod`'
  - '`modifyMethod`'
  - '`printMethod`'
  - '`compareBenchDesigns`'
  - '`compareBDMethod`'
  - '`compareBDData`'
  - '`hashBDData`'
- title: SummarizedBenchmark Methods
  desc: >
    Results from benchmark experiments are stored in [SummarizedBenchmark](SummarizedBenchmark-class.html) objects.
    The following functions are available for working with these objects to define benchmark metrics and
    evaluate or plot the results of a benchmark experiment.
  contents:
  - '`groundTruths`'
  - '`availableMetrics`'
  - '`performanceMetrics`'
  - '`addPerformanceMetric`'
  - '`estimateMetricsForAssay`'
  - '`tidyUpMetrics`'
  - '`plotROC`'
  - '`plotMethodsOverlap`'
- title: Class Definitions
  desc: >
    Two core classes, [BenchDesign](BenchDesign-class.html) and
    [SummarizedBenchmark](SummarizedBenchmark-class.html) are
    defined in the package, along with several smaller classes which help encapsulate data
    used in benchmarking ([BDData](BDData-class.html)) and definitions of methods benchmarked
    ([BDMethod](BDMethod-class.html), [BDMethodList](BDMethodList-class.html)).
  contents:
  - '`BenchDesign-class`'
  - '`BDData-class`'
  - '`BDMethod-class`'
  - '`BDMethodList-class`'
  - '`SummarizedBenchmark-class`'
- title: Class Setters
  desc: >
    In addition to using the methods defined above for [working with BenchDesign objects](#section-benchdesign-methods)
    and [working with SummarizedBenchmark](#section-summarizedbenchmark-methods), some slots and values of
    the classes can be directly modified using the following functions. 
  contents:
  - '`BDData<-`'
  - '`BDMethod<-`'
  - '`BDMethodList<-`'
  - '`performanceMetrics<-`'
  - '`groundTruths<-`'
  - '`mcols<-,SummarizedBenchmark-method`'
  - '`assayNames<-,SummarizedBenchmark,character-method`'
- title: Data Sets
  desc: >
    Example data sets are included to illustrate the functionality of the package in the
    various vignettes and case studies.
  contents:
  - '`allSB`'
  - '`sb`'
  - '`tdat`'