_pkgdown.yml

url: https://quantixed.github.io/TrackMateR/

authors:
  Stephen J. Royle:
    href: https://quantixed.org

template:
  params:
    bootswatch: flatly

repo:
  url:
    home: https://github.com/quantixed/TrackMateR/
    source: https://github.com/quantixed/TrackMateR/blob/master/
    issue: https://github.com/quantixed/TrackMateR/issues/
    user: https://github.com/quantixed/

navbar:
  left:
    - icon: fa-home fa-lg
      href: index.html
    - text: Getting Started
      href: articles/TrackMateR.html
    - text: Guides
      menu:
      - text: Getting Started
        href: articles/TrackMateR.html
      - text: Comparison of multiple datasets
        href: articles/comparison.html
      - text: Recalibration of datasets
        href: articles/recalibration.html
    - text: Reference
      href: reference/index.html
    - text: Change log
      href: news/index.html
  right:
    - icon: fa-github fa-lg
      href: https://github.com/quantixed/TrackMateR

reference:
- title: Loading and correcting TrackMate data
  desc: >
    To start, TrackMate XML data needs to be read into R. It may need recalibrating
    if the data were captured with incorrect parameters.
  contents:
  - readTrackMateXML
  - correctTrackMateData
- title: Automated reports
  desc: >
    TrackMateR can be used manually to have fine control over your analysis, however
    if you just want to analyse your data with default parameters, these two functions will
    process one dataset, or many
  contents:
  - reportDataset
  - compareDatasets
- title: Analysing track dynamics
  desc: >
    To analyse track dynamics, there are several functions to calculate them.
    These functions are called (with set parameters) in the automated workflows
    and all of them must be called to make a report.
  contents:
  - calculateAlpha
  - calculateCVE
  - calculateFD
  - calculateJD
  - calculateMSD
  - calculateTrackDensity
  - fittingJD
- title: Generating reports and summaries
  desc: >
    Reports and summaries are collections of plots. They can be generated automatically
    using the automated workflows, or they can be made manually after fine-tuning the analysis
    of track dynamics.
  contents:
  - makeSummaryReport
  - makeComparison
- title: Plotting functions
  desc: >
    The autoimated workflows and the reports that can be generated with TrackMateR
    use several different plotting functions.
  contents:
  - plot_tm_MSD
  - plot_tm_NMSD
  - plot_tm_allTracks
  - plot_tm_alpha
  - plot_tm_cumdistOverTime
  - plot_tm_dee
  - plot_tm_displacementHist
  - plot_tm_displacementOverTime
  - plot_tm_durationHist
  - plot_tm_fd
  - plot_tm_intensityHist
  - plot_tm_neighbours
  - plot_tm_speed
  - plot_tm_width
- title: Analysis of non-TrackMate data
  desc: >
    TrackMateR can read and process csv files in a similar way to TrackMate XML outputs.
    These are typically "ground truth" data sets that have been generated synthetically,
    but could come from some other package.
  contents:
  - compareGTDatasets
  - readGTFile