_pkgdown.yml

title: isoorbi
url: https://isoorbi.isoverse.org
template:
  bootstrap: 5
  bootswatch: litera
  bslib:
    base_font: {google: "Roboto"}

development:
  mode: auto

navbar:
  title: isoorbi
  type: default
  left:
  - text: Quick Start
    href: articles/quick_start.html
  - text: Shot Noise
    href: articles/shot_noise.html
  - text: Dual Inlet
    href: articles/dual_inlet.html
  - text: Flow Injection
    href: articles/flow_injection.html
  - text: IsoXL demo GUI
    href: articles/isoxl_demo.html
  - text: Reference
    href: reference/index.html
  right:
  - icon: fa-github fa-lg
    href: https://github.com/isoverse/isoorbi

reference:
- title: Core functions
  desc: >
    These core functions are essential to read and process isox data.
  contents:
  - orbi_find_isox
  - orbi_read_isox
  - orbi_define_basepeak
  - orbi_summarize_results

- title: Define data blocks
  desc: >
    These functions are useful for annotating and processing `dual inlet` and `flow injection` data.
  contents:
  - orbi_define_block_for_flow_injection
  - orbi_define_blocks_for_dual_inlet
  - orbi_adjust_block
  - orbi_segment_blocks
  - orbi_get_blocks_info

- title: Curate data
  desc: >
    These functions handle data selection and flagging outliers.
  contents:
  - orbi_filter_isox
  - orbi_flag_outliers
  - orbi_flag_satellite_peaks
  - orbi_flag_weak_isotopocules
  - orbi_get_isotopocule_coverage

- title: Visualize data
  desc: >
    These functions help visualize what happens to the data during processing
  contents:
  - orbi_plot_satellite_peaks
  - orbi_plot_isotopocule_coverage
  - orbi_plot_raw_data
  - orbi_add_blocks_to_plot
  - orbi_default_theme

- title: Shot noise analysis
  desc: >
    These functions are available for analysis of shot noise in collected data and creating shot noise plots.
  contents:
  - orbi_analyze_shot_noise
  - orbi_plot_shot_noise

- title: Export functions
  desc: >
    This function serves to export data to an Excel file.
  contents:
  - orbi_export_data_to_excel
  
- title: Other functions
  desc: >
    These functions are available to simplify or customize the data analysis.
  contents:
  - orbi_simplify_isox
  - orbi_calculate_summarized_ratio

- title: Internal
  desc: >
    These functions are available to simplify or customize the data analysis.
  contents:
  - orbi_get_settings
  - orbi_set_settings

- title: Deprecated functions
  contents:
  - orbi_filter_satellite_peaks
  - orbi_filter_scan_intensity
  - orbi_filter_weak_isotopocules
  - orbi_filter_flagged_data
  - orbi_calculate_ratios