_pkgdown.yml

title: isoprocessor
url: http://isoprocessor.isoverse.org/
template:
  params:
    bootswatch: simplex
    ganalytics: UA-106138361-4
    toc_float: true

home:
  strip_header: true

development:
  mode: unreleased
  version_label: danger
  version_tooltip: "in active development"

navbar:
  title: isoprocessor
  type: default
  left:
  - text: Dual Inlet
    href: articles/dual_inlet.html
  - text: Continuous Flow
    href: articles/continuous_flow.html
  - text: Scan
    href: articles/scan.html
  - text: "Processing Examples"
    menu:
      - text: "Bulk carbon isotope analysis"
        href: articles/ea_irms_example_carbon.html
      - text: "Compound specific carbon isotope analysis"
        href: articles/gc_irms_example_carbon.html
  - text: Reference
    href: reference/index.html
  right:
  - icon: fa-github fa-lg
    href: https://github.com/isoverse/isoprocessor


reference:
- title: Calculation functions
  desc: >
    These functions provide tools to easily calculate ratios, deltas, scale time and convert signal units.
  contents:
  - iso_calculate_ratios
  - iso_calcualte_deltas
  - iso_convert_signals
  - iso_convert_time
  - iso_scale_double_with_units
- title: Peak table functions
  desc: >
    These functions provide tools to work with peak tables in continuous flow files.
  contents:
  - iso_set_peak_table
  - iso_set_peak_table_from_vendor_data_table
  - iso_get_peak_table
  - iso_mutate_peak_table
  - iso_convert_peak_table_units
- title: Peak mapping
  desc: >
    Functions to easily map data table peaks by retention time.
  contents:
   - iso_map_peaks
   - iso_get_problematic_peak_mappings
   - iso_remove_problematic_peak_mappings
- title: Calibration
  desc: >
    Functions to calibrate data.
  contents:
  - iso_add_standards
  - iso_prepare_for_calibration
  - iso_generate_calibration
  - iso_apply_calibration
  - iso_evaluate_calibration_range
  - iso_get_problematic_calibrations
  - iso_remove_problematic_calibrations
- title: Unpacking calibration models
  desc: >
    Generic base functions, can be adapted for non-standard applications.
  contents:
  - iso_unnest_data
  - iso_unnest_calibration_coefs
  - iso_unnest_calibration_summary
  - iso_unnest_calibration_range
  - iso_unnest_calibration_parameters

- title: Visualization
  desc: >
    Visualization functions.
  contents:
  - iso_plot_continuous_flow_data
  - iso_plot_dual_inlet_data
  - iso_plot_calibration_parameters
  - iso_plot_residuals
  - iso_plot_data
  - iso_mark_calibration_range
  - iso_mark_value_range
  - iso_mark_outliers

- title: Reporting & Export
  desc: >
    Reporting and export functions.
  contents:
  - iso_summarize_data_table
  - iso_remove_list_columns
  - iso_export_calibration_to_excel

- title: Package settings
  desc: >
  contents:
  - iso_set_default_processor_parameters
  - iso_show_default_processor_parameters
  - iso_get_default_processor_parameters

- title: Under the hood
  desc: >
    Generic base functions, can be adapted for non-standard applications.
  contents:
  - run_regression
  - apply_regression
  - unnest_select_data
  - unnest_model_column