_pkgdown.yml

url: https://jameshwade.github.io/measure/
template:
  bootstrap: 5
  bslib:
    primary: "#4A90A4"
    secondary: "#6BA5B8"
    success: "#28A745"
    info: "#17A2B8"
    warning: "#FF9933"
    danger: "#DC3545"
    base_font: {google: "Open Sans"}
    heading_font: {google: "Montserrat"}
    code_font: {google: "Fira Code"}
    bg: "#FFFFFF"
    fg: "#212529"
  theme: arrow-light
  light-switch: true

logo:
  src: man/figures/logo.png
  alt: "measure hex logo"
navbar:
  structure:
    left:
    - intro
    - reference
    - articles
    right:
    - search
    - github
  components:
    articles:
      text: Articles
      menu:
      - text: Tutorials
      - text: Getting Started
        href: articles/tutorial-getting-started.html
      - text: Bioreactor Case Study
        href: articles/tutorial-bioreactor.html
      - text: '---'
      - text: How-To Guides
      - text: Baseline Correction
        href: articles/howto-baseline.html
      - text: Integrating with tidymodels
        href: articles/howto-tidymodels.html
      - text: Data Organization & Diagnostics
        href: articles/howto-data-organization.html
      - text: '---'
      - text: Reference
      - text: Preprocessing Techniques
        href: articles/reference-preprocessing.html
      - text: Multi-Dimensional Data
        href: articles/reference-multidimensional.html
      - text: Analytical Validation
        href: articles/reference-validation.html
      - text: '---'
      - text: Explanation
      - text: Internal Class System
        href: articles/explanation-internals.html
development:
  mode: devel
articles:
- title: Tutorials
  desc: Learning-oriented guides that take you through a complete workflow
  contents:
  - articles/tutorial-getting-started
  - articles/tutorial-bioreactor
- title: How-To Guides
  desc: Task-oriented guides for solving specific problems
  contents:
  - articles/howto-baseline
  - articles/howto-tidymodels
  - articles/howto-data-organization
- title: Reference
  desc: Information-oriented technical descriptions
  contents:
  - articles/reference-preprocessing
  - reference-multidimensional
  - reference-validation
- title: Explanation
  desc: Understanding-oriented discussion of concepts and architecture
  contents: explanation-internals
reference:
- title: Input Steps
  desc: Convert raw data to measure's internal format
  contents:
  - step_measure_input_wide
  - step_measure_input_long
- title: Processing Steps
  desc: Apply spectral preprocessing transformations
  contents:
  - step_measure_savitzky_golay
  - step_measure_snv
  - step_measure_msc
  - step_measure_map
- title: Multi-Channel Operations
  desc: Align, combine, and compute ratios between measurement channels
  contents:
  - step_measure_channel_align
  - step_measure_channel_combine
  - step_measure_channel_ratio
- title: Spectral Math
  desc: Mathematical transformations for spectral data
  contents:
  - step_measure_absorbance
  - step_measure_transmittance
  - step_measure_log
  - step_measure_kubelka_munk
  - step_measure_derivative
  - step_measure_derivative_gap
- title: Region Operations
  desc: Trim, exclude, and resample measurement regions
  contents:
  - step_measure_trim
  - step_measure_exclude
  - step_measure_resample
  - step_measure_interpolate
- title: Sample-wise Normalization
  desc: Normalize each spectrum independently
  contents:
  - starts_with("step_measure_normalize")
- title: Variable-wise Scaling
  desc: Scale across samples at each measurement location
  contents:
  - step_measure_center
  - starts_with("step_measure_scale")
- title: Reference-Based Corrections
  desc: Blank subtraction and reference corrections
  contents:
  - step_measure_subtract_blank
  - step_measure_subtract_reference
  - step_measure_ratio_reference
- title: Calibration
  desc: X-axis and Y-axis calibration steps
  contents:
  - step_measure_calibrate_x
  - step_measure_calibrate_y
- title: Output Steps
  desc: Convert internal format back to modeling-ready data
  contents:
  - step_measure_output_wide
  - step_measure_output_long
- title: Peak Operations
  desc: Peak detection, integration, and analysis for chromatography
  contents:
  - step_measure_peaks_detect
  - step_measure_peaks_integrate
  - step_measure_peaks_properties
  - step_measure_peaks_filter
  - step_measure_peaks_deconvolve
  - step_measure_peaks_to_table
  - is_peaks_list
  - find_peaks_cols
- title: Peak Algorithm Registry
  desc: Registration and discovery for peak detection algorithms
  contents:
  - peak_algorithms
  - get_peak_algorithm
  - has_peak_algorithm
  - register_peak_algorithm
  - unregister_peak_algorithm
- title: Peak Model Classes
  desc: S3 class architecture for peak shape models used in deconvolution
  contents:
  - new_peak_model
  - is_peak_model
  - create_peak_model
  - has_peak_model
  - peak_models
  - register_peak_model
  - unregister_peak_model
  - peak_model_value
  - peak_model_gradient
  - peak_model_gradient_numerical
  - peak_model_bounds
  - peak_model_initial_guess
  - peak_model_area
  - peak_model_param_names
  - validate_peak_model_params
  - sum_peak_models
- title: Built-in Peak Models
  desc: Core peak shape models for deconvolution
  contents:
  - gaussian_peak_model
  - emg_peak_model
  - bigaussian_peak_model
  - lorentzian_peak_model
- title: Peak Deconvolution Utilities
  desc: Optimization, initialization, and quality assessment helpers
  contents:
  - optimize_deconvolution
  - initialize_peak_params
  - add_param_jitter
  - assess_deconv_quality
  - check_quality_gates
- title: Smoothing & Noise Reduction
  desc: Noise reduction and spike removal steps
  contents:
  - step_measure_smooth_ma
  - step_measure_smooth_median
  - step_measure_smooth_gaussian
  - step_measure_smooth_wavelet
  - step_measure_filter_fourier
  - step_measure_despike
- title: Alignment & Registration
  desc: Spectral alignment and shift correction
  contents:
  - step_measure_align_shift
  - step_measure_align_reference
  - step_measure_align_dtw
  - step_measure_align_ptw
  - step_measure_align_cow
- title: Quality Control
  desc: Quality metrics and data cleaning
  contents:
  - step_measure_qc_snr
  - step_measure_qc_saturated
  - step_measure_qc_outlier
  - step_measure_impute
- title: Tunable Parameters
  desc: Parameters for hyperparameter tuning with dials
  contents:
  - window_side
  - baseline_lambda
  - peak_location_min
  - derivative_order
  - smooth_window
  - smooth_sigma
  - fourier_cutoff
  - despike_threshold
  - align_max_shift
  - align_segment_length
  - outlier_threshold
  - bin_width
  - emsc_degree
  - osc_n_components
  - starts_with("tunable")
- title: Data
  desc: Included datasets for examples and testing
  contents:
  - meats_long
  - glucose_bioreactors
  - hplc_chromatograms
  - sec_chromatograms
  - sec_calibration
  - maldi_spectra
- title: Baseline Correction
  desc: Baseline correction steps and utilities
  contents:
  - starts_with("step_measure_baseline")
  - step_measure_detrend
  - subtract_rf_baseline
- title: SEC/GPC Analysis
  desc: Molecular weight calculations for size exclusion chromatography
  contents:
  - step_measure_mw_averages
  - step_measure_mw_distribution
  - step_measure_mw_fractions
- title: Feature Engineering
  desc: Extract features from spectral data
  contents:
  - step_measure_integrals
  - step_measure_ratios
  - step_measure_moments
  - step_measure_bin
- title: Extended Scatter Correction
  desc: Advanced scatter correction methods
  contents:
  - step_measure_emsc
  - step_measure_osc
- title: Data Augmentation
  desc: Training data augmentation for improved model robustness
  contents:
  - step_measure_augment_noise
  - step_measure_augment_shift
  - step_measure_augment_scale
- title: Drift & Batch Correction
  desc: Correct for signal drift and batch effects
  contents:
  - step_measure_drift_qc_loess
  - step_measure_drift_linear
  - step_measure_drift_spline
  - step_measure_qc_bracket
  - step_measure_batch_reference
  - measure_detect_drift
- title: Calibration & Quantitation
  desc: Calibration curves, LOD/LOQ, and quantitation
  contents:
  - measure_calibration
  - measure_calibration_fit
  - measure_calibration_predict
  - measure_calibration_verify
  - is_measure_calibration
  - tidy.measure_calibration
  - glance.measure_calibration
  - augment.measure_calibration
  - measure_lod
  - measure_loq
  - measure_lod_loq
  - tidy.measure_lod
- title: Precision & Accuracy
  desc: Method validation for precision and accuracy
  contents:
  - measure_repeatability
  - measure_intermediate_precision
  - measure_reproducibility
  - measure_gage_rr
  - measure_accuracy
  - measure_linearity
  - measure_carryover
- title: Uncertainty
  desc: ISO GUM uncertainty budgets
  contents:
  - measure_uncertainty_budget
  - measure_uncertainty
  - uncertainty_component
  - uncertainty_type_a
  - uncertainty_type_b_rectangular
  - uncertainty_type_b_expanded
  - tidy.measure_uncertainty_budget
- title: Control Charts & QC
  desc: Statistical process control and system suitability
  contents:
  - measure_control_limits
  - measure_control_chart
  - measure_system_suitability
- title: Method Comparison
  desc: Compare analytical methods using Bland-Altman, Deming, and Passing-Bablok
  contents:
  - measure_bland_altman
  - measure_deming_regression
  - measure_passing_bablok
  - measure_proficiency_score
- title: Matrix Effects & Sample Prep
  desc: Matrix effect quantification, standard addition, and sample prep QC
  contents:
  - measure_matrix_effect
  - step_measure_standard_addition
  - step_measure_dilution_correct
  - step_measure_surrogate_recovery
- title: Criteria & Assessment
  desc: Acceptance criteria and pass/fail evaluation
  contents:
  - criterion
  - measure_criteria
  - measure_assess
  - all_pass
  - get_failures
  - criteria_bioanalytical
  - criteria_ich_q2
  - criteria_bland_altman
  - criteria_method_comparison
  - criteria_proficiency_testing
  - criteria_matrix_effects
  - criteria_surrogate_recovery
- title: Metadata Validation
  desc: Validate analytical metadata columns
  contents:
  - measure_validate_metadata
  - measure_standardize_sample_type
  - measure_sample_types
- title: Multi-Way Analysis
  desc: PARAFAC, Tucker, and MCR-ALS decomposition for multi-dimensional data
  contents:
  - step_measure_parafac
  - step_measure_tucker
  - step_measure_mcr_als
- title: Multi-Dimensional Data
  desc: Support for 2D and higher-dimensional measurement data (LC-DAD, EEM, 2D NMR)
  contents:
  - new_measure_nd_tbl
  - new_measure_nd_list
  - is_measure_nd_tbl
  - is_measure_nd_list
  - measure_ndim
  - measure_dim_names
  - measure_dim_units
  - measure_is_regular
  - measure_grid_info
  - measure_apply
  - measure_unfold
  - measure_fold
  - measure_slice
  - measure_project
  - find_measure_nd_cols
  - get_measure_col_ndim
- title: Utilities
  desc: Helper functions and utilities
  contents:
  - new_measure_tbl
  - new_measure_list
  - is_measure_tbl
  - is_measure_list
  - find_measure_cols
  - has_measure_col
  - required_pkgs.recipe
- title: Technique Pack Registry
  desc: Registration and discovery for technique packs
  contents:
  - measure_packs
  - measure_steps
  - register_measure_pack
  - register_measure_step
- title: Exploration & Analysis
  desc: Interactive exploration and summary functions for prototyping
  contents:
  - measure_map
  - measure_map_safely
  - measure_summarize
- title: Data Organization
  desc: Column detection and role assignment helpers
  contents:
  - measure_identify_columns
  - measure_column_summary
  - measure_column_patterns
  - set_measure_roles
  - check_measure_recipe
- title: Axis Validation
  desc: Axis semantics and data quality validation
  contents:
  - validate_measure
  - measure_axis_info
  - infer_axis_type
  - check_axis_consistency
  - measure_quality_summary
- title: Validation Reporting
  desc: Generate reproducible analytical method validation reports
  contents:
  - measure_validation_report
  - render_validation_report
  - has_validation_section
  - get_validation_section
  - add_validation_section
  - print.measure_validation_report
  - summary.measure_validation_report
  - tidy.measure_validation_report
- title: Visualization & Diagnostics
  desc: Plotting and diagnostic functions for measure data
  contents:
  - starts_with("autoplot")
  - starts_with("fortify")
  - plot_measure_comparison
  - measure_plot_summary
redirects:
  - ["articles/measure.html", "articles/tutorial-getting-started.html"]
  - ["articles/sec-analysis-example.html", "articles/tutorial-bioreactor.html"]
  - ["articles/baseline.html", "articles/howto-baseline.html"]
  - ["articles/recipes.html", "articles/howto-tidymodels.html"]
  - ["articles/roles-diagnostics.html", "articles/howto-data-organization.html"]
  - ["articles/preprocessing.html", "articles/reference-preprocessing.html"]
  - ["articles/multidimensional.html", "articles/reference-multidimensional.html"]
  - ["articles/validation.html", "articles/reference-validation.html"]
  - ["articles/internals.html", "articles/explanation-internals.html"]