_pkgdown.yml

destination: ../docs/photobiology
url: https://docs.r4photobiology.info/photobiology/

template:
  bootstrap: 5

reference:
  - title: Package overview
    contents:
    - '`photobiology-package`'

  - title: Radiation
    desc: Classes, methods and objects for storing, manipulating and describing spectral data.
  - subtitle: Waveband and spectral weighting functions
    desc: Constructors and other methods for waveband objects used to store descriptions of wavelength ranges and spectral weighting functions.
    contents:
    - waveband
    - is.waveband
    - split_bands
    - wb2spct
    - wb2rect_spct
    - wb2tagged_spct
    - print.waveband
  - subtitle: Individual spectra
    desc: Constructors and query methods for objects used to store spectral data.
    contents:
    - source_spct
    - is.generic_spct
    - as.generic_spct
    - as.calibration_spct
    - as.raw_spct
    - as.cps_spct
    - as.source_spct
    - as.response_spct
    - as.filter_spct
    - as.reflector_spct
    - as.solute_spct
    - as.object_spct
    - as.chroma_spct
    - setGenericSpct
    - generic_mspct
    - class_spct
    - spct_classes
    - rmDerivedSpct
    - make_var_labels
  - subtitle: Collections of spectra
    desc: Constructor and query methods for objects used to store multiple spectra.
    contents:
    - generic_mspct
    - is.generic_mspct
    - as.generic_mspct
    - as.calibration_mspct
    - as.raw_mspct
    - as.cps_mspct
    - as.source_mspct
    - as.response_mspct
    - as.filter_mspct
    - as.reflector_mspct
    - as.solute_mspct
    - as.object_mspct
    - as.chroma_mspct
    - as.matrix-mspct
    - setGenericSpct
    - mspct_classes
    - rmDerivedMspct
    - shared_member_class
  - subtitle: summary() and print() methods for spectra
    desc: Specializations and variants of R's generic methods for spectral data and accompanying metadata records.
    contents:
    - is.summary_generic_spct
    - head_tail
    - print.generic_spct
    - print.summary_generic_spct
    - print.metadata
    - summary.generic_spct
    - summary_spct_classes
  - subtitle: Summary quantities from individual spectra, related to spectral values
    desc: Methods for the computation of non-spectral derived quantities from spectra. Each spectrum is described by one or up to a few scalar values resulting from integration or averaging of spectral values over wavelengths, or other properties.
    contents:
    - irrad
    - e_irrad
    - q_irrad
    - fluence
    - e_fluence
    - q_fluence
    - illuminance
    - response
    - e_response
    - q_response
    - absorbance
    - absorptance
    - transmittance
    - reflectance
    - average_spct
    - integrate_spct
    - color_of
    - rgb_spct
    - e_ratio
    - q_ratio
    - eq_ratio
    - qe_ratio
    - e_fraction
    - q_fraction
    - Tfr_ratio
    - Tfr_fraction
    - Tfr_normdiff
    - Rfr_ratio
    - Rfr_fraction
    - Rfr_normdiff
  - subtitle: Summary quantities from individual spectra and wavebands, related to wavelength
    desc: Methods for querying about the wavelength values of spectra and wavebands. Each spectrum or wavebdand is described by one or two scalar values.
    contents:
    - min
    - max
    - range
    - expanse
    - midpoint
    - stepsize
  - subtitle: Statistical summaries from groups of spectra
    desc: Methods that compute statistical summaries of spectral data, treating individual spectra as replicates or sampled members from a population of spectra. A summary spectrum or fewer spectra than input are returned.
    contents:
    - compare_spct
    - s_sum
    - s_prod
    - s_mean
    - s_median
    - s_range
    - s_var
    - s_sd
    - s_se
    - s_mean_se
    - s_mean_se_band
    - pull_sample
  - subtitle: Metadata attributes
    desc: Methods for setting and querying metadata from spectral objects.
    contents:
    - is_photon_based
    - setBSWFUsed
    - is_effective
    - getInstrDesc
    - setInstrDesc
    - trimInstrDesc
    - isValidInstrDesc
    - getInstrSettings
    - setInstrSettings
    - trimInstrSettings
    - isValidInstrSettings
    - getMultipleWl
    - setMultipleWl
    - getNormalized
    - setNormalized
    - is_normalized
    - getScaled
    - setScaled
    - is_scaled
    - setRfrType
    - getFilterProperties
    - setFilterProperties
    - getSoluteProperties
    - setSoluteProperties
    - setTfrType
    - getAfrType
    - setAfrType
    - is_absorbance_based
    - getKType
    - setKType
    - is_mole_based
    - getTimeUnit
    - setTimeUnit
    - setResponseType
    - getWhatMeasured
    - setWhatMeasured
    - getWhenMeasured
    - setWhenMeasured
    - getWhereMeasured
    - setWhereMeasured
    - getHowMeasured
    - setHowMeasured
    - getIdFactor
    - setIdFactor
    - is_tagged
    - dim.generic_mspct
    - labels
    - add_attr2tb
    - spct_attr2tb
    - spct_metadata
  - subtitle: Spectral features
    desc: Methods for detection of specific features in spectra.
    contents:
    - peaks
    - valleys
    - wls_at_target
    - spikes
  - subtitle: Transformations and conversions, related to spectral values
    desc: Non-summary methods for transforming or modifying the radiation-related quantity of spectral data objects.
    contents:
    - clean
    - despike
    - normalize
    - normalization
    - fscale
    - fshift
    - convertTimeUnit
    - e2q
    - q2e
    - T2A
    - A2T
    - T2Afr
    - Afr2T
    - any2T
    - convertTfrType
    - convertThickness
    - tag
    - untag
    - cps2irrad
    - smooth_spct
  - subtitle: Transformations, related to wavelength
    desc: Non-summary methods for transforming or modifying the wavelengths of spectral data objects.
    contents:
    - insert_hinges
    - interpolate_wl
    - interpolate_spct
    - clip_wl
    - thin_wl
    - trim_wl
    - trim_spct
    - na.omit
    - wl2wavenumber
  - subtitle: Mathematical operators and functions for spectra
    desc: Specializations of all R's mathematical functions and operators for spectral objects.
    contents:
    - '`plus-.generic_spct`'
    - '`div-.generic_spct`'
    - '`minus-.generic_spct`'
    - '`mod-.generic_spct`'
    - '`slash-.generic_spct`'
    - '`times-.generic_spct`'
    - '`^.generic_spct`'
    - Trig
    - log
    - MathFun
    - sign
    - round
  - subtitle: Extract, replace and combine
    desc: Functions and operators, both specializations of R's ones and new ones specific to spectra and collections of spectra.
    contents:
    - Extract
    - Extract_mspct
    - Subset
    - c
    - rbindspct
    - merge2object_spct
    - split2mspct
    - subset2mspct
    - join_mspct
  - subtitle: Apply
    desc: Apply functions for collections of spectra.
    contents:
    - msmsply
    - convolve_each
  - subtitle: Options
    desc: Convenience functions for setting R options recognized by functions in the 'r4photobiology' suite of R packages.
    contents:
    - using_Tfr
    - energy_as_default
    - wb_trim_as_default
    - verbose_as_default

  - title: Optics
    desc: Computations related to radiation physics.
    contents:
    - diffraction_single_slit
    - Rfr_from_n

  - title: Datasets
    desc: Spectral data used in documentation examples and unit tests
  - subtitle: Data for light sources
    desc: Spectral irradiance data for daylight and artificial light
    contents:
    - sun.spct
    - sun_daily.spct
    - sun_evening.spct
    - white_led.source_spct
    - phenylalanine.spct
    - water.spct
    - A.illuminant.spct
    - D50.illuminant.spct
    - D65.illuminant.spct
    - FEL_spectrum
    - D2_spectrum
    - D2.UV653
  - subtitle: Data for real and theoretical objects
    desc: Spectral transmittance, spectral reflectance and spectral absorptance data for real and theoretical objects
    contents:
    - two_filters.spct
    - clear.spct
    - green_leaf.spct
    - Ler_leaf.spct
    - black_body.spct
  - subtitle: Data for light sensors
    contents:
    - ccd.spct
    - photodiode.spct
    - two_sensors.mspct
  - subtitle: Data for human vision
    desc: Data for the spectral response of the human eye as used in different computaions related to illumination and vision
    contents:
    - ciev10.spct
    - ciev2.spct
    - ciexyzCC10.spct
    - ciexyzCC2.spct
    - ciexyzCMF10.spct
    - ciexyzCMF2.spct
    - cone_fundamentals10.spct
  - subtitle: Data for animal vision
    desc: Data for the spectral response of bee vision
    contents:
    - beesxyzCMF.spct
  - subtitle: Utility data
    desc: List of packages in the R for Photobiology suite
    contents:
    - r4p_pkgs

  - title: Housekeeping and helper functions
    desc: Utilities mainly used internally in the 'r4photobiology' suite of R packages, but safe to use in user code.
    contents:
    - check_spct
    - enable_check_spct
    - check_w.length
    - checkTimeUnit
    - copy_attributes
    - merge_attributes
    - formatted_range
    - normalize_range_arg
    - collect2mspct
    - spct_wide2long
    - uncollect2spct
    - drop_user_cols
    - getSpctVersion
    - getMspctVersion
    - is.old_spct
    - upgrade_spct
    - upgrade_spectra
    - defunct

  - title: Low-level functions
    desc: Internal functions available for use by developers when maximum flexibility is needed. They are not meant for everyday use as they lack error handling and data validation features.
    contents:
    - as_energy
    - as_quantum
    - as_quantum_mol
    - calc_multipliers
    - calc_source_output
    - check_spectrum
    - copy_attributes
    - div_spectra
    - e2qmol_multipliers
    - e2quantum_multipliers
    - e2quantum_multipliers
    - energy_irradiance
    - energy_ratio
    - findMultipleWl
    - find_peaks
    - find_spikes
    - find_wls
    - fit_peaks
    - get_attributes
    - get_peaks
    - insert_spct_hinges
    - integrate_xy
    - interpolate_spectrum
    - irradiance
    - merge_attributes
    - normalized_diff_ind
    - oper_spectra
    - photon_irradiance
    - photon_ratio
    - photons_energy_ratio
    - prod_spectra
    - replace_bad_pixs
    - s_e_irrad2rgb
    - select_spct_attributes
    - split_energy_irradiance
    - split_irradiance
    - split_photon_irradiance
    - subt_spectra
    - sum_spectra
    - trim_tails
    - trim_waveband
    - v_insert_hinges
    - v_replace_hinges
    - w_length_range2rgb
    - w_length2rgb
    - waveband_ratio

navbar:
  structure:
    left:  [intro, reference, articles, tutorials, news]
    right: [search, github]
  components:
    intro:
      icon: fas fa-home fa-lg
      href: index.html
      aria-label: Home
    reference:
      text: Reference
      href: reference/index.html
    news:
      text: Changelog
      href: news/index.html
    articles:
      text: User Guide
      menu:
      - text: '0 The R for Photobiology Suite'
        href: articles/userguide-0-r4p-introduction.html
      - text: '1 Radiation'
        href: articles/userguide-1-radiation.html
      - text: 'SunCalcMeeus Astronomy and Atmosphere'
        href: https://docs.r4photobiology.info/SunCalcMeeus/
    tutorials:
      text: Resources
      menu:
      - text: R for Photobiology web site
        href: https://www.r4photobiology.info/
      - text: A handbook of methods
        href: https://doi.org/10.31885/9789521083631
      - text: Photobiological Sciences Online
        href: http://photobiology.info/
      - text: FOSS for Spectroscopy
        href: https://bryanhanson.github.io/FOSS4Spectroscopy/