_pkgdown.yml

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template:
  # bootstrap: 5
  params:
    bootswatch: cerulean
    noindex: false

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development:
  mode: unreleased # auto

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navbar:
  structure:
    left:  [version, home, intro, articles, tutorials, reference, news]
    right: [github]
  components:
    version:
      icon: fa-book
      menu:
      - text: "Documentation for version of package:"
      - text: Released
        href: https://r-hyperspec.github.io/hyperSpec/
      - text: In-development
        href: https://r-hyperspec.github.io/hyperSpec/dev/
#    intro:
#      text: Get started
#      href: articles/hyperSpec.html
#    articles:
#      text: Articles
#      menu:
#      - text: Introduction to Package "hyperSpec"
#        href: articles/hyperSpec.html
#      - text: Import and Export of Spectra Files
#        href: articles/fileio.html
#      - text: Plotting Functions in "hyperSpec"
#        href: articles/plotting.html
#      - text: Fitting Baselines to Spectra
#        href: articles/baseline.html
#      - text: ----------------------------------
#      - text: More...
#        href: articles/index.html

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articles:
  - title: "Principles"
    navbar: ~
    desc: >
      The main functionality of "hyperSpec".
    contents:
    - hyperSpec
    - fileio
    - plotting
    - baseline
  - title: "Case studies"
    desc: >
      The example workflows.
    contents:
    - flu
    - laser

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authors:
  Bryan A. Hanson:
    href: http://academic.depauw.edu/hanson_web/
  Vilmantas Gegzna:
    href: https://orcid.org/0000-0002-9500-5167

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reference:
- title: '1. Package and class "hyperSpec"' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- contents:
  - has_keyword("package")
  - has_keyword("classes")
  - has_concept("hyperSpec-main")


- title: '2. Utility functions' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- contents:
  - has_concept("utils")


- title: '3. Datasets' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  desc: "Datasets to try functionality of **hyperSpec** functions."
- contents:
  - has_concept("datasets")


- title: '4. Create and convert `hyperSpec` objects' # ~~~~~~~~~~~~~~~~~~~~

- subtitle: Create or convert from/into `hyperSpec`
- contents:
  - "initialize"
  - has_concept("hyperSpec conversion")


- title: '5. Import and export `hyperSpec` objects' # ~~~~~~~~~~~~~~~~~~~~~

- subtitle: Read/Write from/to files
- contents:
  - has_concept("io")
  - has_concept("IO")

- subtitle: '! Moved to package hySpc.read.ENVI'
  desc: |
    You should use analogous functions from package
    [**hySpc.read.ENVI**](https://r-hyperspec.github.io/hySpc.read.ENVI/reference/index.html)
    as these functions will be removed soon.
- contents:
  - has_concept("moved to hySpc.read.ENVI", internal = TRUE)

- subtitle: '! Moved to package hySpc.read.jdx'
  desc: |
    You should use analogous functions from package
    [**hySpc.read.jdx**](https://r-hyperspec.github.io/hySpc.read.jdx/reference/index.html)
    as these functions will be removed soon.
- contents:
  - has_concept("moved to hySpc.read.jdx", internal = TRUE)

- subtitle: '! Moved to package hySpc.read.mat'
  desc: |
    You should use analogous functions from package
    [**hySpc.read.mat**](https://r-hyperspec.github.io/hySpc.read.mat/reference/index.html)
    as these functions will be removed soon.
- contents:
  - has_concept("moved to hySpc.read.mat", internal = TRUE)

- subtitle: '! Moved to package hySpc.read.spc'
  desc: |
    You should use analogous functions from package
    [**hySpc.read.spc**](https://r-hyperspec.github.io/hySpc.read.spc/reference/index.html)
    as these functions will be removed soon.
- contents:
  - has_concept("moved to hySpc.read.spc", internal = TRUE)

- subtitle: '! Moved to package hySpc.read.spe'
  desc: |
    You should use analogous functions from package
    [**hySpc.read.spe**](https://r-hyperspec.github.io/hySpc.read.spe/reference/index.html)
    as these functions will be removed soon.
- contents:
  - has_concept("moved to hySpc.read.spe", internal = TRUE)

- subtitle: '! Moved to package hySpc.read.txt'
  desc: |
    You should use analogous functions from package
    [**hySpc.read.txt**](https://r-hyperspec.github.io/hySpc.read.txt/reference/index.html)
    as these functions will be removed soon.
- contents:
  - has_concept("moved to hySpc.read.txt", internal = TRUE)


- title: '6. Plotting' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- subtitle: Plots
- contents:
  - "plot-methods"
  - has_concept("plot generation")

- subtitle: Color palettes
- contents:
  - has_concept("color palette")

- subtitle: Plotting tools
- contents:
  - has_concept("plotting tools")

- subtitle: '! Moved to package hySpc.ggplot2'
  desc: |
    You should use analogous functions from package
    [**hySpc.ggplot2**](https://r-hyperspec.github.io/hySpc.ggplot2/reference/index.html)
    as these functions will be removed soon.
- contents:
  - has_concept("moved to hySpc.ggplot2", internal = TRUE)


- title: '7. Data manipulation' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- subtitle: Summary and data preview
- contents:
  - has_concept("summary")

- subtitle: Manipulation
- contents:
  - has_concept("manipulation")

- subtitle: Baseline manipulation
- contents:
  - has_concept("baseline")

- subtitle: Binning and smoothing
- contents:
  - has_concept("spectra smoothing")

- subtitle: Data generation functions
- contents:
  - has_concept("data generation")

- subtitle: 'Statistics, analysis, randomization'
- contents:
  - has_concept("stats")

- subtitle: Wavelength manipulation
- contents:
  - has_concept("wavelengths")

- subtitle: Label manipulation
- contents:
  - has_concept("labels")


- title: '8. Other functions' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  desc: "Functions not mentioned above."
- contents:
  - lacks_concepts(c(
    "hyperSpec-main",
    "utils",
    "datasets",
    "hyperSpec conversion", "io", "IO",
    "plot generation", "color palette", "plotting tools",

    "summary", "manipulation", "spectra smoothing", "baseline", "labels",
    "wavelengths", "data generation", "stats",

    "moved to hySpc.ggplot2",
    "moved to hySpc.read.ENVI",
    "moved to hySpc.read.jdx",
    "moved to hySpc.read.mat",
    "moved to hySpc.read.spc",
    "moved to hySpc.read.spe",
    "moved to hySpc.read.txt",

    "deprecated"
    ))


- title: '9. Removed or deprecated functions' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~

- subtitle: Functions moved to other packages
  desc: >
    The following functions were moved to other
    **[r-hyperspec](https://r-hyperspec.github.io/)** family packages.
    In most cases, the functions were also renamed.
    Please, use the analogues of these functions, which are in appropriate
    packages.
- contents:
  - has_concept("moved to hySpc.ggplot2",   internal = TRUE)
  - has_concept("moved to hySpc.read.ENVI", internal = TRUE)
  - has_concept("moved to hySpc.read.jdx",  internal = TRUE)
  - has_concept("moved to hySpc.read.mat",  internal = TRUE)
  - has_concept("moved to hySpc.read.spc",  internal = TRUE)
  - has_concept("moved to hySpc.read.spe",  internal = TRUE)
  - has_concept("moved to hySpc.read.txt",  internal = TRUE)

- subtitle: Deprecated, renamed, or defunct functions
  desc: "You should **not** use these functions any more."
- contents:
  - has_concept("deprecated", internal = TRUE)

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figures:
  dev: grDevices::png
  dpi: 96
  dev.args: []
  fig.ext: png
  fig.width: 4.854
  fig.height: 3
  fig.retina: 2
  fig.asp: 1.618

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