autoSpectra/_pkgdown.yml at main · HugoMachadoRodrigues/autoSpectra · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
url: https://HugoMachadoRodrigues.github.io/autoSpectra/

template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    primary: "#4fc3f7"
    secondary: "#81c784"
    base_font:
      google: "Source Sans Pro"
    heading_font:
      google: "Source Code Pro"

home:
  title: "autoSpectra — Soil Spectral Modelling"
  description: >
    R package for soil spectral modelling, visualization, and prediction.
    Sensor-agnostic soilVAE models trained on OSSL v1.2. Supports VisNIR
    and MIR spectra with two-step Savitzky-Golay preprocessing.
  links:
    - text: "OSSL Documentation"
      href: https://docs.soilspectroscopy.org
    - text: "Zenodo record"
      href: https://doi.org/10.5281/zenodo.19004686

navbar:
  structure:
    left:  [intro, reference, articles, tutorials, news]
    right: [search, github, twitter]
  components:
    twitter:
      icon: "fab fa-twitter fa-lg"
      href: https://twitter.com/Hugo_MRodrigues
      aria-label: Twitter

authors:
  Hugo Rodrigues:
    href: https://orcid.org/0000-0002-8070-8126

footer:
  structure:
    left:  developed_by
    right: built_with

reference:
  - title: "OSSL Data"
    desc: "Download and manage Open Soil Spectral Library data"
    contents:
      - starts_with("ossl_")

  - title: "Pre-trained Models"
    desc: "Download pre-trained soilVAE models from Zenodo (one-time setup)"
    contents:
      - download_ossl_models
      - models_available

  - title: "Model Training"
    desc: "Train soilVAE models on OSSL or custom datasets"
    contents:
      - build_soilVAE
      - train_soilVAE
      - train_ossl_models
      - load_soilVAE
      - save_scaler
      - save_metrics_json
      - metrics_from_y
      - split_idx

  - title: "In-Memory Model Cache"
    desc: "Load models once per session and reuse them without disk I/O"
    contents:
      - get_cached_model
      - preload_ossl_models
      - list_cached_models
      - clear_model_cache

  - title: "Prediction"
    desc: "Predict soil properties and assess applicability domain"
    contents:
      - predict_soil
      - predict_applicability
      - format_predictions
      - get_family
      - family_matches
      - property_label

  - title: "Preprocessing"
    desc: "Spectral preprocessing functions"
    contents:
      - preprocess_visnir
      - preprocess_mir
      - reflectance_to_absorbance
      - apply_pipeline
      - apply_sg_matrix
      - apply_snv
      - parse_sg
      - sg_safe_params
      - resample_to_grid
      - get_wavelengths

  - title: "Visualization"
    desc: "Plotting functions"
    contents:
      - plot_spectra
      - plot_mean_spectrum
      - plot_predictions
      - plot_applicability

  - title: "Registry"
    desc: "Model registry and metadata"
    contents:
      - model_registry
      - ossl_l1_properties
      - ossl_l1_labels
      - ossl_visnir_instruments
      - ossl_mir_instruments

  - title: "Shiny App"
    desc: "Launch the interactive application"
    contents:
      - run_autoSpectra

  - title: "Utilities"
    desc: "Internal helper functions"
    contents:
      - feature_minmax
      - dir_create
      - vneed

news:
  releases:
    - text: "v0.3.0 — OSSL-only sensor-agnostic redesign"
      href: https://github.com/HugoMachadoRodrigues/autoSpectra/releases/tag/v0.3.0
    - text: "v0.2.0 — R package + OSSL integration"
      href: https://github.com/HugoMachadoRodrigues/autoSpectra/releases/tag/v0.2.0
    - text: "v0.1.0 — Initial Shiny app"
      href: https://github.com/HugoMachadoRodrigues/autoSpectra/releases/tag/v0.1.0