_pkgdown.yml

url: https://sipss.github.io/AlpsNMR/
destination: docs
template:
  bootstrap: 5
  bootswatch: cerulean
authors:
  Nestlé Institute of Health Sciences:
    href: https://www.nestlehealthscience.com/
  Institute for Bioengineering of Catalonia:
    href: https://www.ibecbarcelona.eu/sensingsys


reference:
- title: "Basic functions"
  desc: >
    Functions you'll use on a first analysis
  contents:
  - AlpsNMR-package
  - nmr_read_samples
  - nmr_meta_add
  - nmr_interpolate_1D
  - nmr_exclude_region
  - plot.nmr_dataset_1D
  - nmr_baseline_removal
  - nmr_detect_peaks
  - nmr_align
  - nmr_normalize
  - nmr_integrate_peak_positions
  - nmr_data_analysis
- title: "Metadata related functions"
  desc: >
    Functions to handle metadata
  contents: 
  - nmr_meta_add
  - nmr_meta_export
  - nmr_meta_get_column
  - nmr_meta_get
  - nmr_meta_groups
- title: "Import / Export functions"
  desc: >
    Functions to read NMR files into AlpsNMR datasets or to export to other
    packages
  contents:
  - load_and_save_functions
  - nmr_read_bruker_fid
  - nmr_read_samples
  - nmr_zip_bruker_samples
  - nmr_export_data_1r
  - files_to_rDolphin
  - save_files_to_rDolphin
  - nmr_data_1r_to_SummarizedExperiment
  - SummarizedExperiment_to_nmr_data_1r
  - SummarizedExperiment_to_nmr_dataset_peak_table
  - to_ChemoSpec
  - to_ASICS
  - nmr_batman_options
  - nmr_batman
  - nmr_dataset_peak_table_to_SummarizedExperiment
  - save_profiling_output
- title: "Data analysis / Modelling functions"
  desc: >
    Functions for machine learning or data analysis, to be used once the
    data has been preprocessed
  contents:
  - bp_kfold_VIP_analysis
  - bp_VIP_analysis
  - models_stability_plot_bootstrap
  - models_stability_plot_plsda
  - nmr_data_analysis_method
  - nmr_data_analysis
  - permutation_test_model
  - permutation_test_plot
  - plot_bootstrap_multimodel
  - plot_plsda_multimodel
  - plot_plsda_samples
  - plot_vip_scores
  - plsda_auroc_vip_compare
  - plsda_auroc_vip_method
  - random_subsampling
- title: "nmr_dataset manipulation functions"
  desc: >
    Functions to manage and filter nmr_dataset objects
  contents:
  - filter.nmr_dataset_family
  - format.nmr_dataset_1D
  - format.nmr_dataset_peak_table
  - format.nmr_dataset
  - is.nmr_dataset_1D
  - is.nmr_dataset_peak_table
  - is.nmr_dataset
  - new_nmr_dataset_1D
  - new_nmr_dataset_peak_table
  - new_nmr_dataset
  - nmr_data
  - nmr_dataset_1D
  - nmr_dataset_family
  - nmr_dataset_peak_table
  - nmr_dataset
  - plot_interactive
  - plot_webgl
  - plot.nmr_dataset_1D
  - print.nmr_dataset_1D
  - tidy.nmr_dataset_1D
  - print.nmr_dataset_peak_table
  - print.nmr_dataset
  - "[.nmr_dataset_1D"
  - "[.nmr_dataset_peak_table"
  - "[.nmr_dataset"
  - validate_nmr_dataset_family
  - validate_nmr_dataset_peak_table
  - validate_nmr_dataset
- title: "Metabolite identification"
  desc: >
    Functions and tables related to metabolite identification
  contents:
  - HMDB_blood
  - HMDB_cell
  - HMDB_urine
  - hmdb
  - Parameters_blood
  - Parameters_cell
  - Parameters_urine
  - ROI_blood
  - ROI_cell
  - ROI_urine
  - nmr_identify_regions_blood
  - nmr_identify_regions_cell
  - nmr_identify_regions_urine
- title: "Alignment functions"
  desc: >
    Functions to align spectra
  contents:
  - nmr_align_find_ref
  - nmr_align
- title: "Baseline correction"
  desc: >
    Functions to remove or estimate the baseline
  contents:
  - nmr_baseline_removal
  - nmr_baseline_estimation
- title: "Peak detection"
  desc: >
    Functions to detect peaks and visualize the resulting peak lists
  contents:
  - nmr_detect_peaks_plot_overview
  - nmr_detect_peaks_plot_peaks
  - nmr_detect_peaks_plot
  - nmr_detect_peaks_tune_snr
  - nmr_detect_peaks
  - nmr_baseline_threshold_plot
  - nmr_baseline_threshold
  - Peak_detection
  - peaklist_accept_peaks
  - peaklist_fit_lorentzians
- title: "Peak clustering / matching / Peak tables"
  desc: >
    Functions to build peak tables from peak lists
  contents:
  - nmr_peak_clustering
  - nmr_peak_clustering_plot
  - nmr_build_peak_table
  - nmr_get_peak_distances
  - nmr_integrate_regions
  - nmr_integrate_peak_positions

- title: "Outlier detection"
  desc: >
    Functions to detect and report outliers in the dataset
  contents:
  - nmr_pca_build_model
  - nmr_pca_outliers_filter
  - nmr_pca_outliers_plot
  - nmr_pca_outliers_robust
  - nmr_pca_outliers
  - nmr_pca_plots

- title: "Other functions"
  desc: >
    Other, not catalogued, AlpsNMR functions
  contents: 
  - download_MTBLS242
  - file_lister
  - get_integration_with_metadata
  - Pipelines
  - nmr_ppm_resolution
  - ppm_resolution
  - nmr_autophase