_pkgdown.yml

# ===================================================================== #
#  Licensed as GPL-v3.0.                                                #
#                                                                       #
#  Developed as part of the AMRverse (https://github.com/AMRverse):     #
#  https://github.com/AMRverse/AMRgen                                   #
#                                                                       #
#  We created this package for both routine data analysis and academic  #
#  research and it was publicly released in the hope that it will be    #
#  useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
#                                                                       #
#  This R package is free software; you can freely use and distribute   #
#  it for both personal and commercial purposes under the terms of the  #
#  GNU General Public License version 3.0 (GNU GPL-3), as published by  #
#  the Free Software Foundation.                                        #
# ===================================================================== #

# Site metadata
url: 'https://amrgen.org'
title: 'AMRgen'

# Template settings
template:
  bootstrap: 5
  bootswatch: "united"
  bslib:
    base_font: {google: "Nunito"}
    heading_font: {google: "Nunito"}
    code_font: {google: "Fira Code"}
    # (colours based on the AMRgen logo)
    primary:          "#7030A0" # deep purple (main text "AMRgen" and rightmost circle)
    secondary:        "#C52574" # strong magenta/pink (leftmost circle and logo accents)
    success:          "#25c475" # green contrast (not in logo, but for success messages in site)
    info:             "#8151A4" # medium lavender/purple (upper circles in logo)
    warning:          "#EBADC7" # pale pink highlight (lighter background circles/links)
    danger:           "#D35691" # vivid pink-red (circle accent, darker magenta tone)
    link-color:       "#C52574" # magenta link color (aligns with secondary)
    link-hover-color: "#7030A0" # hover state purple (aligns with primary)

# Navbar configuration
navbar:
  title: "AMRgen"
  left:
    - text: "Home"
      icon: "fa-home"
      href: "index.html"
    - text: 'Reference'
      icon: "fa-book-open"
      href: "reference/index.html"
    - text: "Vignettes"
      icon: "fa-book"
      href: "articles"
  right:
    - text: "Source Code"
      icon: "fab fa-github"
      href: "https://github.com/AMRverse/AMRgen"

articles:
  - title: "Vignettes"
    contents:
      - AnalysingGenoPhenoData
      - DownloadGenoPhenoData
      - Concordance
      - NeisseriaGonoExamples
      - SalmonellaExamples
      - StaphAureusClindamycin
      - KlebsiellaMultipleGenotypers
      - DeletionVariantsCatB3

# Reference section grouping
reference:
  - title: "Data Import & Preprocessing"
    desc: >
      Functions to import, harmonise, and prepare genotype and phenotype data from public repositories or internal formats.
    contents:
      - starts_with("import")
      - starts_with("export")
      - starts_with("convert")
      - starts_with("download")
      - starts_with("summarise")
      - starts_with("format")
      - get_binary_matrix
      - get_combo_matrix
      - starts_with("query_ncbi")

  - title: "Resistance Interpretation"
    desc: >
      Core tools for interpreting antimicrobial resistance based on EUCAST breakpoints and custom models.
    contents:
      - starts_with("compare")
      - matches("eucast")
      - merge_logreg_soloppv
      - interpret_pheno

  - title: "Modelling and analysis"
    desc: >
      Statistical models for resistance prediction and inference, including logistic regression and Firth regression.
    contents:
      - amr_upset
      - solo_ppv
      - amr_ppv
      - amr_logistic
      - glm_details
      - logistf_details
      - getBreakpoints
      - checkBreakpoints
      - concordance
      - concordance_from_tables
      - print.amr_concordance

  - title: "Visualisation & Reporting"
    desc: >
      Tools to visualise results, including MIC distributions, model outputs, and genotype-phenotype relationships.
    contents:
      - matches("plot")
      - assay_by_var

  - title: "Data"
    desc: >
      Example datasets for demonstration and reproducible analysis.
    contents:
      - ecoli_pheno
      - ecoli_pheno_raw
      - ecoli_geno_raw
      - ecoli_cip_vs_ref
      - ecoli_cip_mic_data
      - staph_pheno_ncbi
      - staph_pheno_ncbi_raw
      - staph_pheno_ncbi_cloud_raw
      - staph_geno_ncbi_cloud_raw
      - staph_pheno_ebi
      - staph_geno_ebi
      - amrfp_drugs_table
      - pheno_eco_2075
      - geno_eco_2075
      - eurogasp_geno_raw
      - ngono_cro_geno_raw
      - ngono_tet_geno_raw
      - ngono_cro_pheno_raw
      - eurogasp_pheno_raw
      - azm_comparison
      - cip_comparison
      - cro_comparison
      - cfm_comparison
      - ngono_tet_pheno_raw
      - salm_raw
      - kleborate_raw
      - kleborate_raw_v313
      - kleborate_classes
      - pheno_CLI_public
      - afp_CLI_public
      - ST_data_CLI
      - DASSIM_pheno_raw
      - btESBL_pheno
      - DASSIM_geno
      - NCBI_Ecoli_pheno_chl
      - MICROBIGGE_Ecoli_CHLR
      - rgi_raw
      - rgi_short_name_table
      - rgi_drugs_table
      - rgi_EuSCAPE_raw
      - kp_mero_euscape
      - kp_mero_amrfp
      - sirscan_codes

# Footer configuration
footer:
  structure:
    left: [devtext]
    right: [logo]
  components:
    devtext: 'Free and Open Source (GPL-3), brought by AMRverse/AMRgen Development Team'
    logo: 'AMRverse is an ecosystem for AMR data science. We aim to make common tasks easier and faster, via interoperable tools and resources.'