_pkgdown.yml

url: http://isoreader.isoverse.org

title: Isoreader
template:
  params:
    bootswatch: simplex
    ganalytics: UA-106138361-3

development:
  mode: auto

home:
  strip_header: true    

navbar:
  title: isoreader
  type: default
  left:
  - text: Quick Start
    href: articles/quick_start.html
  - text: Full Examples
    menu:
    - text: Dual Inlet
      href: articles/dual_inlet.html
    - text: Continuous Flow
      href: articles/continuous_flow.html
    - text: Scan
      href: articles/scan.html
  - text: Advanced
    menu:
    - text: Operations
      href: articles/operations.html
    - text: Development
      href: articles/development.html
  - text: Reference
    href: reference/index.html
  right:
  - icon: fa-github fa-lg
    href: https://github.com/isoverse/isoreader

reference:
- title: Reading IRMS data files
  desc: >
    These functions provide the core functionality for the package. They parse the raw isotope ratio mass spectrometry data files.
  contents:
  - iso_read_continuous_flow
  - iso_read_dual_inlet
  - iso_read_scan
  - iso_reread_files

- title: Data wrangeling
  desc: >
    These functions provide tools to easily filter files and update file information. 
    The package also provides a few functions that expand on useful text processing provided by the readr package (summarized in `extract_data`).
  contents:
  - iso_add_file_info
  - iso_rename_file_info
  - iso_select_file_info
  - iso_mutate_file_info
  - iso_parse_file_info
  - iso_set_file_root
  - iso_filter_files
  - extract_data
  - extract_substring
  - extract_word

- title: Data units
  desc: >
    These functions provide tools to work easily with numbers that have units associated with them. 
  contents:
  - iso_double_with_units
  - iso_is_double_with_units
  - iso_get_units
  - iso_strip_units
  - iso_make_units_explicit
  - iso_make_units_implicit
  - iso_format

- title: Aggregating the data
  desc: >
    These functions aggregate the data collected from one or many IRMS data files.
  contents:
  - iso_get_data_summary
  - iso_get_all_data
  - iso_get_file_info
  - iso_get_raw_data
  - iso_get_bgrd_data
  - iso_get_vendor_data_table
  - iso_get_resistors
  - iso_get_standards

- title: "Exporting/saving data: Feather, Excel, and R Data Storage"
  desc: >
    These functions provide tools to save the data to specific file formats.
  contents:
  - iso_save
  - iso_export_files_to_excel
  - iso_export_files_to_feather

- title: Package information and default parameters
  desc: >
    These functions provide information about the package capabilities, easy access to example files, and ways to set default parameters across the package.
  contents:
  - iso_get_supported_file_types
  - iso_get_reader_example
  - iso_caching
  - iso_cleanup_reader_cache
  - iso_info_messages
  - iso_set_default_read_parameters
  - iso_get_default_reader_parameters

- title: Dealing with read problems
  desc: >
    
  contents:
  - iso_problem_functions
  - iso_has_problems
  - iso_get_problems_summary
  - iso_get_problems
  - iso_filter_files_with_problems

- title: File system functions
  desc: >
    Functions to find IRMS data files and root file paths.
  contents:
  - iso_expand_paths
  - iso_root_paths
  - iso_find_absolute_path_roots
  - iso_shorten_relative_paths

- title: Low-level IO, debugging, and development tools
  desc: >
    See the advanced vignette for details.
  contents:
  - iso_read_files
  - iso_register_dual_inlet_file_reader
  - iso_register_continuous_flow_file_reader
  - iso_register_scan_file_reader
  - iso_is_file
  - iso_is_file_list
  - iso_is_continuous_flow
  - iso_is_dual_inlet
  - iso_is_scan
  - iso_debug_mode
  - iso_source_file_op_error
  - iso_get_source_file_structure
  - iso_print_source_file_structure
  - read_iso_file
  - reread_iso_files
  - set_temp
  - print.binary_isodat_file
  - print.iso_file_list
  - print.iso_file
  - vec_arith.iso_double_with_units
  - vec_cast.iso_double_with_units
  - vec_ptype2.iso_double_with_units 

- title: Deprecated
  contents:
  - deprecated

# additional modification notes on 
# https://www.r-bloggers.com/building-a-website-with-pkgdown-a-short-guide/
# http://hadley.github.io/pkgdown/articles/pkgdown.html