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Changelog

Source: NEWS.md

eemanalyzeR 1.4.0

(2026-05-14)

  • Renamed metadata default column names to be more descriptive. If an old metadata sheet is read in, the column names will automatically be renamed to sample_id and sample_name.

    • data_identifier is now sample_id

    • description is now sample_name

    • Notes is now notes

  • Renamed a few of the items within eem and abs to be consistent with the metadata sheet.

    • meta_name is now sample_id

    • description is now sample_name

    • Notes is now notes

  • The names returned in the index outputs were updated. The column names are now sample_id and sample_name which corresponds to those entries in the eem. Previously these were sample_name and sample which corresponded to the description and sample entries.

  • Added an option to use the sample_name as the plot title, previously only sample_id and sample were supported.

eemanalyzeR 1.3.0

(2026-05-07)

  • Major updates to how the user interacts with the user and session configurations. Now there is a more unified vocabulary among the session and the user configuration functions.

    • list_session_config and read_user_config both return lists of their the corresponding configuration options
    • validate_session_config and validate_user_config will check the configuration options against package defaults to make sure they are valid options to use for EEMs processing
    • reset_session_config and reset_user_config will reset the current session configuration and user configuration file back to package defaults, respectively.
    • modify_session_config and edit_user_config allow the user to apply changes to either the session or the saved user configuration file. Modifying the user configuration can be done by hand or by providing name-value pairs to the function arguments.
    • load_user_config checks that the saved user configuration file is valid and, if so, applies these configuration options to the session.
    • repair_user_config attempts to repair the user configuration by replacing any invalid options in the user configuration file with default options from the package.

  • Package install, loading, and updates.

    • On package loading, we now provide some default behavior and messaging if this is a new or upgraded installation.
      • First we check that eemanalyzeR is installed into the default installation directory (which depends on the type of system).
      • Next, we check that the user configuration file exists, and if it doesn’t we prompt the user to create one.
      • If the user configuration file exists, we check the saved package version against the installed package. A version mismatch may indicate that the user has upgraded the package and needs to update the user configuration files, as these may have changed since the last package version.
      • Finally, we validate and load the saved configuration so it is used for processing EEMs in the R session.

eemanalyzeR 1.2.0

(2026-04-16)

  • Moving some of the checks of the QA/QC samples to the run_eems function so they don’t warn the user multiple times as the check_mdl and check_std are run several times throughout run_eems.

  • Updated validate_blanks

    • to clip to the area of interest before plotting so it is easier to see any issues

    • increased the width of the scattering to remove a little to better see any issues

    • added a message directing users to check out the output-documentation for checking the blank which prints once per session.

  • Updating vignettes.

    • Added custom-process-steps to describe how to update and save changes to defaults and use multiple methods.

    • Added figures and snippets of the output files in output-documentation and getting-started.

    • Added section in output-documentation to describe what to look for in the blank validation step. (#19)

eemanalyzeR 1.1.0

(2026-03-31)

  • Updated create_mdl and create_std functions to ask to update the default qaqc_dir in the user_config if it’s NA and not directory is provided. This fixes the issue caused by version 1.0.2 which de-automated creating and then using the QA/QC standard files (#22).

  • Modified how mdl and std files are saved, adding an argument method to the functions which is used to give a unique name for different QA/QC methods (#24).

  • Created a new helper function get_qaqc which will look for QA/QC files, ask the user which set to use if there’s more than one set, update the readme with the files used, and return the QA/QC files (#24).

eemanalyzeR 1.0.3

(2026-03-30)

  • Added an argument (sum_plot) to export_data to skip the summary plot to fix bug when processing a large (>50) samples at a time (#28).

  • Added check when running check_mdl or check_std to warn if the wavelengths differ between the QA/QC file and the samples (#24).

  • Further updated the pattern defaults to be a little more flexible for skip in dir_read to work with our example data (#20).

eemanalyzeR 1.0.2

(2026-03-26)

  • Updating all functions to remove the use of helper function .qaqc_dir and replace with get_qaqc_dir which pulls from the config file (#22).

  • Updated the default value for qaqc_dir in the config file to .na.character.

  • When creating MDL and check standard files, if no qaqc_dir is specified it will return the file as an R object with a warning.

eemanalyzeR 1.0.1

(2026-03-09)

  • Updated defaults for skip in dir_read to be more robust and to skip samples with “abs” in the name (#20).

eemanalyzeR 1.0.0

(2026-01-02)

Initial publicly available version.