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maldipickr 1.3.2

Fixed

  • Fix typo that invalidated Zenodo integration

maldipickr 1.3.1

Added

Features / Documentation

  • Add gather_spectra_stats() to aggregate spectra quality-check statistics (#45)
  • Add "Get Started" vignette for a quickstart (#48)
  • Add graphical overview
  • Add example of filtering when delineating with identification (#42)

Visibility / Readability / FAIR

  • Setup integration of Github repository with Zenodo with additional metadata (#49)
  • Setup correct Opengraph metadata for the website
  • Setup analytics via the NFDI4Microbiota instance of matomo
  • Add maldipickr logo in vector format to edit in the future (#42)
  • Setup R-hub checks via Github Actions

Changed

  • Use directly a simpler and more compact README.md instead of README.Rmd

Fixed

  • Fix implicit TRUE as T in R code.
  • Bump Github Actions Node.js to v20 to fix warnings (#47)

maldipickr 1.3.0

Fixed

  • Fix non-unique names possibility during spectra processing (#37)

Changed

  • Deprecate ability to write RDS in process_spectra() (#38)
  • Deprecate ability to read RDS in merge_processed_spectra()
  • Change warnings in check_spectra() to messages pointing to use remove_spectra()

Added

  • Add get_spectra_names() to extract, format spectra names and warn against non-uniqueness
  • Add remove_spectra() to better handle discarding raw or processed spectra
  • Add {lifecycle} to better handle deprecation
  • Add sections to the function reference list to improve clarity on website

maldipickr 1.2.0

Changed

  • (BREAKING) Change homemade clustering to robust hierarchical clustering in delineate_with_similarity() (#32). The default method of hierarchical clustering is the complete linkage (also known as farthest neighbor clustering) to ensure that the within-group minimum similarity of each cluster respects the threshold
  • Change sapply() calls to more type-robust vapply() calls

Added

  • (BREAKING) Set a minimum R version >= 3.2.0 (#31)
  • Add hierarchical clustering linkage method as argument to delineate_with_similarity()
  • Add tolerance argument to check_spectra() to allow flexible spectra length checks
  • Add more unit tests to key functions: pick_spectra() (#26) and merge_processed_spectra() (#27)

Fixed

  • Fix missing spectra names when merging spectra lists with peak-less spectra
  • Fix coverage update issue by adding codecov token (#34)

maldipickr 1.1.1

Fixed

  • Fix typos for CRAN re-submission: missing brackets in reference, and spelling errors.

maldipickr 1.1.0

Fixed

  • (URGENT) Fix delineate_with_similarity() that did not include friends-of-friends in clusters after removal of {igraph} in #18. Add a relevant similarity matrix to test it accordingly.

maldipickr 1.0.2

Changed

  • Fix the invalid file URIs in NEWS.md and README.md

maldipickr 1.0.1

Changed

  • Fix title to title case for CRAN

maldipickr 1.0.0

Changed

  • (BREAKING) read_biotyper_report() first column is now name instead of spot, meaning read_many_biotyper_reports() renames all the name columns to original_name. This was to pick_spectra() easily usable with taxonomy identification reports (38a614173fd21315a40e0823600a2082fa0935bb)
  • (BREAKING) All functions now follow the verb_concept nomenclature, meaning clustering functions are now renamed accordingly (#24):
    • Change similarity_to_clusters() to delineate_with_similarity()
    • Change identification_to_clusters() to delineate_with_identification()
  • Refactor the delineate_with_similarity() clustering function (formerly: similarity_to_clusters()) without using the {igraph} nor {tidygraph} R packages, for fewer dependencies and simpler codebase (#18)
  • Update the DESCRIPTION to include the Strejcek reference (#22) and better highlight the package added-value
  • Refactor the pkgdown website with a more accessible font and color schema inline with the logo color palette
  • Change the vignettes titles and outline to better structure the documents
  • Refactor cosine similarity computation example by highlighting the dedicated coop::tcosine() instead of the t() %>% coop::cosine()

Added

  • Add long or wide output format for read_biotyper_report() (#12)
  • Document how to quickstart with the {maldipickr} package for those in a hurry (#15)
  • Document more precisely how to install tagged release of {maldipickr} package
  • Add better tests for merge_processed_spectra() (b39c1313fd38239b4b1821a243c9debf467fd092)
  • Document authors list according to CRAN policy
  • Add CRAN comments file to track submission notes

Removed

  • Deprecate the CHANGELOG.md in favor of the R specific NEWS.md (#20)
  • Remove redundant check after symbolic links creation (#19)

Fixed

  • Fix summarise() usage in pick_spectra(), with code simplification (#11)
  • Remove symbolic links created for importing acqu spectra files (#21)
  • Fix CRAN warnings regarding qpdf (3b19dd36a6ec0f5dc277418c98977c526981b6e3)
  • Fix masked relevant to_pick column in the vignette (#17)

maldipickr 0.1.1

Added

Changed

  • Improve the package description according to CRAN recommendations

maldipickr 0.1.0

  • First stable version

maldipickr 0.0.0.9000

  • Added a NEWS.md file to track changes to the package.