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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

• Add citation file for R (CITATION) and for GitHub CITATION.cff
• Add a CHANGELOG.md (Common Changelog)

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.