NEWS.md

In maldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra

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.

maldipickr documentation built on Sept. 13, 2024, 1:12 a.m.