Changes in version 1.3.2 Fixed - Fix typo that invalidated Zenodo integration Changes in version 1.3.1.9000 Fixed - Fix unwanted conversion to NAs when sample names were well numbers like E1 or E2 (#51, thanks for spotting this @sarah-lital) Changes in version 1.3.1 (2024-09-12) 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) Changes in version 1.3.0 (2023-12-14) 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 Changes in version 1.2.0 (2023-10-25) 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) Changes in version 1.1.1 (2023-09-07) Fixed - Fix typos for CRAN re-submission: missing brackets in reference, and spelling errors. Changes in version 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. Changes in version 1.0.2 Changed - Fix the invalid file URIs in NEWS.md and README.md Changes in version 1.0.1 Changed - Fix title to title case for CRAN Changes in version 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) Changes in version 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 Changes in version 0.1.0 - First stable version Changes in version 0.0.0.9000 - Added a NEWS.md file to track changes to the package.