Changelog • maldipickr

maldipickr (development version)

CRAN release: 2023-12-14

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()

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

CRAN release: 2023-10-25

(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

(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)

CRAN release: 2023-09-07

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

(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.

(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()

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