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process_spectra()
(#38)merge_processed_spectra()
check_spectra()
to messages pointing to use remove_spectra()
get_spectra_names()
to extract, format spectra names and warn against non-uniquenessremove_spectra()
to better handle discarding raw or processed spectra{lifecycle}
to better handle deprecationdelineate_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 thresholdsapply()
calls to more type-robust vapply()
callsdelineate_with_similarity()
check_spectra()
to allow flexible spectra length checkspick_spectra()
(#26) and merge_processed_spectra()
(#27)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.URIs
in NEWS.md
and README.md
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
)verb_concept
nomenclature, meaning clustering functions are now renamed accordingly (#24):
similarity_to_clusters()
to delineate_with_similarity()
identification_to_clusters()
to delineate_with_identification()
delineate_with_similarity()
clustering function (formerly: similarity_to_clusters()
) without using the {igraph}
nor {tidygraph}
R packages, for fewer dependencies and simpler codebase (#18)DESCRIPTION
to include the Strejcek reference (#22) and better highlight the package added-valuepkgdown
website with a more accessible font and color schema inline with the logo color palettecoop::tcosine()
instead of the t() %>% coop::cosine()
read_biotyper_report()
(#12){maldipickr}
package for those in a hurry (#15){maldipickr}
packagemerge_processed_spectra()
(b39c1313fd38239b4b1821a243c9debf467fd092
)CHANGELOG.md
in favor of the R specific NEWS.md
(#20)summarise()
usage in pick_spectra()
, with code simplification (#11)qpdf
(3b19dd36a6ec0f5dc277418c98977c526981b6e3
)to_pick
column in the vignette (#17)CITATION
) and for GitHub CITATION.cff
CHANGELOG.md
(Common Changelog)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.