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ChangeLog
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ChangeLog
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2023-05-17 Helge Hecht v1.3.0
* Added test cases for several functions [PR #3](https://github.com/RECETOX/RAMClustR/pull/3)
* Extracted functions for several duplicate code [PR #23](https://github.com/RECETOX/RAMClustR/pull/23)
* Added option for dataframe input [PR #25](https://github.com/RECETOX/RAMClustR/pull/25)
* Updated ramclustR function with individual function calls [PR #32](https://github.com/RECETOX/RAMClustR/pull/32)
* Added `sample_names` attribute to `ramclustObj` [PR#33](https://github.com/RECETOX/RAMClustR/pull/33)
* Replaced sample.names from phenoData with sample_names attribute in rc.feature files [PR #33](https://github.com/RECETOX/RAMClustR/pull/33)
* Updated featnames with the xcms feature names in rc.get.xcms.data [PR #46](https://github.com/RECETOX/RAMClustR/pull/46)
2022-04-05 Helge Hecht v1.2.4
* Adapted tests to also be working on MAC M1
2022-03-16 Corey Broeckling v1.2.3
* fixed machineIntegerMax limit. (courtesy Helge Hecht)
* import Sirius output
* import ADAP KDB annotations
2021-08-11 Corey Broeckling v1.2.2
* fixed clri bug in write.msp
* fixed annotation bug - no structures from MSFinder were being assigned
* fixed a neutral loss format error used for findMain
2021-04-19 Corey Broeckling v1.2.1
* removed closeAllConnections() call from rc.cmpd.get.pubchem for CRAN compatibility
2021-04-19 Corey Broeckling v1.2.0
* added pubchem retreival functionality
* added blank filter to remove background features
* added normalization to QC samples
2020-04-14 Corey Broeckling v1.1.0
* splitting ramclustR function into several smaller functions
* adjust $history to a list.
2019-09-17 Corey Broeckling v1.0.8
* remove dependency on XCMS, replace with XCMS as suggestion
2019-08-27 Corey Broeckling v1.0.8
* add reporting, fix processing history narrative issues.
2019-04-23 Corey Broeckling v1.0.7
* trying to improve stability of getClassyFire - bug fix in tryCatch part of problem.
2019-04-23 Corey Broeckling v1.0.6
* adapted getClassyFire to limit number of new structure ClassyFications to 5/minute per server regulations
* bug fix in annotate, get.synonyms
2019-02-15 Corey Broeckling v1.0.5
* fixed bug in do.findmain
2019-02-12 Corey Broeckling v1.0.4
* fixed bug in batch.qc correction for MSe data
2019-01-30 Corey Broeckling v1.0.3
* added write.methods function to export processing history
2019-01-30 Corey Broeckling v1.0.2
* changed behavior of msfinder import and annotation. Structure results from a relevant database can be used to set the formula, rather than formula being independently assigned.
* added rt.only.low.n option to control behavior of clustering with low n (< 5)
2019-01-18 Corey Broeckling v1.0.1
* fixed bug in ramclustR function when fewer than five samples.
* added function to convert foodb download to MSFinder structure database import format.
2019-01-17 Corey Broeckling
* update R, CRAN check, 1.0.0
2019-01-11 Corey Broeckling
* check() returns zero errors or warnings, two notes.
* check.windows() returns BioC warning, unclear how to fix (no reference to BioC apparent)
* updated do.findmain, altered ramclustR scoring algorithm, made ramclustR default, and changed selection criterion for find.main vs ramclustR scoring when mass assignment is conflicted between the two.
2018-06-26 Corey Broeckling
* check() returns zero errors, warnings, or notes.
2014-09-02 Steffen Neumann <[email protected]>
* Fix some minor stuff to make R CMD check happy