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 * Fix some minor stuff to make R CMD check happy