Merge branch 'cbroeckl:master' into dev

Author: hechth

.Rbuildignore

@@ -5,4 +5,5 @@ cran-comments.md
 ^CRAN-SUBMISSION$
 ^conda
 ^.vscode
-^.github
+^.github
+^docs

ChangeLog

@@ -1,4 +1,4 @@
-unreleased - dev
+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)

DESCRIPTION

@@ -2,7 +2,7 @@ Package: RAMClustR
 Type: Package
 Title: Mass Spectrometry Metabolomics Feature Clustering and Interpretation
 Version: 1.3.0
-Date: 2022-04-05
+Date: 2023-05-17
 Authors@R:
     c(person(given = "Corey D.", family = "Broeckling",
              role = c("aut"),
@@ -16,38 +16,10 @@ Authors@R:
              email = "[email protected]",
              role = c("cre"),
              comment = c(ORCID = "0000-0001-6744-996X")))
-Depends:
-  R (>= 3.5.0)
-Imports:
-  dynamicTreeCut,
-  fastcluster,
-  ff,
-  httr,
-  jsonlite,
-  preprocessCore,
-  e1071,
-  gplots,
-  pcaMethods,
-  stringr,
-  utils,
-  webchem,
-  ggplot2,
-  methods
-Suggests: 
-  knitr,
-  rmarkdown,
-  xcms,
-  testthat,
-  patrick,
-  MSnbase,
-  InterpretMSSpectrum,
-  BiocManager,
-  xml2,
-  stringi,
-  readxl,
-  curl,
-  rentrez
-License: GPL (>= 2)
+Imports: dynamicTreeCut, fastcluster, preprocessCore, e1071, gplots, pcaMethods, utils, ggplot2, InterpretMSSpectrum
+Depends: R (>= 3.5.0)
+Suggests: knitr, rmarkdown, xcms, testthat, BiocManager, stringi, curl
+License: MIT
 Description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectrometry <DOI: 10.1021/ac501530d> data. 
 URL: https://github.com/cbroeckl/RAMClustR
 Encoding: UTF-8

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Corey Broeckling
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,50 +1,30 @@
 # Generated by roxygen2: do not edit by hand
 
 export(RCQC)
-export(adap.to.rc)
 export(add_params)
-export(annotate)
-export(annotation.summary)
-export(assign.z)
-export(change.annotation)
-export(cmpd.summary)
 export(compute_SpecAbundAve)
 export(compute_do.sets)
 export(compute_wt_mean)
 export(create_ramclustObj)
 export(defineExperiment)
 export(define_samples)
-export(do.findmain)
-export(export.msfinder.formulas)
+export(doFindmain)
 export(exportDataset)
 export(filter_blanks)
 export(filter_good_features)
 export(filter_signal)
 export(find_good_features)
 export(findfeature)
 export(findmass)
-export(fooddb2msfinder)
-export(get.taxon.cids)
 export(getData)
-export(getSmilesInchi)
 export(get_ExpDes)
 export(get_instrument_platform)
-export(impRamSearch)
-export(import.adap.kdb)
-export(import.msfinder.formulas)
-export(import.msfinder.mssearch)
-export(import.msfinder.structures)
-export(import.sirius)
-export(manual.annotation.template)
 export(mean_signal_intensities)
 export(mergeRCobjects)
 export(ramclustR)
 export(rc.calibrate.ri)
 export(rc.cmpd.filter.blanks)
 export(rc.cmpd.filter.cv)
-export(rc.cmpd.get.classyfire)
-export(rc.cmpd.get.pubchem)
-export(rc.cmpd.get.smiles.inchi)
 export(rc.cmpd.replace.na)
 export(rc.expand.sample.names)
 export(rc.export.msp.rc)
@@ -58,20 +38,20 @@ export(rc.feature.replace.na)
 export(rc.get.csv.data)
 export(rc.get.df.data)
 export(rc.get.xcms.data)
+export(rc.merge.split.clusters)
 export(rc.qc)
 export(rc.ramclustr)
 export(rc.remove.qc)
 export(rc.restore.qc.samples)
 export(remove_blanks)
 export(replace_na)
+export(write.gcei.mat)
 export(write.methods)
 export(write.msp)
 export(write_csv)
 importFrom(dynamicTreeCut,cutreeDynamicTree)
 importFrom(e1071,skewness)
 importFrom(fastcluster,hclust)
-importFrom(ff,ff)
-importFrom(gplots,heatmap.2)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,pdf)
 importFrom(graphics,"legend")
@@ -83,9 +63,7 @@ importFrom(graphics,abline)
 importFrom(graphics,axis)
 importFrom(graphics,boxplot)
 importFrom(graphics,hist)
-importFrom(httr,http_error)
-importFrom(jsonlite,fromJSON)
-importFrom(methods,new)
+importFrom(methods,is)
 importFrom(pcaMethods,pca)
 importFrom(preprocessCore,normalize.quantiles)
 importFrom(stats,aggregate)