################################################################################ ##### ##### ##### CHANGELOG ##### ##### ##### ################################################################################ 0.2: Stable release version that contains previous updates from versions 0.1.* 0.1.*: UPDATES -------------------------------------------------------------------------------- ß* 88: testthat function for fluidigmAnalysisWrapper added * 87: Bugfix in fluidigmAnalysisWrapper that crashed the function call * 86: More verbose output added for verbosity>1 * 85: Fixed the wrapper function and added missing options from individual function calls * 84: similarityMatrix tests added * 83: Verbosity issues in getPairwiseSimilarityLoci fixed * 82: Adjustment for better consistency in finding package installation path * 81: Tests for calculatePairwiseSimilarities added * 80: Better examples added to estiamteErrors function * 79: estimateErrors has now a outdir option to define the output folder as well * 78: Added tests for fluidigm2PLINK * 77: Added a FAQ section to the vignette to address the most common problems the package might cause * 76: Updated fluidigm2PLINK help to provide more details on harmonising marker names mismach issues * 75: New option 'outdir' in fluidigm2PLINK function * 74: Example dataset added * 73: Notes in DESCRIPTION file adjusted * 72: Package description added to the manual * 71: Help, function and vignette for similarityMatrix adjusted * 70: Vignette chapter about getPairwiseSimilarityLoci added * 69: Additional and more detailed input checks for getPairwiseSimilarityLoci added * 68: Help file description for getPairwiseSimilarityLoci adjusted * 67: Vignette chapter about calculatePairwiseSimilarities added * 66: Additional and more detailed input checks for calculatePairwiseSimilarities added * 65: Help file description for calculatePairwiseSimilarities adjusted * 64: Vignette updated for replicates and negative controls * 63: Bugfix: estimateErrors concidered sp.markers only when sexing was performed, they act no independent * 62: Changed sexing=FALSE as new default in estimateErrors() * 61: Added more careful input checks to estimateErrors * 60: Updated the function description for estimateErrors * 59: Harmonised the output from 'cat' and 'print' to 'message' in fluidigm2PLINK * 58: Bugfix: The out option in fluidigm2PLINK was not working properly * 57: Option overwrite added to fluidigm2PLINK function * 56: Vignette part of fluidigm2PLINK added * 55: Details in Rd file for fluidigm2PLINk added * 54: More input checks for fluidigm2PLINK * 53: Input checks added to calculatePairwiseSimilarities.R * 52: More details to calculatePairwiseSimilarities.R added * 51: Added manual skeletons for Details and Examples * 50: Added the vignette skeleton * 49: Added co-authors and contributers * 48: Missing function parameters added to the documentation * 47: Adding verbosity option for more detailed function feedback (split from verbose logical/numerical mix) * 46: Placed importFrom under usethis control ( usethis::use_import_from("grDevices", "png") ) * 45: Added sexing option tocalculatePairwiseSimilarities() function (=run PLINK with --allow-no-sex option) * 44: Adjusted the fluidigmAnalysisWrapper function so that it works again * 43: Added more input checks to fluidigm2PLINK() function * 42: Added option sexing=TRUE to estimateErrors() function * 41: Added option fixNames=TRUE to fluidigm2PLINK() function