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NEWS file of the MCseqReplic package
Changes in version 1.0.0 [2026-04-29]
Changes in existing functions
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seqdistMCSEargumentsilentreplaced by an argumentverbose
Misc
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Package released on CRAN.
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CITATION file.
Changes in version 0.3.4 [2026-02-21]
New function
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MCpj()Generates a distribution Pj of the timing error probability that complies with expected size of timing errors and the probability of no error.
Changes in version 0.3.3 [2025-10-10]
Changes in existing functions
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MCseqdistSE()The standards error of each distance (MC.se) is now the square root of the sum of the variance of the simulated distances and the squared bias. The standard deviation of the distances is returned asMC.sd. Plot and summary methods have been adjusted conformably. -
MCratios()z-ratios now take account of the new definition ofMC.se
Changes in version 0.3.2 [2025-03-18]
Changes in existing functions
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MCdisslist()new logical argumentuse.udiss, which when set asTRUE, tells the function to derive MC-distances from the distances between unique merged replicated sequences. -
MCudist()adapted for distances to reference sequences, which can be passed with new argumentseqref.
Bug fixes
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MCclustqualoption clustmeth="ward.D" (or any otherhclustmethod) did not work. -
MCnuniquewrong result ofcheck = TRUE.
Changes in version 0.3.1 [2025-03-06]
New functions
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MCdisscorr()Correlations between observed and MC-simulated distances. -
MCclustqual()Cluster quality for a range of partition sizes per MC-set.
Changes in existing functions
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MCdisslist()gains argumentseqrefto specify reference sequences to analyze distances to these references. -
MCseqdistSE()and associatedprintandsummarymethods now supports list of matrices of distances to reference sequences. -
MCratios()and associatedprintandsummarymethod now also apply to outcome ofMCseqdistSE()(classdistMC)for distances to reference sequences. -
summary.MCratios()gains a threshold argumentthreshand returns the number and proportion ofdiss.zratios lower than this threshold. -
MCclustcompnow returns all the indexes provided by packagearicodefor each MC-set.
Bug fixes
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MCseqReplicate()error when all dss have same length.
Changes in version 0.3.0 [2025-01-10]
Misc.
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Packaged created from seqdistMCSE 0.2.0
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Implements the generation of replicated sets of sequences with timing changes.