Changes in version 1.0.0 (2026-04-29)                  

Changes in existing functions

    o   
	seqdistMCSE argument silent replaced by an argument verbose

Misc

    o   
	Package released on CRAN.

    o   
	CITATION file.

                        Changes in version 0.3.4                        

New function

    o   
	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                        

Changes in existing functions

    o   
	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 as MC.sd. Plot and summary methods have
	been adjusted conformably.

    o   
	MCratios() z-ratios now take account of the new definition of
	MC.se

                        Changes in version 0.3.2                        

Changes in existing functions

    o   
	MCdisslist() new logical argument use.udiss, which when set as
	TRUE, tells the function to derive MC-distances from the
	distances between unique merged replicated sequences.

    o   
	MCudist() adapted for distances to reference sequences, which
	can be passed with new argument seqref.

Bug fixes

    o   
	MCclustqual option clustmeth="ward.D" (or any other hclust
	method) did not work.

    o   
	MCnunique wrong result of check = TRUE.

                        Changes in version 0.3.1                        

New functions

    o   
	MCdisscorr() Correlations between observed and MC-simulated
	distances.

    o   
	MCclustqual() Cluster quality for a range of partition sizes
	per MC-set.

Changes in existing functions

    o   
	MCdisslist() gains argument seqref to specify reference
	sequences to analyze distances to these references.

    o   
	MCseqdistSE() and associated print and summary methods now
	supports list of matrices of distances to reference sequences.

    o   
	MCratios() and associated print and summary method now also
	apply to outcome of MCseqdistSE() (class distMC) for distances
	to reference sequences.

    o   
	summary.MCratios() gains a threshold argument thresh and
	returns the number and proportion of diss.z ratios lower than
	this threshold.

    o   
	MCclustcomp now returns all the indexes provided by package
	aricode for each MC-set.

Bug fixes

    o   
	MCseqReplicate() error when all dss have same length.

                        Changes in version 0.3.0                        

Misc.

    o   
	Packaged created from seqdistMCSE 0.2.0

    o   
	Implements the generation of replicated sets of sequences with
	timing changes.