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NEWS	R Documentation

NEWS file of the MCseqReplic package

MCpj() Generates a distribution Pj of the timing error probability that complies with expected size of timing errors and the probability of no error.

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

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

MCclustqual option clustmeth="ward.D" (or any other hclust method) did not work.
MCnunique wrong result of check = TRUE.

MCdisslist() gains argument seqref to specify reference sequences to analyze distances to these references.
MCseqdistSE() and associated print and summary methods now supports list of matrices of distances to reference sequences.
MCratios() and associated print and summary method now also apply to outcome of MCseqdistSE() (class distMC) for distances to reference sequences.
summary.MCratios() gains a threshold argument thresh and returns the number and proportion of diss.z ratios lower than this threshold.
MCclustcomp now returns all the indexes provided by package aricode for each MC-set.