DNAmixtures

Statistical analysis of DNA mixtures with artefacts

by Therese Graversen

A detailed svn log of changes can be found at the DNAmixtures project summary page.

DNAmixtures 0.1-4 released 2015-01-22

  • Small fix to ensure that alleles are correctly matched based on their repeat number (Thanks to Øyvind Bleka for reporting this).

DNAmixtures 0.1-3 released 2014-04-05

  • The likelihood function can now optionally be maximised without imposing an order on unknown contributors.
  • Highly implausible parameter values are better handled.
  • Small bug-fixes to predict regarding a missing propagation step and the handling of mixtures with non-overlapping sets of markers.

DNAmixtures 0.1-2 released 2014-01-22

  • A significant speedup has been implemented.

DNAmixtures 0.1-1 released 2013-12-08

  • Function setPeakInfo for taking into account the observed peaks using a specified model parameter has been added. Both discrete information about presence/absence of peaks and the full peak heights can be used.
  • A function removePeakInfo for removing information about observed peaks has been added.
  • set.cpt has been renamed to setCPT; Functions set.CPT.[O/D/Q] are renamed to setCPT.[O/D/Q].
  • The functions setCPT and setCPT.O no longer automatically include the peak height information.
  • Functions parameters and condPeakHeights have been removed, and information of the state of the networks (e.g. specified parameters) is no longer maintained in the DNAmixture objects. It is up to the user to ensure that the Bayesian networs represent the distribution of interest.
  • The package functions may during computations change the state of the Bayesian networks in a DNAmixture, both in terms of propagated evidence and of the model parameters used. In particular, many functions now initially retract all evidence to ensure the networks represent the correct distribution. In special cases, the user may wish to keep some evidence during the computations; this can be achieved through an argument initialize=FALSE.
  • Printing a summary of map.genotypes can now be done for selected markers only.
  • mixML returns the mle as class mixpar.
  • varEst has been improved
  • Plot methods have been improved.
  • logL.K now ensures that phi has the right ordering.
  • get.shapes has been renamed to getShapes.

DNAmixtures 0.1-0 released 2013-06-10

  • First release.