updog 2.1.1

  1. Added an upper bound to the sequencing error rate in flexdog_full() (and, hence, flexdog() and multidog()). This protects against some poor behavior observed in a corner case. Specifically, F1 populations where the offspring are all the same genotype and is sequenced at moderate to low depth.
  2. Fixed some stale URLs, fixed some style issues found by lintr.

updog 2.1.0

  1. The parallel backend in multidog() is now handled by the future package. If you use the nc argument in multidog(), it should still run in parallel using multiple R sessions on your local machine. However, you can now use the functionality of future to choose your own evaluation strategy, after setting nc = NA. This will also allow you to use schedulers in high performance computing environments through the future.batchtools package. See the multidog() function documentation for more details.
  2. The vignette “Genotyping Many SNPs with multidog()” goes through an example of using the future package.
  3. A new experimental function, export_vcf(), is in the works to export multidog objects to a VCF file. This is not yet exported because I still have a few bugs to fix.
  4. plot.multidog() will now plot the parent read-counts in F1 and S1 populations.
  5. Internally, multidog() now uses iterators through the iterators package to send only subsets of the data to each R process.
  6. A new internal .combine function is used in the foreach() call of multidog() in order to decrease the memory usage of multidog().

updog 2.0.2

This is a massive edit of the updog software. Major changes include:

  1. No more support of model = "ash". It seemed that model = "norm" was always better and faster, so I just got rid of the "ash" option. This also extremely simplified the code.
  2. Removal of mupdog(). I think this was a good idea, but the computation was way too slow to be usable.
  3. Revision of model = "f1pp" and model = "s1pp". These now include interpretable parameterizations that are meant to be identified via another R package. But support is only for tetraploids right now.
  4. multidog() now prints some nice ASCII art when it’s run.
  5. format_multidog() now allows you to format multiple variables in terms of a multidimensional array.
  6. Fixes a bug where format_multidog() was reordering the SNP dimensions. This was fine as long as folks used dimnames properly, but now it should allow folks to also use dim positions.
  7. Updog now returns genotype log-likelihoods.

updog 1.2.1

updog 1.2.0

updog 1.1.3

updog 1.1.1

updog 1.1.0

updog 1.0.1

updog 0.99.0