Insertion Deletion Analysis While Accounting for Possible Missing Data

Genome-wide gene insertion and deletion rates can be modelled in a maximum likelihood framework with the additional flexibility of modelling potential missing data using the models included within. These models simultaneously estimate insertion and deletion (indel) rates of gene families and proportions of "missing" data for (multiple) taxa of interest. The likelihood framework is utilized for parameter estimation. A phylogenetic tree of the taxa and gene presence/absence patterns (with data ordered by the tips of the tree) are required. See Dang et al. (2016) for more details.


News

indelmiss v1.0-8 (Release date: 2018-01-30)

Changes:

  • Maintainance.
  • Updated citation.

indelmiss v1.0-7 (Release date: 2016-08-21)

Changes:

  • nmiss changed to pmiss. pmiss is the proportion of missingness to be simulated.
  • Some fine tuning to examples in the indelrates.Rd file.

indelmiss v1.0-6 (Release date: 2016-01-19)

Changes:

  • Allows for user-specified root probabilities.
  • Allows for user-specification of starting values for the rates.

indelmiss v1.0-5 (Release date: 2015-11-25)

Changes:

  • Optimizations to code. Runs faster now.

indelmiss v1.0-4 (Release date: 2015-11-17)

Changes:

  • Match tips from usertree to data from userphyl for datasource=="user".
  • Specifying toi with taxa names.
  • BIC typo corrected.
  • Added a minimal check for bg "listofnodes" argument, which will stop and warn users if any branch is not being listed in the branch grouping.
  • Quashed a bug that would pop up when building unique phyletic patterns (used within the algorithm) observed when discrete characters in the phyletic patterns included numbers greater than 9.
  • Quashed a bug that popped up when fitting a model with a single branch having a unique rate separate from the surrounding branches.
  • Both matrices and dataframes are now accepted for the discrete character data argument.
  • Argument matching for some arguments.
  • More tests for arguments in model specification.

Reference manual

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install.packages("indelmiss")

1.0.9 by Utkarsh J. Dang, 9 months ago


Browse source code at https://github.com/cran/indelmiss


Authors: Utkarsh J. Dang and G. Brian Golding


Documentation:   PDF Manual  


GPL (>= 2) license


Imports Rcpp, ape, numDeriv, phangorn

Suggests testthat

Linking to Rcpp


See at CRAN