Plots dependency logos from a set of aligned input sequences.

Traditional phasing programs are limited to diploid organisms.
 Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
 (MCMC) approaches, and builds a generic framework that allows haplotype searches
 in a multiple infection setting. This package is primarily developed as part of
 the Pf3k project, which is a global collaboration using the latest
 sequencing technologies to provide a high-resolution view of natural variation
 in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from
 patient blood sample, which often contains more than one parasite strain, with
 unknown proportions. This package is used for deconvoluting mixed haplotypes,
 and reporting the mixture proportions from each sample.

Fits (multigroup) mixtures of latent or hidden Markov models on mixed categorical and continuous (timeseries) data. The 'Rdonlp2' package can optionally be used for optimization of the log-likelihood and is available from R-forge. See Visser et al. (2009, <DOI:10.1007/978-0-387-95922-1_13>) for examples and applications.

Fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models, see Visser & Speekenbrink (2010, <DOI:10.18637/jss.v036.i07>).

Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.

Manage your source code dependencies
  by decorating your existing R code with special,
  'roxygen'-style comments.

Could be used to obtain spatial depths, spatial ranks and outliers of multivariate random variables. Could also be used to visualize DD-plots (a multivariate generalization of QQ-plots).

Data depth concept offers a variety of powerful and user friendly
    tools for robust exploration and inference for multivariate data. The offered
    techniques may be successfully used in cases of lack of our knowledge on
    parametric models generating data due to their nature. The
    package consist of among others implementations of several data depth techniques
    involving multivariate quantile-quantile plots, multivariate scatter estimators,
    multivariate Wilcoxon tests and robust regressions.