Depends: survival, lpSolve, mlogit, coxphf

Description: Proportional hazards estimation in the presence of a partially monotone likelihood has difficulties, in that finite estimators do not exist.  These difficulties are related to those arising from logistic and multinomial regression.  References for methods are given in the separate function documents.  Supported by grant NSF DMS 1712839.

Title: Penalised Maximum Likelihood Estimation for Hidden Semi-Markov
Description: Provides tools for penalised maximum likelihood estimation of hidden semi-Markov models (HSMMs) with flexible state dwell-time distributions. These include functions for model fitting, model checking and state-decoding. The package considers HSMMs for univariate time series with state-dependent gamma, normal, Poisson or Bernoulli distributions. For details, see Pohle, J., Adam, T. and Beumer, L.T. (2021): Flexible estimation of the state dwell-time distribution in hidden semi-Markov models. <arXiv:2101.09197>.

Title: Functions for phylogenetically-based statistical analyses.
Author: Ram�n D�az-Uriarte <ramon-diaz@teleline.es> and Theodore Garland, Jr <tgarland@facstaff.wisc.edu>.
Description: Manipulation and analysis of phylogenetically simulated data sets (as
obtained from PDSIMUL in PDAP package) and phylogenetically-based analyses

Title: Functions for phylogenetically based statistical analyses
Author: Ram�n D�az-Uriarte <ramon-diaz@teleline.es> and Theodore Garland, Jr <tgarland@facstaff.wisc.edu>, <tgarland@citrus.ucr.edu>
Description: Manipulation and analysis of phylogenetically simulated data sets
and phylogenetically based analyses using GLS.

Title: Functions for Phylogenetically Based Statistical Analyses
Author: Ramon Diaz-Uriarte <rdiaz@cnio.es> and Theodore Garland, Jr
Description: Manipulation and analysis of phylogenetically simulated
data sets and phylogenetically based analyses using GLS.

Author: Ram�n D�az-Uriarte <rdiaz@cnio.es> and Theodore Garland, Jr <tgarland@facstaff.wisc.edu>, <tgarland@citrus.ucr.edu>