Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.


News

_N_e_w_s _f_o_r _P_a_c_k_a_g_e '_o_u_c_h'

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_4:

    • Depends on R>=3.6.  This change necessitated by modifications
      to the default RNG with R version 3.6.

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_3:

    • Changes to the organization of the package.

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_2:

    • Upgrade the package license to GPL version 3.

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_1:

    • Improvements to the underlying C code, which now registers
      callable functions.

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1_0:

    • In ‘glssoln’, when the Choleski decomposition fails, a
      warning is issued and ‘NA’s are returned.  In previous
      versions, an error was thrown.

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._8:

    • 'as(tree,"data.frame")' now returns a data-frame with
      rownames identical to the node-names ([email protected]s).

    • Functions that have been deprecated since 2.1-1 have been
      removed.  The argument 'alpha' that was deprecated in favor
      of 'sqrt.alpha' in version 2.6-1 has been removed.

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._7:

    • Fixed typo in the documentation of 'hansen'.  Thanks to
      Roland Sookias for bringing this to my attention.

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._6:

    • In the 'hansen' function, the use of the argument 'alpha' was
      confusing.  This vector parameterizes the "selection" portion
      of the OU model, which since version 2 has been assumed to be
      a positive-definite matrix (corresponding to stabilizing
      selection).  In particular, it contains the entries of the
      lower-triangular matrix square root of this positive definite
      matrix.  To make the name more mnemonic, this argument has
      been renamed 'sqrt.alpha'.  This is a superficial change
      meant to improve intelligibility: the algorithm itself has
      not changed.  To prevent loss of backward compatibility, use
      of argument 'alpha' will continue to work, though it will
      generate a warning.  In some future release, use of 'alpha'
      as an argument to 'hansen' will no longer generate a warning
      but will instead be passed through to the control list for
      'optim' if method='optim' and will otherwise generate an
      error.

_C_h_a_n_g_e_s _i_n _o_u_c_h _v_e_r_s_i_o_n _2._1:

    • Version 2 of ouch represents a major revision.  ouch's
      capabilities have been substantially extended.

    • support is now provided for multivariate characters.
      Inference based on multivariate Ornstein-Uhlenbeck and
      multivariate Brownian motion models is now provided.

    • nonultrametric trees are supported.

    • the root character state need no longer be estimated.
      Instead, the root state is assumed to be distributed
      according to the stationary distribution of the OU process.

    • convenience functions for parametric bootstrap confidence
      intervals are provided.

    • the new function 'paint' simplifies the specification of
      adaptive regimes in complex phylogenies.

    • the new function 'ape2ouch' translates trees in the 'phylo'
      format of the ape package into 'ouchtree' format (thanks to
      Dan Ackerly).

    • The new package is a complete rewrite, using S4 classes.  The
      old functionality from ouch v. 1 remains available, but is
      now deprecated.

Reference manual

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install.packages("ouch")

2.14-1 by Aaron A. King, 7 months ago


https://kingaa.github.io/ouch/


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


Authors: Aaron A. King <[email protected]> and Marguerite A. Butler <[email protected]>


Documentation:   PDF Manual  


Task views: Analysis of Ecological and Environmental Data, Statistical Genetics, Phylogenetics, Especially Comparative Methods


GPL-3 license


Depends on methods, stats, graphics, subplex

Suggests ape, geiger


Imported by mvSLOUCH, pmc.

Depended on by surface.


See at CRAN