News for Package 'ouch'

Changes in ouch version 2.19:

        • There is a new ‘as.data.frame’ method.

Changes in ouch version 2.17:

        • Both left and right plot margins can be adjusted to allow,
          for example, for long taxon names or long legend labels.

        • There is now an example showing how to plot a tree with long
          taxon names.

        • Error messages and examples have been improved somewhat.

        • The manual and help pages have been streamlined.

Changes in ouch version 2.16:

        • The arguments to the various ‘plot’ methods have changed.
          There is now much finer control over the plotting.  In
          particular, one can specify a different palette of colors,
          adjust the width of the margin in which taxon labels are
          printed, and pass options separately to the base-graphics
          ‘plot’, ‘text’, and ‘legend’ commands under0lying the ‘ouch’
          ‘plot’ methods.

        • A layout bug in ‘plot’ has been fixed.

Changes in ouch version 2.15:

        • The ‘plot’ function now spaces the terminal taxa evenly.

        • The documentation has received an overhaul.

Changes in ouch version 2.14:

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

Changes in ouch version 2.13:

        • Changes to the organization of the package.

Changes in ouch version 2.12:

        • Upgrade the package license to GPL version 3.

Changes in ouch version 2.11:

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

Changes in ouch version 2.10:

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

Changes in ouch version 2.8:

        • 'as(tree,"data.frame")' now returns a data-frame with
          rownames identical to the node-names (tree@nodes).

        • 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.

Changes in ouch version 2.7:

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

Changes in ouch version 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.

Changes in ouch version 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.

