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 NAs 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.