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