ouch-deprecated {ouch} | R Documentation |
These functions are deprecated.
is.valid.ouch.tree(node, ancestor, times, regimes = NULL) tree.plot(node, ancestor, times, names = NULL, regimes = NULL) brown.fit(data, node, ancestor, times) brown.dev(n = 1, node, ancestor, times, sigma, theta) hansen.fit(data, node, ancestor, times, regimes = NULL, interval = c(0, 100), tol = 1e-12) hansen.prof(alpha, data, node, ancestor, times, regimes = NULL) hansen.dev(n = 1, node, ancestor, times, regimes = NULL, alpha, sigma, theta)
data |
Phenotypic data for extant species, i.e., at the terminal ends of the phylogenetic tree. |
node |
Specification of the names of the nodes. |
ancestor |
Specification of the topology of the phylogenetic tree. This is in the form of a character vector of node names, one for each node in the tree. The i-th name is that of the ancestor of the i-th node. The root node is distinguished by having no ancestor (i.e., NA). |
times |
A vector of nonnegative numbers, one per node in the tree, specifying the time at which each node is located. The root node should be assigned time 0. |
regimes |
A vector of codes, one for each node in the tree, specifying the selective regimes hypothesized to have been operative. Corresponding to each node, enter the code of the regime hypothesized for the branch segment terminating in that node. For the root node, because it has no branch segment terminating on it, the regime specification is irrelevant. |
names |
Optional vector of species names. |
n |
Number of pseudorandom data sets to generate. |
sigma |
the value of σ to be used in the simulations. |
alpha |
Value of selection-strength parameter α. |
theta |
the value of theta to be used in the simulations. |
interval |
The interval which will be searched for the optimal α. By default, 0 < α < 100. |
tol |
Convergence tolerance. |
Phylogenetic trees in ouch are now implemented using the S4
class ouchtree
. The validity checks formerly implemented by
is.valid.ouch.tree
are now performed when an ouchtree
is
contructed; see ouchtree
, ouchtree-class
.
The ouchtree
class has a plot
method, obviating the need
for tree.plot
; see ouchtree-class
.
Brownian motion (BM) models are now built around the S4 class
browntree
. Fitting BM models is now accomplished by means of
brown
; generating random deviates from a fitted model,
by the simulate
method for browntree
-class objects. See
browntree-class
.
The Ornstein-Uhlenbeck-based Hansen models are now implemented using
the S4 class hansentree
. They are fit using
hansen
; see hansentree-class
for
documentation of the simulate
method for this class.
Aaron A. King <kingaa at umich dot edu>