.Defunct(msg = '\'klastorin\' has been removed from ape,
see help("ape-defunct") for details.')
-mlphylo <-
- function(x, phy, model = DNAmodel(), search.tree = FALSE,
- quiet = FALSE, value = NULL, fixed = FALSE)
+mlphylo <- function(...)
.Defunct(msg = '\'mlphylo\' has been removed from ape,
see help("ape-defunct") for details.')
-DNAmodel <- function(model = "K80", partition = 1,
- ncat.isv = 1, invar = FALSE,
- equal.isv = TRUE, equal.invar = 1)
+DNAmodel <- function(...)
.Defunct(msg = '\'DNAmodel\' has been removed from ape,
see help("ape-defunct") for details.')
-sh.test <- function(..., x, model = DNAmodel(), B = 100)
+sh.test <- function(...)
.Defunct(msg = '\'sh.test\' has been removed from ape,
see help("ape-defunct") for details.')
-heterozygosity <- function (x, variance = FALSE)
- .Defunct(msg = '\'heterozygosity\' has been moved from ape to pegas,
+evolve.phylo <- function(phy, value, var)
+ .Defunct(msg = '\'evolve.phylo\' has been removed from ape,
see help("ape-defunct") for details.')
-H <- function(x, variance = FALSE)
- heterozygosity (x, variance = FALSE)
-
-nuc.div <- function(x, variance = FALSE, pairwise.deletion = FALSE)
- .Defunct(msg = '\'nuc.div\' has been moved from ape to pegas,
+plot.ancestral <- function(...)
+ .Defunct(msg = '\'plot.ancestral\' has been removed from ape,
see help("ape-defunct") for details.')
-theta.h <- function(x, standard.error = FALSE)
- .Defunct(msg = '\'theta.h\' has been moved from ape to pegas,
+chronogram <- function(...)
+ .Defunct(msg = '\'chronogram\' has been removed from ape,
see help("ape-defunct") for details.')
-theta.k <- function(x, n = NULL, k = NULL)
- .Defunct(msg = '\'theta.k\' has been moved from ape to pegas,
+ratogram <- function(...)
+ .Defunct(msg = '\'ratogram\' has been removed from ape,
see help("ape-defunct") for details.')
-theta.s <- function(s, n, variance = FALSE)
- .Defunct(msg = '\'theta.s\' has been moved from ape to pegas,
+NPRS.criterion <- function(...)
+ .Defunct(msg = '\'NPRS.criterion\' has been removed from ape,
see help("ape-defunct") for details.')