.Defunct(msg = '\'klastorin\' 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,
+mlphylo <-
+ function(x, phy, model = DNAmodel(), search.tree = FALSE,
+ quiet = FALSE, value = NULL, fixed = FALSE)
+ .Defunct(msg = '\'mlphylo\' 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,
- see help("ape-defunct") for details.')
-
-theta.h <- function(x, standard.error = FALSE)
- .Defunct(msg = '\'theta.h\' has been moved from ape to pegas,
- 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,
+DNAmodel <- function(model = "K80", partition = 1,
+ ncat.isv = 1, invar = FALSE,
+ equal.isv = TRUE, equal.invar = 1)
+ .Defunct(msg = '\'DNAmodel\' 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,
+sh.test <- function(..., x, model = DNAmodel(), B = 100)
+ .Defunct(msg = '\'sh.test\' has been removed from ape,
see help("ape-defunct") for details.')