1 ## diversi.gof.R (2006-10-16)
3 ## Tests of Constant Diversification Rates
5 ## Copyright 2002-2006 Emmanuel Paradis
7 ## This file is part of the R-package `ape'.
8 ## See the file ../COPYING for licensing issues.
10 diversi.gof <- function(x, null = "exponential", z = NULL)
13 if (null == "exponential") {
15 z <- 1 - exp(-delta * sort(x))
18 nmsz <- deparse(substitute(z))
19 z <- sort(z) # utile ???
22 W2 <- sum((z - (2*i - 1)/(2*n))^2) + 1/12*n
23 A2 <- -sum((2*i - 1)*(log(z) + log(1 - rev(z))))/n - n
24 if (null == "exponential") {
28 else W2 <- (W2 - 0.4/n + 0.6/n^2)/(1 + 1/n)
29 cat("\nTests of Constant Diversification Rates\n\n")
30 cat("Data:", deparse(substitute(x)), "\n")
31 cat("Number of branching times:", n, "\n")
33 if (null == "exponential") cat("exponential\n\n")
34 else cat(nmsz, "(user-specified)\n\n")
35 cat("Cramer-von Mises test: W2 =", round(W2, 3))
36 if (null == "exponential") {
37 if (W2 < 0.177) cat(" P > 0.1\n")
38 if (W2 >= 0.177 && W2 < 0.224) cat(" 0.05 < P < 0.1\n")
39 if (W2 >= 0.224 && W2 < 0.273) cat(" 0.025 < P < 0.05\n")
40 if (W2 >= 0.273 && W2 < 0.337) cat(" 0.01 < P < 0.025\n")
41 if (W2 > 0.337) cat(" P < 0.01\n")
44 if (W2 < 0.347) cat(" P > 0.1\n")
45 if (W2 >= 0.347 && W2 < 0.461) cat(" 0.05 < P < 0.1\n")
46 if (W2 >= 0.461 && W2 < 0.581) cat(" 0.025 < P < 0.05\n")
47 if (W2 >= 0.581 && W2 < 0.743) cat(" 0.01 < P < 0.025\n")
48 if (W2 > 0.743) cat(" P < 0.01\n")
50 cat("Anderson-Darling test: A2 =", round(A2, 3))
51 if (null == "exponential") {
52 if (A2 < 1.078) cat(" P > 0.1\n")
53 if (A2 >= 1.078 && A2 < 1.341) cat(" 0.05 < P < 0.1\n")
54 if (A2 >= 1.341 && A2 < 1.606) cat(" 0.025 < P < 0.05\n")
55 if (A2 >= 1.606 && A2 < 1.957) cat(" 0.01 < P < 0.025\n")
56 if (A2 > 1.957) cat(" P < 0.01\n")
59 if (A2 < 1.933) cat(" P > 0.1\n")
60 if (A2 >= 1.933 && A2 < 2.492) cat(" 0.05 < P < 0.1\n")
61 if (A2 >= 2.492 && A2 < 3.070) cat(" 0.025 < P < 0.05\n")
62 if (A2 >= 3.070 && A2 < 3.857) cat(" 0.01 < P < 0.025\n")
63 if (A2 > 3.857) cat(" P < 0.01\n")