From dfe58641d0e6fe53612710cd92401306273609f4 Mon Sep 17 00:00:00 2001 From: paradis Date: Wed, 13 Feb 2013 06:52:04 +0000 Subject: [PATCH] fix from Pierre Legendre git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@208 6e262413-ae40-0410-9e79-b911bd7a66b7 --- R/CDAM.global.R => CADM.global.R | 0 R/CDAM.post.R => CADM.post.R | 2 +- NEWS | 5 +++++ man/chronos.Rd | 4 ++-- 4 files changed, 8 insertions(+), 3 deletions(-) rename R/CDAM.global.R => CADM.global.R (100%) rename R/CDAM.post.R => CADM.post.R (99%) diff --git a/R/CDAM.global.R b/CADM.global.R similarity index 100% rename from R/CDAM.global.R rename to CADM.global.R diff --git a/R/CDAM.post.R b/CADM.post.R similarity index 99% rename from R/CDAM.post.R rename to CADM.post.R index 00b3d76..8530cd3 100644 --- a/R/CDAM.post.R +++ b/CADM.post.R @@ -257,7 +257,7 @@ } } Mantel.prob <- as.matrix(as.dist(Mantel.prob/(nperm+1))) - diag(Mantel.prob) <- 1 + diag(Mantel.prob) <- NA # Corrected 08feb13 } }) diff --git a/NEWS b/NEWS index 59c6fed..9bc3f6c 100644 --- a/NEWS +++ b/NEWS @@ -15,6 +15,11 @@ BUG FIXES 'phy' are not in the same order than the list of trees (thanks to Rupert Collins for the report). + o CADM.post() displayed "1" on the diagonal of the matrix of + Mantel p-values. It now displays "NA" on the diagonal, + indicating that no test of significance is computed between a + distance matrix and itself. + CHANGES IN APE VERSION 3.0-7 diff --git a/man/chronos.Rd b/man/chronos.Rd index 22c15f1..d85f5f7 100644 --- a/man/chronos.Rd +++ b/man/chronos.Rd @@ -102,9 +102,9 @@ chronos.control(...) inference: bridging the parsimony-likelihood gap. \emph{Systematic Biology}, \bold{57}, 665--674. - Paradis, E. (2012) Molecular dating of phylogenies by likelihood + Paradis, E. (2013) Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information - criterion. \emph{Manuscript}. + criterion. \emph{Molecular Phylogenetics and Evolution}, in press. Sanderson, M. J. (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood -- 2.39.2