[Picante-commits] r56 - pkg/man

[noreply at r-forge.r-project.org]

Author: skembel
Date: 2008-04-17 06:20:49 +0200 (Thu, 17 Apr 2008)
New Revision: 56

Modified:
   pkg/man/Kcalc.Rd
   pkg/man/phylosignal.Rd
Log:
Improve phylosignal/Kcalc documentation

Modified: pkg/man/Kcalc.Rd
===================================================================
--- pkg/man/Kcalc.Rd	2008-04-13 18:25:58 UTC (rev 55)
+++ pkg/man/Kcalc.Rd	2008-04-17 04:20:49 UTC (rev 56)
@@ -1,6 +1,6 @@
 \name{Kcalc}
 \alias{Kcalc}
-%- Also NEED an '\alias' for EACH other topic documented here.
+
 \title{ K statistic of phylogenetic signal }
 \description{
   Calculates K statistic of phylogenetic signal
@@ -17,7 +17,7 @@
 \value{
   \item{K }{K statistic}
 }
-\references{ Blomberg and Garland 2002 Evolution}
+\references{ Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745.}
 \author{ Simon Blomberg <s.blomberg1 at uq.edu.au> and David Ackerly <dackerly at berkeley.edu> }
 
 \seealso{ \code{\link{phylosignal}} }

Modified: pkg/man/phylosignal.Rd
===================================================================
--- pkg/man/phylosignal.Rd	2008-04-13 18:25:58 UTC (rev 55)
+++ pkg/man/phylosignal.Rd	2008-04-17 04:20:49 UTC (rev 56)
@@ -1,6 +1,6 @@
 \name{phylosignal}
 \alias{phylosignal}
-%- Also NEED an '\alias' for EACH other topic documented here.
+
 \title{ Measure phylogenetic signal }
 \description{
   Calculates K statistic of phylogenetic signal as well as P-value based on variance of phylogenetically independent contrasts relative to tip shuffling randomization.
@@ -22,7 +22,12 @@
   \item{PIC.variance.P }{P-value of observed vs. random variance of PICs}
    \item{PIC.variance.z }{Z-score of observed vs. random variance of PICs}
 }
-\references{ Blomberg and Garland. 2002. Evolution. }
+\references{ Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. }
 \author{ Steve Kembel <skembel at berkeley.edu> }
 \seealso{ \code{\link{Kcalc}} }
-\keyword{univar}
+\examples{
+randtree <- rcoal(20)
+randtraits <- evolve.brownian(randtree)
+phylosignal(randtraits[randtree$tip.label],randtree)
+}
+\keyword{univar}
\ No newline at end of file