[Caic-commits] r75 - pkg/inst/doc

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

Author: petzoldt
Date: 2008-10-04 12:55:07 +0200 (Sat, 04 Oct 2008)
New Revision: 75

Modified:
   pkg/inst/doc/caic-benchmarks.rnw
Log:
caic-benchmarks.rnw

Modified: pkg/inst/doc/caic-benchmarks.rnw
===================================================================
--- pkg/inst/doc/caic-benchmarks.rnw	2008-10-04 10:06:07 UTC (rev 74)
+++ pkg/inst/doc/caic-benchmarks.rnw	2008-10-04 10:55:07 UTC (rev 75)
@@ -73,7 +73,8 @@
 The next section of code duplicates these CAIC analyses using the \texttt{crunch()} function. Note that the default internal branch length used in calculations at a polytomy (\texttt{polytomy.brlen}) needs to be changed from the 0, which is the default in \texttt{crunch()}, to 1, which was the default in CAIC. The \texttt{caic.table()} function is used to extract a contrast table from the \texttt{crunch()} output, including CAIC style node labels.
 
 <<>>=
-load("../../benchmarks/Benchmark.rda")
+#load("../../benchmarks/Benchmark.rda")
+load("Benchmark.Rda")
 library(CAIC)
 crunch.CrDi213 <- crunch(contResp ~ contExp1 + contExp2, data=BenchData, phy=BENCH, names.col=node, polytomy.brlen=1)
 crunch.CrDi213.tab <- caic.table(crunch.CrDi213, CAIC.codes=TRUE)