X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fape-internal.Rd;h=73d53e6cf85a1c829dc85cff67aaa6d46e4aeba5;hb=821974300c3d4c88584832e3f4b2c99ed56601cb;hp=242afb5774b604760dcc92b7584922076fdee5f5;hpb=c827059eeafc8cbe41c812b26979543ab287803e;p=ape.git

diff --git a/man/ape-internal.Rd b/man/ape-internal.Rd
index 242afb5..73d53e6 100644
--- a/man/ape-internal.Rd
+++ b/man/ape-internal.Rd
@@ -8,24 +8,6 @@
 \alias{mant.zstat}
 \alias{lower.triang}
 \alias{clado.build}
-\alias{getDurations}
-\alias{getEdgeLengths}
-\alias{getExternalParams}
-\alias{getNEdges}
-\alias{getNFreeParams}
-\alias{getRates}
-\alias{objFuncLogScale}
-\alias{optimTree}
-\alias{phylogram}
-\alias{prepareTree}
-\alias{setTree}
-\alias{buildTreeFromPhylo}
-\alias{destroyTree}
-\alias{getError}
-\alias{nEdges}
-\alias{nNodes}
-\alias{klastorin_nTips}
-\alias{getMisawaTajima}
 \alias{phylogram.plot}
 \alias{cladogram.plot}
 \alias{circular.plot}
@@ -40,16 +22,18 @@
 \alias{pos.move}
 \alias{BOTHlabels}
 \alias{chronopl.cv}
-\alias{prepareDNA}
 \alias{floating.pie.asp}
 \alias{checkLabel}
 \alias{getMRCA}
+\alias{plotCophylo2}
+\alias{plotPhyloCoor}
+\alias{integrateTrapeze}
+\alias{CDF.birth.death}
 \title{Internal Ape Functions}
 \description{
-  Internal ape functions.
+  Internal \pkg{ape} functions.
 }
 \note{
-  These are not to be called by the user (or in some cases are just
-  waiting for proper documentation to be written).
+  These are not to be called by the user (unless you know what you're doing).
 }
 \keyword{internal}