[Seqinr-commits] r2053 - pkg/man

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

Author: jeanlobry
Date: 2017-07-04 13:29:20 +0200 (Tue, 04 Jul 2017)
New Revision: 2053

Added:
   pkg/man/kaks-torture.Rd
Log:
new test file for kaks

Added: pkg/man/kaks-torture.Rd
===================================================================
--- pkg/man/kaks-torture.Rd	                        (rev 0)
+++ pkg/man/kaks-torture.Rd	2017-07-04 11:29:20 UTC (rev 2053)
@@ -0,0 +1,33 @@
+\name{kaksTorture}
+\alias{kaksTorture}
+\docType{data}
+\title{Expected numeric results for Ka and Ks in extreme cases}
+\description{
+This data set is what should be obtained when runing \code{kaks()}
+on the test file kaks-torture.fasta in the sequences directory of the
+seqinR package.
+}
+\usage{data(kaksTorture)}
+\format{
+  A list with 4 components of class dist.
+  \describe{
+    \item{ka}{Ka}
+    \item{ks}{Ks}
+    \item{vka}{variance for Ka}
+    \item{vks}{variance for Ks}
+  }
+}
+\source{
+See comments in kaks-torture.fasta for R code used to produce it.
+}
+\references{
+\code{citation("seqinr")}
+}
+\examples{
+data(kaksTorture)
+kaks.torture <- read.alignment(file = system.file("sequences/kaks-torture.fasta", 
+  package = "seqinr"), format = "fasta")
+stopifnot(identical(kaksTorture, kaks(kaks.torture)))
+stopifnot(identical(kaksTorture, kaks(kaks.torture, rmgap = FALSE)))
+}
+\keyword{datasets}