[Phylobase-commits] r557 - in pkg: R man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 21 20:53:01 CEST 2009
Author: bbolker
Date: 2009-08-21 20:52:59 +0200 (Fri, 21 Aug 2009)
New Revision: 557
Modified:
pkg/R/checkdata.R
pkg/man/check.phylo4.Rd
pkg/tests/misctests.Rout.save
pkg/tests/phylotorture.Rout.save
pkg/tests/testprune.Rout.save
Log:
changed "multroot" to "multiroot" in checkdata.R;
updated test output appropriately; update docs
for checkRoot
Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R 2009-08-21 18:29:43 UTC (rev 556)
+++ pkg/R/checkdata.R 2009-08-21 18:52:59 UTC (rev 557)
@@ -11,7 +11,7 @@
}
checkTree <- function(object,
- warn=c("retic","singleton","multroot"),
+ warn=c("retic","singleton","multiroot"),
err=NULL) {
## case of empty phylo4 object
@@ -43,7 +43,7 @@
if(length(object at tip.label) != ntips)
return("number of tip labels not consistent with number of tips")
E <- edges(object)
- tips <- sort(E[,2][!E[,2] %in% E[,1]])
+ tips <- unique(sort(E[,2][!E[,2] %in% E[,1]]))
nodes <- unique(sort(c(E)))
intnodes <- nodes[!nodes %in% tips]
roots <- E[which(is.na(E[,1])),2]
@@ -150,9 +150,9 @@
if (nRoots>1) {
currmsg <- "tree has more than one root"
- if ("multroot" %in% err)
+ if ("multiroot" %in% err)
return(currmsg)
- if ("multroot" %in% warn)
+ if ("multiroot" %in% warn)
msg <- c(msg,currmsg)
}
if (any(nDesc==1)) {
Modified: pkg/man/check.phylo4.Rd
===================================================================
--- pkg/man/check.phylo4.Rd 2009-08-21 18:29:43 UTC (rev 556)
+++ pkg/man/check.phylo4.Rd 2009-08-21 18:52:59 UTC (rev 557)
@@ -7,13 +7,20 @@
}
\usage{
checkPhylo4(object)
-checkTree(object,warn="retic",err=NULL)
+checkTree(object,
+ warn=c("retic","singleton","multiroot"),
+ err=NULL)
}
\arguments{
\item{object}{A prospective S4 object}
\item{warn}{a character vector listing phenomena to warn about:
- current options are "poly" and "retic"}
- \item{err}{a character vector listing phenomena to trigger errors}
+ current options are [\code{"poly"} (polytomies),
+ \code{"retic"} (reticulations),
+ \code{"singleton"} ("singleton" nodes, i.e.
+ nodes with a single descendant), \code{"multiroot"}
+ (multiple roots) ]}
+ \item{err}{a character vector listing phenomena to trigger errors:
+ choices as above}
}
\value{
As required by \code{\link[methods]{validObject}}, returns an
Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save 2009-08-21 18:29:43 UTC (rev 556)
+++ pkg/tests/misctests.Rout.save 2009-08-21 18:52:59 UTC (rev 557)
@@ -83,8 +83,8 @@
mean : 0.2116037
variance : 0.01503145
distribution :
- Min. 1st Qu. Median 3rd Qu. Max.
-0.07552 0.10370 0.23040 0.27250 0.38530
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+0.07552 0.10370 0.23040 0.21160 0.27250 0.38530
Comparative data:
@@ -131,8 +131,8 @@
mean : 0.1988313
variance : 0.0167175
distribution :
- Min. 1st Qu. Median 3rd Qu. Max.
-0.04857 0.07552 0.20610 0.28460 0.38530
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+0.04857 0.07552 0.20610 0.19880 0.28460 0.38530
Comparative data:
@@ -334,4 +334,4 @@
>
> proc.time()
user system elapsed
- 3.464 0.076 3.520
+ 3.396 0.064 3.490
Modified: pkg/tests/phylotorture.Rout.save
===================================================================
--- pkg/tests/phylotorture.Rout.save 2009-08-21 18:29:43 UTC (rev 556)
+++ pkg/tests/phylotorture.Rout.save 2009-08-21 18:52:59 UTC (rev 557)
@@ -40,8 +40,6 @@
longer object length is not a multiple of shorter object length
3: In tips == 1:ntips :
longer object length is not a multiple of shorter object length
-4: In tips == 1:ntips :
- longer object length is not a multiple of shorter object length
> OKvals <- sapply(p1,class)!="try-error"
> table(sapply(p1[!OKvals],as.character))
@@ -94,7 +92,7 @@
>
> try(as(broke1, "phylo4") -> tree, silent=TRUE) # makes a phylo4 object with no warning
Warning message:
-In checkTree(object) : tree is reticulated:tree contains singleton nodes
+In checkTree(object) : tree contains singleton nodes
> try(phylo4(broke1$edge), silent=TRUE) # constructor makes a phylo4 object with no warning
label node ancestor edge.length node.type
6 <NA> 6 NA NA internal
@@ -107,10 +105,8 @@
4 T4 4 9 NA tip
5 T5 5 9 NA tip
Warning messages:
-1: In checkTree(object) :
- tree is reticulated:tree contains singleton nodes
-2: In checkTree(object) :
- tree is reticulated:tree contains singleton nodes
+1: In checkTree(object) : tree contains singleton nodes
+2: In checkTree(object) : tree contains singleton nodes
> ## error message comes from ape, not phylo? -- AND
> ## error is about singles, not disconnected nodes
> ## print(try(plot(tree), silent=TRUE )) ## pdc couldn't get this to work, so temporarily commenting
@@ -202,4 +198,4 @@
>
> proc.time()
user system elapsed
- 1.680 0.064 1.733
+ 1.744 0.044 1.807
Modified: pkg/tests/testprune.Rout.save
===================================================================
--- pkg/tests/testprune.Rout.save 2009-08-21 18:29:43 UTC (rev 556)
+++ pkg/tests/testprune.Rout.save 2009-08-21 18:52:59 UTC (rev 557)
@@ -40,8 +40,8 @@
mean : 0.2116037
variance : 0.01503145
distribution :
- Min. 1st Qu. Median 3rd Qu. Max. NA's
-0.07552 0.10370 0.23040 0.27250 0.38530 1.00000
+ Min. 1st Qu. Median Mean 3rd Qu. Max.
+0.07552 0.10370 0.23040 0.21160 0.27250 0.38530
Comparative data:
@@ -77,4 +77,4 @@
>
> proc.time()
user system elapsed
- 1.162 0.047 1.203
+ 1.700 0.068 1.744
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