[Adephylo-commits] r121 - pkg/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jan 19 12:00:06 CET 2009
Author: jombart
Date: 2009-01-19 12:00:06 +0100 (Mon, 19 Jan 2009)
New Revision: 121
Modified:
pkg/R/abouheif.R
pkg/R/distances.R
pkg/R/orthobasis.R
pkg/R/orthogram.R
pkg/R/partition.R
pkg/R/ppca.R
pkg/R/proximities.R
pkg/R/table.phylo4d.R
pkg/R/utils.R
Log:
Changes in naming conventions in phylobase.
pkg check is ok with the 2 usual warnings.
Changes are as follow:
from -> to
attach_data attachData
check_data checkData
check_phylo4 checkPhylo4
check_tree checkTree
getedges getEdge
hasSingles hasSingle
Modified: pkg/R/abouheif.R
===================================================================
--- pkg/R/abouheif.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/abouheif.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -14,8 +14,8 @@
W <- as.matrix(W)
} else { # otherwise computed W from x, a phylo4d object
if(!inherits(x, "phylo4d")) stop("if W is not provided, x has to be a phylo4d object")
- if (is.character(chk <- check_phylo4(x))) stop("bad phylo4d object: ",chk)
- if (is.character(chk <- check_data(x))) stop("bad phylo4d object: ",chk)
+ if (is.character(chk <- checkPhylo4(x))) stop("bad phylo4d object: ",chk)
+ if (is.character(chk <- checkData(x))) stop("bad phylo4d object: ",chk)
W <- proxTips(x, method=method, a=a, normalize="row", symmetric=TRUE)
}
@@ -25,8 +25,8 @@
## take data from x if it is a phylo4d
if(inherits(x, "phylo4d")){
- if (is.character(chk <- check_phylo4(x))) stop("bad phylo4d object: ",chk)
- if (is.character(chk <- check_data(x))) stop("bad phylo4d object: ",chk)
+ if (is.character(chk <- checkPhylo4(x))) stop("bad phylo4d object: ",chk)
+ if (is.character(chk <- checkData(x))) stop("bad phylo4d object: ",chk)
x <- tdata(x)
}
Modified: pkg/R/distances.R
===================================================================
--- pkg/R/distances.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/distances.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -15,7 +15,7 @@
tips.names <- names(tips)
## some checks
- if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+ if (is.character(checkval <- checkPhylo4(x))) stop(checkval)
if(any(is.na(tips))) stop("wrong tips specified")
## create all couples of observations
@@ -52,7 +52,7 @@
c(allPath[[i]], allPairs[i,1], allPairs[i,2]) )
names(allPath) <- allPath.names
- edge.idx <- lapply(allPath, function(e) getedges(x, e) ) # list of indices of edges
+ edge.idx <- lapply(allPath, function(e) getEdge(x, e) ) # list of indices of edges
allEdgeLength <- edgeLength(x)
res <- lapply(edge.idx, function(idx) sum(allEdgeLength[idx], na.rm=TRUE) )
} # end patristic
@@ -116,7 +116,7 @@
root <- getNode(x, N+1) # so that we have a named node
## some checks
- if(is.character(checkval <- check_phylo4(x))) stop(checkval)
+ if(is.character(checkval <- checkPhylo4(x))) stop(checkval)
if(any(is.na(tips))) stop("wrong tips specified")
@@ -133,7 +133,7 @@
allPath <- lapply(1:length(allPath), function(i) c(allPath[[i]], tips[i]) )
names(allPath) <- allPath.names
- edge.idx <- lapply(allPath, function(e) getedges(x, e) ) # list of indices of edges
+ edge.idx <- lapply(allPath, function(e) getEdge(x, e) ) # list of indices of edges
allEdgeLength <- edgeLength(x)
res <- sapply(edge.idx, function(idx) sum(allEdgeLength[idx], na.rm=TRUE) )
} # end patristic
Modified: pkg/R/orthobasis.R
===================================================================
--- pkg/R/orthobasis.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/orthobasis.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -11,7 +11,7 @@
if(is.null(prox)){ # have to compute prox
x <- as(x, "phylo4")
- if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+ if (is.character(checkval <- checkPhylo4(x))) stop(checkval)
W <- proxTips(x, tips="all", method=method, a=a, normalize="row", symmetric=TRUE)
} else { # prox is provided
W <- as.matrix(prox)
Modified: pkg/R/orthogram.R
===================================================================
--- pkg/R/orthogram.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/orthogram.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -41,7 +41,7 @@
## check that tre is provided and valid
if(is.null(tre)) stop("tre, orthobasis or prox must be provided")
tre <- as(tre, "phylo4")
- if (is.character(checkval <- check_phylo4(tre))) stop(checkval)
+ if (is.character(checkval <- checkPhylo4(tre))) stop(checkval)
orthobas <- treePart(tre, result="orthobasis")
} else { # else orthobasis from the proxi matrix.
orthobas <- orthobasis.phylo(prox=prox)
Modified: pkg/R/partition.R
===================================================================
--- pkg/R/partition.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/partition.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -17,7 +17,7 @@
x <- as(x, "phylo4")
## check phylo4 object
- if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+ if (is.character(checkval <- checkPhylo4(x))) stop(checkval)
## computations
nodIdx <- nTips(x)+1
@@ -44,7 +44,7 @@
result <- match.arg(result)
## check phylo4 object
- if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+ if (is.character(checkval <- checkPhylo4(x))) stop(checkval)
n <- nTips(x) # number of tips
HTU.idx <- (n+1):(n+nNodes(x)) # index of internal nodes (HTU)
Modified: pkg/R/ppca.R
===================================================================
--- pkg/R/ppca.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/ppca.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -11,8 +11,8 @@
## handle arguments
if(!require(ade4)) stop("The package ade4 is not installed.")
- if (is.character(chk <- check_phylo4(x))) stop("bad phylo4d object: ",chk)
- if (is.character(chk <- check_data(x))) stop("bad phylo4d object: ",chk)
+ if (is.character(chk <- checkPhylo4(x))) stop("bad phylo4d object: ",chk)
+ if (is.character(chk <- checkData(x))) stop("bad phylo4d object: ",chk)
tre <- as(x, "phylo4")
method <- match.arg(method)
Modified: pkg/R/proximities.R
===================================================================
--- pkg/R/proximities.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/proximities.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -16,7 +16,7 @@
tips <- getNode(x, tips)
## some checks
- if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+ if (is.character(checkval <- checkPhylo4(x))) stop(checkval)
if(any(is.na(tips))) stop("wrong tips specified")
## compute distances
Modified: pkg/R/table.phylo4d.R
===================================================================
--- pkg/R/table.phylo4d.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/table.phylo4d.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -10,8 +10,8 @@
{
## preliminary stuff and checks
- if (is.character(chk <- check_phylo4(x))) stop("bad phylo4d object: ",chk)
- # if (is.character(chk <- check_data(x))) stop("bad phylo4d object: ",chk) <- needed?
+ if (is.character(chk <- checkPhylo4(x))) stop("bad phylo4d object: ",chk)
+ # if (is.character(chk <- checkData(x))) stop("bad phylo4d object: ",chk) <- needed?
if(!require(ape)) stop("the ape package is required")
if(cex.label<0.1) {
Modified: pkg/R/utils.R
===================================================================
--- pkg/R/utils.R 2009-01-12 14:11:37 UTC (rev 120)
+++ pkg/R/utils.R 2009-01-19 11:00:06 UTC (rev 121)
@@ -48,7 +48,7 @@
x <- as(x, "phylo4")
## some checks
- if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+ if (is.character(checkval <- checkPhylo4(x))) stop(checkval)
t1 <- getNode(x, tip1)
t2 <- getNode(x, tip2)
if(any(is.na(c(t1,t2)))) stop("wrong tip specified")
@@ -170,7 +170,7 @@
nameBy <- match.arg(nameBy)
## check phylo4 object
- if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+ if (is.character(checkval <- checkPhylo4(x))) stop(checkval)
## computations
nodIdx <- nTips(x)+1
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