[Phylobase-commits] r722 - in pkg: R inst/doc src

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Jan 26 16:28:06 CET 2010 

Author: francois
Date: 2010-01-26 16:28:06 +0100 (Tue, 26 Jan 2010)
New Revision: 722

Added:
   pkg/src/ncl/
Modified:
   pkg/R/checkdata.R
   pkg/R/formatData.R
   pkg/R/methods-phylo4.R
   pkg/R/prune.R
   pkg/R/treewalk.R
   pkg/inst/doc/developer.pdf
Log:
bringing ncl-2.1.09 into the main branch

Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R	2010-01-26 15:26:14 UTC (rev 721)
+++ pkg/R/checkdata.R	2010-01-26 15:28:06 UTC (rev 722)
@@ -84,7 +84,7 @@
     if (is.null(names(object at label))) {
         stop(c("Tip and node labels must have names matching node IDs. ",
             lab.msg))
-             
+
     } else {
         if (!all(tips %in% names(na.omit(object at label)))) {
             stop(c("All tips must have associated tip labels. ",
@@ -123,11 +123,11 @@
     }
 
     ## make sure that tip and node labels are unique
-    lb <- labels(object, "all")
-    lb <- lb[nchar(lb) > 0]
-    lb <- na.omit(lb)
-    if(any(table(lb) > 1))
-        stop("All labels must be unique")
+    #lb <- labels(object, "all")
+    #lb <- lb[nchar(lb) > 0]
+    #lb <- na.omit(lb)
+    #if(any(table(lb) > 1))
+    #    stop("All labels must be unique")
 
     ## all done with fatal errors.  Now construct a list
     ##  of warnings and paste them together

Modified: pkg/R/formatData.R
===================================================================
--- pkg/R/formatData.R	2010-01-26 15:26:14 UTC (rev 721)
+++ pkg/R/formatData.R	2010-01-26 15:28:06 UTC (rev 722)
@@ -31,30 +31,72 @@
     if (any(dim(dt)==0)) {
         return(data.frame(row.names=ids.out))
     }
-        
+
     label.type <- match.arg(label.type)
-    stopifnot(label.column %in% 1:ncol(dt))
+    ## TODO -- needs testing
+    if (label.type == "column") {
+        if (is.numeric(label.column))
+            stopifnot(label.column %in% 1:ncol(dt))
+        else
+            stopifnot(label.column %in% names(dt))
+    }
+
     missing.data <- match.arg(missing.data)
     extra.data <- match.arg(extra.data)
 
     if(match.data) {
+        
+        
         ## extract values to be matched to nodes
         ndNames <- switch(label.type,
                           rownames = rownames(dt),
                           column = dt[,label.column])
+        ## Deal with duplicated labels
+        if (any(duplicated(labels(phy, type)))) {
+            tmpDt <- getNode(phy, ndNames)
+            
+        }
+        
+        ## check whether labels are unique
+        ##if (any(duplicated(labels(phy, type)))) {
+        ##    if (allowDuplicateLabels) {
+        ##       lb <- as(phy, "data.frame")[nodeId(phy, type), 1:2]
+        ##        if (label.type == "rownames") {
+        ##            dt <- data.frame(lbl=rownames(dt), dt)
+        ##            label.column <- 1 # just to be safe
+        ##            label.type <- "column"
+        ##        }
+        ##        dt <- merge(x=lb, y=dt, by.x=1, by.y=label.column)
+        ##        dt <- dt[,-1]
+        ##        ndNames <- dt$node
+        ##    }
+        ##    else stop("All labels must be unique")
+        ##}
         ## either force matching on labels, or match on node
         ## numbers for any number-like elements and labels otherwise
         if (rownamesAsLabels) {
             ids.in <- getNode(phy, as.character(ndNames), missing="OK")
-        } else {
-            ids.in <- as.numeric(rep(NA, length(ndNames)))
-            treatAsNumber <- nchar(gsub("[0-9]", "", ndNames))==0
-            ids.in[treatAsNumber] <- getNode(phy,
-                as.integer(ndNames[treatAsNumber]), missing="OK")
-            ids.in[!treatAsNumber] <- getNode(phy,
-                as.character(ndNames[!treatAsNumber]), missing="OK")
         }
+        else {
+           ids.in <- lapply(ndNames, function(ndnm) {
+                if (nchar(gsub("[0-9]", "", ndnm)) == 0) {
+                    getNode(phy, as.integer(ndnm), missing="OK")
+                }
+                else {
+                    getNode(phy, as.character(ndnm), missing="OK")
+                }
+            })
+            ids.in <- unlist(ids.in)
 
+            #ids.in <- as.numeric(rep(NA, length(ndNames)))
+            #treatAsNumber <- nchar(gsub("[0-9]", "", ndNames))==0
+            #ids.in[treatAsNumber] <- getNode(phy,
+            #    as.integer(ndNames[treatAsNumber]), missing="OK")
+            #ids.in[!treatAsNumber] <- getNode(phy,
+            #    as.character(ndNames[!treatAsNumber]), missing="OK")
+            browser()
+        }
+
         ## Make sure that data are matched to appropriate nodes
         if (type=="tip" && any(na.omit(ids.in) %in% nodeId(phy,
             "internal"))) {
@@ -90,6 +132,9 @@
                    fail = stop(msg))
         }
         ## Format data to have correct dimensions
+        ## TODO -- here build empty dataframe to match in case
+        ## of duplicates.
+        browser()
         dt <- dt[!is.na(ids.in), , drop=FALSE]
         rownames(dt) <- ids.in[!is.na(ids.in)]
         dt.out <- dt[match(ids.out, rownames(dt)), , drop=FALSE]
@@ -97,7 +142,6 @@
         if(label.type == "column") dt.out <- dt.out[, -label.column, drop=FALSE]
 
     } else {
-
         ## Check if too many or not enough rows in input data
         expected.nrow <- length(nodeId(phy, type))
         diffNr <- nrow(dt) - expected.nrow

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2010-01-26 15:26:14 UTC (rev 721)
+++ pkg/R/methods-phylo4.R	2010-01-26 15:28:06 UTC (rev 722)
@@ -507,6 +507,7 @@
 
 orderIndex <- function(x, order=c("preorder", "postorder")) {
 
+    browser()
     order <- match.arg(order)
     if(!isRooted(x)){
         stop("Tree must be rooted to reorder")
@@ -596,7 +597,7 @@
     order   <- match.arg(order)
     index   <- orderIndex(x, order)
     x at order <- order
-    x at edge  <- x at edge[index, ]
+    x at edge  <- edges(x)[index, ]
     if(hasEdgeLabels(x)) {
         x at edge.label  <- x at edge.label[index]
     }

Modified: pkg/R/prune.R
===================================================================
--- pkg/R/prune.R	2010-01-26 15:26:14 UTC (rev 721)
+++ pkg/R/prune.R	2010-01-26 15:28:06 UTC (rev 722)
@@ -26,6 +26,7 @@
         if (edgeOrder(x) == "postorder") {
             edge.post <- edges(x)
         } else {
+            browser()
             edge.post <- edges(reorder(x, "postorder"))
         }
         for (i in seq_along(edge.post[,2])) {
@@ -59,6 +60,7 @@
         edge.length.new <- edge.length.new[-match(edge.names.drop,
             names(edge.length.new))]
         edge.label.new[edge.name.new] <- NA
+        browser()
         edge.label.new <- edge.label.new[-match(edge.names.drop,
             names(edge.label.new))]
 

Modified: pkg/R/treewalk.R
===================================================================
--- pkg/R/treewalk.R	2010-01-26 15:26:14 UTC (rev 721)
+++ pkg/R/treewalk.R	2010-01-26 15:28:06 UTC (rev 722)
@@ -20,7 +20,10 @@
 
     ## match node to tree
     if (is.character(node)) {
-        irval <- match(node, labels(x, type))
+        ndTmp <- paste("^", node, "$", sep="")
+        irval <- lapply(ndTmp, function(ND) grep(ND, labels(x, type)))
+        irval <- unlist(irval)
+        ##irval <- match(node, labels(x, type))
     } else if (is.numeric(node) && all(floor(node) == node, na.rm=TRUE)) {
         irval <- match(as.character(node), names(labels(x, type)))
     } else {
@@ -293,7 +296,7 @@
             ## hack to return NA for tip nodes when type='ancestor'
             if(length(res)==0) res <- NA
             names(res) <- rep(nid, length(res))
-        }   
+        }
         names(res) <- rep(nid, length(res))
         res
     })

Modified: pkg/inst/doc/developer.pdf
===================================================================
--- pkg/inst/doc/developer.pdf	2010-01-26 15:26:14 UTC (rev 721)
+++ pkg/inst/doc/developer.pdf	2010-01-26 15:28:06 UTC (rev 722)
@@ -1,937 +1,912 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/phylobase -r 722

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