[Dplr-commits] r996 - in pkg/dplR: R man

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

Author: andybunn
Date: 2015-06-04 23:46:43 +0200 (Thu, 04 Jun 2015)
New Revision: 996

Modified:
   pkg/dplR/R/treeMean.R
   pkg/dplR/man/treeMean.Rd
Log:
Added an argument to treeMean to limit averaging to a period with >1 core in cases where there are two more samples per tree. Just passing na.rm to rowMeans.

Question: what to do if there is no overlap between two cores? E.g.,  core A runs from 1800 to 1850 and core B from 1852 to 2014. Sometimes (silly) users set their data up this way. This would make internal NA which is a bad practice.


Modified: pkg/dplR/R/treeMean.R
===================================================================
--- pkg/dplR/R/treeMean.R	2015-06-03 20:49:29 UTC (rev 995)
+++ pkg/dplR/R/treeMean.R	2015-06-04 21:46:43 UTC (rev 996)
@@ -1,4 +1,4 @@
-treeMean <- function(rwl, ids) {
+treeMean <- function(rwl, ids, na.rm=FALSE) {
     rwl2 <- as.matrix(rwl)
     if (!is.data.frame(ids) || !("tree" %in% names(ids))) {
         stop("'ids' must be a data.frame with column 'tree'")
@@ -24,7 +24,7 @@
     matches <- match(trees, uTrees)
     res <- matrix(NA_real_, nrow=nrow(rwl2), ncol=length(uTrees))
     for (i in seq_along(uTrees)) {
-        res[, i] <- rowMeans(rwl2[, matches == i, drop=FALSE], na.rm=TRUE)
+      res[,i] <- rowMeans(rwl2[, matches == i, drop=FALSE], na.rm=na.rm)
     }
     res[is.nan(res)] <- NA_real_
     res <- as.data.frame(res, row.names = rownames(rwl2))

Modified: pkg/dplR/man/treeMean.Rd
===================================================================
--- pkg/dplR/man/treeMean.Rd	2015-06-03 20:49:29 UTC (rev 995)
+++ pkg/dplR/man/treeMean.Rd	2015-06-04 21:46:43 UTC (rev 996)
@@ -6,7 +6,7 @@
   This function calculates the mean value for each tree in a rwl or rwi object.
 }
 \usage{
-treeMean(rwl, ids)
+treeMean(rwl, ids, na.rm=FALSE)
 }
 \arguments{
   \item{rwl}{a \code{data.frame} of ring widths with
@@ -17,13 +17,21 @@
     \code{"tree"} giving a \code{numeric} \acronym{ID} for each tree and
     column two named \code{"core"} giving a \code{numeric} \acronym{ID}
     for each core. }
+  \item{na.rm}{ \code{logical} passed to \code{\link{rowMeans}}. Should 
+    missing values be removed?}    
 }
 \details{
-  Here.
+  This function averages together multiple cores to give a mean value of growth.
+  It is very common in dendrochronology to take more than one core per tree. In
+  those cases it is occassionally desirable to have an average of the cores.
+  This function merely loops through the \code{rwl} object and calculates the
+  \code{\link{rowMeans}} for each tree. If \code{na.rm=TRUE} trees with >1 
+  sample will be averaged only over the period where the samples overlap. 
+  If FALSE the output can vary in the number of samples. See examples.
 }
 \value{
-  An object of class \code{c("rwl", "data.frame")} with the means of
-  each tree.
+  An object of class \code{c("rwl", "data.frame")} with the mean annual value 
+  for each tree.
 }
 
 \author{ Andy Bunn. Patched and improved by Mikko Korpela. }
@@ -33,20 +41,21 @@
 \examples{
 data(gp.rwl)
 gp.ids <- read.ids(gp.rwl, stc = c(0, 2, 1))
+
 gp.treeMean <- treeMean(gp.rwl, gp.ids)
-# plot using S3method for class "rwl"
-plot(gp.treeMean,plot.type="spag")
+gp.treeMean2 <- treeMean(gp.rwl, gp.ids, na.rm=TRUE)
 
+# look at an example of a single tree with different averaging periods
+tree40 <- data.frame(gp.rwl[, c("40A","40B")],
+                     gp.treeMean[, "40", drop=FALSE],
+                     gp.treeMean2[, "40", drop=FALSE])
+names(tree40) <- c("coreA", "coreB", "treeMean1", "treeMean2")
+head(tree40,50)
+
 data(ca533)
 ca533.treeMean <- treeMean(ca533, autoread.ids(ca533))
-# look at an example of two cores per tree
-tail(ca533[, c("CAM031", "CAM032"), drop=FALSE])
-tail(rowMeans(ca533[, c("CAM031", "CAM032"), drop=FALSE], na.rm=TRUE))
-tail(ca533.treeMean[, "3", drop=FALSE])
-# look at an example of single tree
-ca533[, "CAM011", drop=FALSE]
-ca533.treeMean[, 1]
-ca533[905, "CAM011"]
-ca533.treeMean[905, 1]
+# plot using S3method for class "rwl"
+plot(ca533.treeMean,plot.type="spag")
+
 }
 \keyword{ manip }