R: Calculate mean across cores in a tree

treeMean {dplR} | R Documentation

## Calculate mean across cores in a tree

### Description

This function calculates the mean value for each tree in a rwl or rwi object.

### Usage

    treeMean(rwl, ids, na.rm=FALSE)

### Arguments

`rwl` | a `data.frame` of ring widths with `rownames(rwl)` containing years and `colnames(rwl)` containing each series ID such as produced by `read.rwl`
`ids` | a `data.frame` with column one named `"tree"` giving a `numeric` ID for each tree and column two named `"core"` giving a `numeric` ID for each core.
`na.rm` | `logical` passed to `rowMeans`. Should missing values be removed?

### Details

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 `rwl` object and calculates the `rowMeans` for each tree. If `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 `c("rwl", "data.frame")` with the mean annual value for each tree.

### Author(s)

Andy Bunn. Patched and improved by Mikko Korpela.

### See Also

`read.rwl`, `read.ids`

### Examples

    data(gp.rwl)
    gp.ids <- read.ids(gp.rwl, stc = c(0, 2, 1))

    gp.treeMean <- treeMean(gp.rwl, gp.ids)
    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))
    # plot using S3method for class "rwl"
    plot(ca533.treeMean,plot.type="spag")

[Package dplR version 1.7.2 Index]