overall.concordance.period: Overall Concordance period

In dplRCon: Concordance for Dendroclimatology

Description

Produces the concordance indices for each year over the period of interest and the average of these indices. Trimmed and different levels of concordance indices in the overall concordance, size adjusted (mean concordance indices)

Usage

overall.concordance.period(x, y, x.boot, y.boot, min.series,
  concordance.indices, period, trim.alpha = 0, concordance.beta = 0.5)

Arguments

x	A matrix containing the standardized ring width indices for subset X, column heading tree ID, row names is time
y	As x, but for subset Y
x.boot	the bootstrapped replicates for matrix x. with bootstrapped replicate as row names, and time as the column headings
y.boot	the bootstrapped replicates for matrix y.
min.series	is a number indicating the minimum number of series for calculating the concordance statistic, recommend 10.
concordance.indices	The function used for calculating the concordance indices for each t.
period	Time period for which the concordance is to be calculated, vector of form c(start, end)
trim.alpha	this is the amount of trimming of the extreme concordance indices, default is 0 (no trimming). Recommend that a 0.005 be used.
concordance.beta	This is used to calculated the proportion of indices above this cut off. Default is proportion above 0.5.

Value

pre.in	Concordance indices.
min.series	Minimum number of series used to calculate concordance.
num.series.at.t.x	Number of series in matrix X for each time, t.
num.series.at.t.y	Number of series in matrix Y for each time, t.
pre.in.greater.ts.period	Concordance indices, as time series, when minimum number of series was available.
period	The time period used to calculate the concordance.
pre.overall.period	The Concordance Statistic.

Examples

#loading data
## Not run: 
data(ring.raw)
data(ring.stand)
data(dbh.po.nc)

#Subset near-pith is the material within 0 -20cm from the estimated pith
spline200.sub0.20.n   <- TruncSeriesPithoffset( ring.raw, ring.stand, dbh.po.nc, c(1,200))
# Subset far-pith is the material further than 20cm from the estimated pith
spline200.sub20.2000.n  <- TruncSeriesPithoffset( ring.raw, ring.stand, dbh.po.nc, c(200,200000))

# series.bootstapped
boot.0.20   <-  series.bootstrap( spline200.sub0.20.n$sub.series.stand,
   stat, 999, names.stat, aver.by.tree = FALSE)
boot.20.2000   <- series.bootstrap(spline200.sub20.2000.n$sub.series.stand,
   stat, 999, names.stat, aver.by.tree = FALSE)

overall.precision.HUP <- overall.concordance.period(spline200.sub20.2000.n$sub.series.stand ,
   spline200.sub0.20.n$sub.series.stand,
   boot.20.2000$boot.series.mean,  boot.0.20$boot.series.mean ,
   1 , concordance.indices, c(1880,1999), trim.alpha=0.005, concordance.beta=0.5)

## End(Not run)

dplRCon documentation built on May 2, 2019, 2:02 p.m.