doAll: Do all implemented analyses, write tables and figures.

In pavel-fibich/TRADER: Tree Ring Analysis of Disturbance Events in R

Do all implemented analyses, write tables and figures.

Description

The TRADER package provides only one way for disturbance reconstruction from tree-ring data. TRADER is a unique package bringing the first instrument for analysis of forest disturbance history in complementary ways. Final advantage of TRADER is the possibility of results comparison between individual studies. This is enabled by easy parameter changes in data processing, as well as by clearly arranged graphical and tabular outputs. We developed TRADER in open source R environment, to further support the on-going open-source software development for dendrochronological methods and data availability.

Usage

doAll(data, m1 = 10, m2 = 10, abs.threshold = NULL, boundary = NULL, buffer = 2, 
  criteriaNA = 0.2, criteria2NA = 0.5, 
  criteriaBA = 0.2, criteria2BA = 0.5, segmentBA = 0.5, segment2BA = 0.5,
  criteriaS = 0.2, criteria2S = 0.5, segmentS = 0.5, segment2S = 0.5,
  gfun = mean, length = 2, notop = 10, notop2 = 10, 
  storedev = pdf, drawing=TRUE, prefix = NULL, ...)

Arguments

data	A data.frame with series as columns and years as rows such as that produced by read.* function of dplR .
m1	Determines the number of years to be averaged (including target year) for period prior the potential releas.
m2	Determines the number of years to be averaged (including target year) for period prior the potential releas.
abs.threshold	Threshold of absolute-increase method.
boundary	Boundary line function of one argument, eg. boundary=function(x) {5.0067*exp(-0.664*x)}
buffer	Number of years determining how close to one another two releases can be.
criteriaNA	Threshold for detection of moderate release in NA method.
criteria2NA	Threshold for detection of major release in NA method.
criteriaBA	Threshold for detection of moderate release in BA method.
criteria2BA	Threshold for detection of major release in BA method.
criteriaS	Threshold for detection of moderate release in S method.
criteria2S	Threshold for detection of major release in S method.
segmentBA	Determines length of the segment on which prior growth will be divided in BA method.
segment2BA	Determines length of the segment on which first mm of prior growth will be divided in BA method.
segmentS	Determines length of the segment on which prior growth will be divided in S method.
segment2S	Determines length of the segment on which first mm of prior growth will be divided in S method.
prefix	Prefix of saved files.
gfun	Determines if M1 and M2 values are mean or median for selected period.
length	Determines how many years have to be given critera exceeded to be considered as release.
notop	Number of highest data points for fitting the boundary line.
notop2	Number of highest data points for fitting the boundary line in the segments for first mm.
storedev	Format for saving the graphical outputs, eg. pdf or jpeg.
drawing	If TRUE, graphical outputs for individual trees.
...	Parameters passed to plot function.

Details

For details look at methods that are evaluated: absoluteIncrease, noblabrams and splechtna.

Value

Write many tables and figures in the current directory.

Note

Check reference.

Author(s)

Pavel Fibich <[e-mail]>, Jan Altman <[e-mail]>, Tuomas Aakala <[e-mail]>, Jiri Dolezal <[e-mail]>

References

Nowacki, G.J. & Abrams, M.D. 1997. Radial-growth averaging criteria for reconstructing disturbance histories from presettlement-origin oaks. Ecological Monographs, 67, 225-249.
Black, B.A. & Abrams, M.D. 2003. Use of boundary-line growth patterns as a basis for dendroecological release criteria. Ecological Applications, 13, 1733-1749.
Fraver, S. & White, A.S. 2005. Identifying growth releases in dendrochronological studies of forest disturbance. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere, 35, 1648-1656.
Splechtna, B.E., Gratzer, G. & Black, B.A. 2005. Disturbance history of a European old-growth mixed-species forest - A spatial dendro-ecological analysis. Journal of Vegetation Science, 16, 511-522.

See Also

absoluteIncreaseALL, growthAveragingALL, boundaryLineALL, splechtnaALL

Examples

data(relData)
 doAll(relData1,length=5,stodev=pdf) 

pavel-fibich/TRADER documentation built on Feb. 12, 2024, 1:27 a.m.