Tree Ring Analysis of Disturbance Events in R

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.

Details

library(TRADER)

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>

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

doAll

Examples

data(relData)

plotFirstYears(relData1)
plotGrowth(relData1)

absoluteIncreaseALL(relData1,length=3,buffer=4,storedev=jpeg)
growthAveragingALL(relData1,length=3,buffer=4,storedev=pdf)
boundaryLineALL(relData1,length=2,buffer=2,storedev=pdf,
  boundary=function(x) {5.0067*exp(-0.664*x)} )  
splechtnaALL(relData1,length=3,buffer=4,storedev=pdf,
  boundary=function(x) {5.0067*exp(-0.664*x)} )
doAll(relData1,length=3,buffer=4,storedev=pdf)

knownBL

Compute absolute threshold

Description

"Blind" definition of the absolute-increase threshold of Fraver & White 2005 (1.25*standard deviation).

Usage

absTreshold(abs, tvalue = 1.25)

Arguments

Details

You can specifie threshold value or use 1.25 * standard deviation used in Fraver & White 2005.

Value

Returns one threshold value.

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

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.

See Also

help absoluteIncrease

Examples

data(relData)
abs<-absIncrease(relData1)
absTreshold(abs)

Analysis by Fraver & White 2005 called "absolute increase"

Description

Absolute-increase method is the alternative to percent-increase method.

Usage

absoluteIncrease(data, abs = NULL, abs.threshold = NULL, 
  m1 = 10, m2 = 10, buffer = 2, gfun = mean, length = 2,
  prefix = NULL)

Arguments

Details

In cases where species autecology (mean growth rate, species sensitivity, and range of growth responses) is well known, it is possible to determine the absolute threshold for release detection, instead of thresholds based on relative growth. Empirically determined absolute-increase threshold for each species roughly corresponded to 1.25 times the standard deviation (Fraver & White 2005). The absolute-increase method has only one threshold, and no distinction is made between moderate and major releases.

Value

Return list object with

Note

Check reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

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.

See Also

absoluteIncreaseALL, plotRelease, reduceByLB

Examples

data(relData)

abs<-absIncrease(relData1)
mabs.threshold<- absTreshold(abs)
fw <- absoluteIncrease(relData1,abs,mabs.threshold)
 plotRelease(relData1,abs,fw, 1, method="FraverWhite") 

Overal function for Fraver & White 2005 method called "absolute increase"

Description

Absolute-increase method is the alternative to percent-increase method.

Usage

absoluteIncreaseALL(data, abs = NULL, abs.threshold = NULL, 
  m1 = 10, m2 = 10, buffer = 2, drawing = TRUE, 
  gfun = mean, length = 2, storedev = pdf, prefix = NULL, ...)

Arguments

Details

In cases where species autecology (mean growth rate, species sensitivity, and range of growth responses) is well known, it is possible to determine the absolute threshold for release detection, instead of thresholds based on relative growth. Empirically determined absolute-increase threshold for each species roughly corresponded to 1.25 times the standard deviation (Fraver & White 2005). The absolute-increase method has only one threshold, and no distinction is made between moderate and major releases.

Value

Write many tables and figures in the current directory.

Note

Check reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

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.

See Also

absoluteIncrease, doAll

Examples

data(relData)
absoluteIncreaseALL(relData1)
absoluteIncreaseALL(relData1,length=3,buffer=4,storedev=pdf)

Fit multiple boundary lines.

Description

Fit multiple boundary lines, write their results and choose the best one.

Usage

boundaryFit(boundaries, x, y, boundary = NULL, 
  store = TRUE, storedev = pdf, initNLS = NULL, prefix = NULL)

Arguments

Details

Boundary-line method scales the percent growth change of Nowacki & Abrams (1997) according to growth rate prior to disturbance. In their example, Black & Abrams (2003) defined moderate and major releases as those falling within 20-49.9%, and 50-100% of the boundary line, respectively. Advantage of the boundary-line is standardization, which takes into account the relationships among tree age, size, and canopy class determining radial growth rate (Black et al. 2004). On the downside, Black et al. (2009) suggest approximately 50000 ring width measurements is necessary for boundary line determination for a given species (Black et al. 2009).

Value

Return list object with

Note

Check reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

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.
Black, B.A., Abrams, M.D., Gagen, M., Daniels, L.D., Kipfmueller, K.F., Speer, J.H. & Anchukaitis, K.J. (2004) Development and application of boundary-line release criteria. Dendrochronologia, 22, 31-42.
Black, B.A., Abrams, M.D., Rentch, J.S. & Gould, P.J. (2009) Properties of boundary-line release criteria in North American tree species. Annals of Forest Science, 66.

See Also

boundaryGet, plotBoundary, nls

Examples

data(relData)
bo<-boundaryGet(relData1)
bofit<-boundaryFit(bo$bo,bo$x,bo$y)

 plotBoundary(bo$bo,bo$x,bo$y,boundary=bofit$fun,rsq=bofit$rsq) 
 plotBoundary(bo$bo,bo$x,bo$y,boundary=function(x) {5.0067*exp(-0.664*x)}) 

Get values for fitting boundary line.

Description

Get values for fitting boundary line.

Usage

boundaryGet(data, prior = NULL, change = NULL, m1 = 10, m2 = 10, 
  segment = 0.5, segment2 = 0.5, notop = 10, notop2 = 10, 
  gfun = mean, bfun = mean)

Arguments

Details

Boundary-line method scales the percent growth change of Nowacki & Abrams (1997) according to growth rate prior to disturbance. In their example, Black & Abrams (2003) defined moderate and major releases as those falling within 20-49.9%, and 50-100% of the boundary line, respectively. Advantage of the boundary-line is standardization, which takes into account the relationships among tree age, size, and canopy class determining radial growth rate (Black et al. 2004). On the downside, Black et al. (2009) suggest approximately 50000 ring width measurements is necessary for boundary line determination for a given species (Black et al. 2009).

Value

Return list object with

Note

Check reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

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.
Black, B.A., Abrams, M.D., Gagen, M., Daniels, L.D., Kipfmueller, K.F., Speer, J.H. & Anchukaitis, K.J. (2004) Development and application of boundary-line release criteria. Dendrochronologia, 22, 31-42.
Black, B.A., Abrams, M.D., Rentch, J.S. & Gould, P.J. (2009) Properties of boundary-line release criteria in North American tree species. Annals of Forest Science, 66.

See Also

boundaryFit, plotBoundary

Examples

data(relData)
bo<-boundaryGet(relData1)
plot(bo)
 plotBoundary(bo$bo,bo$x,bo$y,boundary=function(x) {5.0067*exp(-0.664*x)}) 

Overal function for Black and Abrams 2003 method or "pure boundary line".

Description

Boundary-line method scales the percent growth change of Nowacki & Abrams (1997).

Usage

boundaryLineALL(data, releases = NULL, m1 = 10, m2 = 10, boundary = NULL, 
  buffer = 2, criteria = 0.2, criteria2 = 0.5, segment = 0.5, 
  segment2 = 0.5, drawing = TRUE, gfun = mean, 
  length = 2, notop = 10, notop2 = 10, storedev = pdf, prefix = NULL, ...)

Arguments

Details

Boundary-line method scales the percent growth change of Nowacki & Abrams (1997) according to growth rate prior to disturbance. In their example, Black & Abrams (2003) defined moderate and major releases as those falling within 20-49.9%, and 50-100% of the boundary line, respectively. Advantage of the boundary-line is standardization, which takes into account the relationships among tree age, size, and canopy class determining radial growth rate (Black et al. 2004). On the downside, Black et al. (2009) suggest approximately 50000 ring width measurements is necessary for boundary line determination for a given species (Black et al. 2009).

Value

Write many tables and figures in the current directory.

Note

Check reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

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.
Black, B.A., Abrams, M.D., Gagen, M., Daniels, L.D., Kipfmueller, K.F., Speer, J.H. & Anchukaitis, K.J. (2004) Development and application of boundary-line release criteria. Dendrochronologia, 22, 31-42.
Black, B.A., Abrams, M.D., Rentch, J.S. & Gould, P.J. (2009) Properties of boundary-line release criteria in North American tree species. Annals of Forest Science, 66.

See Also

noblabrams, doAll

Examples

data(relData)
boundaryLineALL(relData1)
 boundaryLineALL(relData1,length=3,buffer=4,storedev=pdf,
  boundary=function(x) {5.0067*exp(-0.664*x)} ) 

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

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 <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

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) 

Overal function for Nowacki and Abrams 1997 method.

Description

Radial-growth averaging criteria developed by Nowacki & Abrams (1997).

Usage

growthAveragingALL(data, releases = NULL, m1 = 10, m2 = 10, 
  buffer = 2, drawing = TRUE, criteria = 0.25, criteria2 = 0.5, 
  gfun = mean, length = 2, storedev = pdf, prefix = NULL, ...)

Arguments

Details

Radial-growth averaging criteria developed by Nowacki & Abrams (1997) is one of the most often used techniques from this category. This method computes the percentage growth change (%GC) between average radial growth over the preceding 10-year period, M1 (including the target year), and average radial growth over the subsequent 10-year period, M2 (excluding the target year): %GC = [(M2-M1)/M1] * 100. Minimum threshold for release is 25% growth change for moderate and >50% for major release. The advantage of this method is its broad applicability even for a small number of samples, and that information about species autecology is not necessary. On the other hand, this generality of radial-growth averaging may lead to detection of false releases and missing of true releases (Black & Abrams 2003; Fraver & White 2005). These inaccuracies are primarily caused by different growth rates in young, small, and suppressed trees when compared to older, larger and dominant trees.

Value

Write many tables and figures in the current directory.

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

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.

See Also

noblabrams, doAll

Examples

data(relData)
growthAveragingALL(relData1)
 growthAveragingALL(relData1,length=3,buffer=4,storedev=pdf) 

Help functions.

Description

Help function used in other functions.

Usage

absIncrease(data, m1 = 10, m2 = 10, gfun = mean)
PGC(data, m1 = 10, m2 = 10, gfun = mean)
PGCreleases(change, criteria = 0.2)
PGCreleasesSplechtna(change, criteria = 0.5)
priorGrowth(data, m1 = 10, m2 = 10, gfun = mean, dom1 = 0)
writeReleaseStats(release_list, mytext)
removeMajorFromModerate(mod,maj,zero,on)
relListToDataFrame(release_list,data)

Arguments

Details

Just helping functions.

Value

Various.

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

Altman J, Fibich P, Dolezal J & Aakala T (2014) TRADER: a package for Tree Ring Analysis of Disturbance Events in R. Dendrochonologia 32: 107-112.

See Also

doAll

Examples

data(relData)

abs<-absIncrease(relData1)

Nowacki and Abrams 1997, Black and Abrams 2003 or "pure boundary line".

Description

There is a split of behaviour of this function according parameter black.

Usage

noblabrams(data = NULL, prior = NULL, change = NULL, m1 = 10, m2 = 10, 
  boundary = NULL, buffer = 2, criteria = 0.25, criteria2 = 0.5, 
  segment = 0.5, segment2 = 0.5, black = FALSE, gfun = mean, length = 2, 
  notop = 10, notop2 = 10, storedev = pdf, prefix = NULL)

Arguments

Details

If black=TRUE: Boundary-line method scales the percent growth change of Nowacki & Abrams (1997) according to growth rate prior to disturbance. In their example, Black & Abrams (2003) defined moderate and major releases as those falling within 20-49.9%, and 50-100% of the boundary line, respectively. Advantage of the boundary-line is standardization, which takes into account the relationships among tree age, size, and canopy class determining radial growth rate (Black et al. 2004). On the downside, Black et al. (2009) suggest approximately 50000 ring width measurements is necessary for boundary line determination for a given species (Black et al. 2009).
If black=FALSE: Radial-growth averaging criteria developed by Nowacki & Abrams (1997) is one of the most often used techniques from this category. This method computes the percentage growth change (%GC) between average radial growth over the preceding 10-year period, M1 (including the target year), and average radial growth over the subsequent 10-year period, M2 (excluding the target year): %GC = [(M2-M1)/M1] * 100. Minimum threshold for release is 25% growth change for moderate and >50% for major release. The advantage of this method is its broad applicability even for a small number of samples, and that information about species autecology is not necessary. On the other hand, this generality of radial-growth averaging may lead to detection of false releases and missing of true releases (Black & Abrams 2003; Fraver & White 2005). These inaccuracies are primarily caused by different growth rates in young, small, and suppressed trees when compared to older, larger and dominant trees.

Value

Return list object with

Note

Rather use functions with ALL suffix.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

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.
Black, B.A., Abrams, M.D., Gagen, M., Daniels, L.D., Kipfmueller, K.F., Speer, J.H. & Anchukaitis, K.J. (2004) Development and application of boundary-line release criteria. Dendrochronologia, 22, 31-42.
Black, B.A., Abrams, M.D., Rentch, J.S. & Gould, P.J. (2009) Properties of boundary-line release criteria in North American tree species. Annals of Forest Science, 66.

See Also

growthAveragingALL, boundaryLineALL, plotRelease, reduceByLB

Examples

data(relData)
rna<-noblabrams(relData1,black=FALSE) # for Nowacki and Abrams 1997
rba<-noblabrams(relData1,black=TRUE) # Black and Abrams 2003

 plotRelease(relData1,rna$change,rna, 1, method="NowackiAbrams",addHLines=c(0.2))
 plotRelease(relData1,rba$change,rba, 1, method="BlackAbrams",addHLines=c(0.2,0.5))

Plot boundary line.

Description

Plot boundary line.

Usage

plotBoundary(boundaries, x, y, boundary, rsq = NULL, 
  criteria = 0.2, criteria2 = 0.5, store = TRUE, storedev = pdf,
  prefix = NULL)

Arguments

Details

Boundary-line method scales the percent growth change of Nowacki & Abrams (1997) according to growth rate prior to disturbance. In their example, Black & Abrams (2003) defined moderate and major releases as those falling within 20-49.9%, and 50-100% of the boundary line, respectively. Advantage of the boundary-line is standardization, which takes into account the relationships among tree age, size, and canopy class determining radial growth rate (Black et al. 2004). On the downside, Black et al. (2009) suggest approximately 50000 ring width measurements is necessary for boundary line determination for a given species (Black et al. 2009).

Value

Plot boundary line and priors.

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

Altman J, Fibich P, Dolezal J & Aakala T (2014) TRADER: a package for Tree Ring Analysis of Disturbance Events in R. Dendrochonologia 32: 107-112.

See Also

boundaryGet, boundaryFit

Examples

data(relData)
bo<-boundaryGet(relData1)
bofit<-boundaryFit(bo$bo,bo$x,bo$y)

plotBoundary(bo$bo,bo$x,bo$y,boundary=bofit$fun,rsq=bofit$rsq)

Plot first years of trees.

Description

Plot first years of trees including option of adding misspiths.

Usage

plotFirstYears(data = NULL, misspith = NULL, store = TRUE, 
  storedev = pdf, prefix=NULL, ...)

Arguments

Details

First year plotting function.

Value

Plot and store number of trees in years.

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

Altman J, Fibich P, Dolezal J & Aakala T (2014) TRADER: a package for Tree Ring Analysis of Disturbance Events in R. Dendrochonologia 32: 107-112.

See Also

plotGrowth

Examples

data(relData)
plotFirstYears(relData1)

plotFirstYears(relData1,relMissPith)

Plot growth of all trees.

Description

Plot growth of all trees and fit polynom for them.

Usage

plotGrowth(data = NULL, polynom = 4, store = TRUE, storedev = pdf, 
            prefix=NULL, ...)

Arguments

Details

Plot function focusing on the trend of the growth of trees.

Value

Plot growth of all trees.

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

Altman J, Fibich P, Dolezal J & Aakala T (2014) TRADER: a package for Tree Ring Analysis of Disturbance Events in R. Dendrochonologia 32: 107-112.

See Also

plotFirstYears

Examples

data(relData)
plotGrowth(relData1)

Plot number of releases.

Description

Barplot number of releases according given criteria.

Usage

plotNORelease(data, inyears, in2years = NULL, criteria, criteria2 = NULL, 
  store = TRUE, storedev = pdf, prefix = NULL)

Arguments

Details

Plot number of releases and return data frame with release statistic.

Value

Return data frame with releases statistic per year.

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

Altman J, Fibich P, Dolezal J & Aakala T (2014) TRADER: a package for Tree Ring Analysis of Disturbance Events in R. Dendrochonologia 32: 107-112.

See Also

plotRelease

Examples

data(relData)

abs<-absIncrease(relData1)
abs.threshold<- absTreshold(abs)
fw <- absoluteIncrease(relData1,abs,abs.threshold)

release_list <- reduceByLB(releases=fw$releases,above=fw$all_releases,type=1)
rs<-writeReleaseStats(release_list,"Total number of releases is")
plotNORelease(relData1,rs, criteria=round(abs.threshold,3) )

Plot releases according the given method.

Description

Plot releases according the given method.

Usage

plotRelease(data, abs, rel, treeno = 1, method = "FraverWhite", 
  type = "l", xlab = NULL, ylab = NULL, main = NULL, 
  col = c("black", "lightblue"), 
  addHLinesCol = c("olivedrab", "red", "darkblue"), 
  addHLines = c(NULL, NULL, NULL), addHLinesText = c("", "", ""), 
  smallcex = 0.85, plotfirst = TRUE, plotpoints = FALSE, 
  store=TRUE, storedev=pdf, prefix=NULL, ...)

Arguments

Details

Complex plotting function of releases.

Value

Plot releases for given tree (treeno).

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

Altman J, Fibich P, Dolezal J & Aakala T (2014) TRADER: a package for Tree Ring Analysis of Disturbance Events in R. Dendrochonologia 32: 107-112.

See Also

absoluteIncreaseALL, growthAveragingALL, boundaryLineALL, splechtnaALL

Examples

data(relData)
rna<-noblabrams(relData1,black=FALSE) # for Nowacki and Abrams 1997
rba<-noblabrams(relData1,black=TRUE) # Black and Abrams 2003

plotRelease(relData1,rna$change,rna, 1, method="NowackiAbrams")
plotRelease(relData1,rba$change,rba, 1, method="BlackAbrams",addHLines=c(0.2,0.5))

Reduce releases by length and buffer.

Description

Reduce peaks of releases according length and buffer.

Usage

reduceByLB(releases, above, buffer = 2, type = 1, length = 2, val = NULL)

Arguments

Details

Check the reference.

Value

Return list of releases reduced by length and buffer.

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

Altman J, Fibich P, Dolezal J & Aakala T (2014) TRADER: a package for Tree Ring Analysis of Disturbance Events in R. Dendrochonologia 32: 107-112.

See Also

growthAveragingALL, boundaryLineALL, splechtnaALL

Examples

data(relData)
rna<-noblabrams(relData1,black=FALSE) # for Nowacki and Abrams 1997

reduceByLB(rna$releases,rna$all_releases)

Release data

Description

Input release data and know boundary lines.

Usage

data(relData)

Format

knownBL data frame with published boundary lines for species and their references.
relData1 example input rwl data (15 trees and 142 years).
relMissPith example of miss piths for relData1.
relData2 big example input rwl data (192 spruce trees and 217 years).

Details

knownBL is just data frame consisting of boundary lines. relData1 and relData2 are subsests of our measurements, not published yet.

Source

Own non published measurements.

References

Altman J, Fibich P, Dolezal J & Aakala T (2014) TRADER: a package for Tree Ring Analysis of Disturbance Events in R. Dendrochonologia 32: 107-112.

Examples

data(relData)

knownBL
plotFirstYears(relData1)

Splechtna et al. 2005 type of releases analysis.

Description

Splechtna is a combination of radial-growth averaging and boundary-line technique.

Usage

splechtna(data, change = NULL, prior = NULL, m1 = 10, m2 = 10, 
  boundary = NULL, buffer = 2, criteria = 0.2, criteria2 = 0.5, 
  segment = 0.5, gfun = mean, length = 2, segment2 = 0.5, 
  notop = 10, notop2 = 10, storedev = pdf, prefix=NULL )

Arguments

Details

Splechtna is a combination of radial-growth averaging and boundary-line technique. This method was developed by Splechtna, Gratzer & Black (2005) and as a potential release accepts only growth pulses exceeding 50% growth change according to Nowacki & Abrams (1997). Only these potential releases were then scaled relative to the boundary line.

Value

Return list object with

Note

Check the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

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

splechtnaALL plotRelease reduceByLB

Examples

data(relData)
rel<-splechtna(relData1)
 plotRelease(relData1,rel$change,rel,1,method="Splechtna") 

Overal function for Splechtna et al. 2005 type of releases analysis.

Description

Splechtna is a combination of radial-growth averaging and boundary-line technique.

Usage

splechtnaALL(data, releases = NULL, m1 = 10, m2 = 10, boundary = NULL, 
  buffer = 2, drawing = TRUE, criteria = 0.2, criteria2 = 0.5, 
  segment = 0.5, segment2 = 0.5, gfun = mean, 
  length = 2, notop = 10, notop2 = 10, storedev = pdf, 
  prefix = NULL, ...)

Arguments

Details

Splechtna is a combination of radial-growth averaging and boundary-line technique. This method was developed by Splechtna, Gratzer & Black (2005) and as a potential release accepts only growth pulses exceeding 50% growth change according to Nowacki & Abrams (1997). Only these potential releases were then scaled relative to the boundary line.

Value

Write many tables and figures in the current directory.

Note

Cehck the reference.

Author(s)

Pavel Fibich <pavel.fibich@prf.jcu.cz>, Jan Altman <altman.jan@gmail.com>, Tuomas Aakala <tuomas.aakala@helsinki.fi>, Jiri Dolezal <jiriddolezal@gmail.com>

References

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

splechtna, doAll

Examples

data(relData)
splechtnaALL(relData1)
 splechtnaALL(relData1,length=3,buffer=4,storedev=pdf,boundary=function(x) {5.0067*exp(-0.664*x)} )