TRADER-package: Tree Ring Analysis of Disturbance Events in R

Description Details Author(s) References See Also Examples

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

Package: TRADER
Type: Package
Version: 1.2-3
Date: 2017-01-13
License: GPL-2 | GPL-3

library(TRADER)

Author(s)

Pavel Fibich <[email protected]>, Jan Altman <[email protected]>, Tuomas Aakala <[email protected]>, Jiri Dolezal <[email protected]>

Maintainer: Pavel Fibich <[email protected]>

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

 1
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 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
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

Example output

png 
  2 
[1] "## Fraver & White analysis!"
[1] "Absolute threshold  1.2 m1 10 m2 10 Buffer 4 Length 3"
[1] "Total number of releases is 16"
inyears
1895 1896 1904 1935 1936 1938 1939 1944 1978 
   1    3    1    4    1    2    1    1    2 
[1] "## Nowacki & Abrams analysis!"
[1] "Criteria 0.25 Criteria2 0.5 m1 10 m2 10 Buffer 4 Length 3"
[1] "Total number of releases >= 0.25 & < 0.5 is 6"
inyears
1888 1920 1935 1936 1978 1980 
   1    1    1    1    1    1 
[1] "Total number of releases >= 0.5 is 22"
inyears
1895 1896 1903 1927 1935 1936 1938 1942 1947 1978 1986 1993 
   1    3    1    1    4    4    2    1    1    2    1    1 
[1] "## Black & Abrams analysis!"
[1] "Criteria 0.2 Criteria2 0.5 m1 10 m2 10 Buffer 2 Length 2 Segment 0.5 Segment2 0.5"
[1] "Total number of releases >= 0.2 & < 0.5 is 14"
inyears
1888 1899 1935 1936 1938 1940 1947 1978 1980 1984 1986 
   1    1    1    2    3    1    1    1    1    1    1 
[1] "Total number of releases >= 0.5 is 25"
inyears
1893 1894 1895 1896 1899 1903 1907 1935 1936 1938 1939 1940 1941 1942 1978 
   1    1    1    3    1    1    1    6    2    2    1    1    1    1    2 
[1] "## Splechtna analysis!"
[1] "Criteria 0.2 Criteria2 0.5 m1 10 m2 10 Buffer 4 Length 3 Segment 0.5 Segment2 0.5"
[1] "Total number of releases >= 0.2 & < 0.5 is 16"
inyears
1896 1927 1935 1936 1938 1942 1947 1978 1986 1993 
   1    1    4    3    1    1    1    2    1    1 
[1] "Total number of releases >= 0.5 is 9"
inyears
1896 1935 1936 1942 1978 
   1    3    2    1    2 
[1] "## Fraver & White analysis!"
[1] "Absolute threshold  1.2 m1 10 m2 10 Buffer 4 Length 3"
[1] "Total number of releases is 16"
inyears
1895 1896 1904 1935 1936 1938 1939 1944 1978 
   1    3    1    4    1    2    1    1    2 
[1] "## Nowacki & Abrams analysis!"
[1] "Criteria 0.25 Criteria2 0.5 m1 10 m2 10 Buffer 4 Length 3"
[1] "Total number of releases >= 0.25 & < 0.5 is 6"
inyears
1888 1920 1935 1936 1978 1980 
   1    1    1    1    1    1 
[1] "Total number of releases >= 0.5 is 22"
inyears
1895 1896 1903 1927 1935 1936 1938 1942 1947 1978 1986 1993 
   1    3    1    1    4    4    2    1    1    2    1    1 
[1] "## Black & Abrams analysis!"
[1] "Criteria 0.2 Criteria2 0.5 m1 10 m2 10 Buffer 4 Length 3 Segment 0.5 Segment2 0.5"
[1] "--Summary of y=a+bx fit."

Call:
lm(formula = tops ~ segments, data = boundaries)

Residuals:
      1       2       3       4       5       6       7 
-2.1637  1.7473  1.3473 -0.1650 -0.1749 -0.2988 -0.2922 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)  
(Intercept)   2.6631     1.0656   2.499   0.0545 .
segments     -0.7266     0.5287  -1.374   0.2277  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.399 on 5 degrees of freedom
Multiple R-squared:  0.2742,	Adjusted R-squared:  0.129 
F-statistic: 1.889 on 1 and 5 DF,  p-value: 0.2277

[1] "--Summary of y=a+bx+cx^2 fit."

Call:
lm(formula = tops ~ segments + I(segments^2), data = boundaries)

Residuals:
      1       2       3       4       5       6       7 
-1.2627  1.7473  0.8067 -0.8858 -0.7155 -0.2988  0.6088 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)
(Intercept)     1.1766     1.5661   0.751    0.494
segments        1.7961     2.0898   0.859    0.439
I(segments^2)  -0.7208     0.5796  -1.244    0.282

Residual standard error: 1.328 on 4 degrees of freedom
Multiple R-squared:  0.4765,	Adjusted R-squared:  0.2148 
F-statistic: 1.821 on 2 and 4 DF,  p-value: 0.274

[1] "--Summary of y=ae^bx fit."

Formula: tops ~ a * exp(b * segments)

Parameters:
  Estimate Std. Error t value Pr(>|t|)
a   2.4721     1.4860   1.664    0.157
b  -0.3441     0.4231  -0.813    0.453

Residual standard error: 1.48 on 5 degrees of freedom

Number of iterations to convergence: 19 
Achieved convergence tolerance: 7.85e-06

[1] "y=c+ae^bx nls error: step factor 0.000488281 reduced below 'minFactor' of 0.000976562"
[1] "y=c+dx+ae^bx nls error: singular gradient"
[1] "y=ae^bx+ce^dx nls error: Missing value or an infinity produced when evaluating the model"
[1] "--Summary of y=a+blog(x) fit."

Formula: tops ~ a + b * log(segments)

Parameters:
  Estimate Std. Error t value Pr(>|t|)  
a   1.5195     0.6389   2.378   0.0633 .
b  -0.4241     0.7248  -0.585   0.5839  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.588 on 5 degrees of freedom

Number of iterations to convergence: 1 
Achieved convergence tolerance: 8.688e-09

[1] "--Summary of y=a+bx+clog(x)+dxlog(x) fit."

Call:
lm(formula = tops ~ segments + log(segments) + segments:log(segments), 
    data = boundaries)

Residuals:
        1         2         3         4         5         6         7 
-0.007628  0.001627  0.189574 -0.418157  0.170181  0.193449 -0.129045 

Coefficients:
                       Estimate Std. Error t value Pr(>|t|)   
(Intercept)              30.061      4.285   7.016  0.00595 **
segments                -26.547      4.156  -6.388  0.00777 **
log(segments)            14.067      1.957   7.189  0.00555 **
segments:log(segments)   10.384      1.852   5.606  0.01121 * 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.313 on 3 degrees of freedom
Multiple R-squared:  0.9782,	Adjusted R-squared:  0.9564 
F-statistic: 44.86 on 3 and 3 DF,  p-value: 0.005431

[1] "The fitted boundary line summary!"
[1] "Logarithmic model y=a+bx+clog(x)+dxlog(x) was the best!"

Call:
lm(formula = tops ~ segments + log(segments) + segments:log(segments), 
    data = boundaries)

Residuals:
        1         2         3         4         5         6         7 
-0.007628  0.001627  0.189574 -0.418157  0.170181  0.193449 -0.129045 

Coefficients:
                       Estimate Std. Error t value Pr(>|t|)   
(Intercept)              30.061      4.285   7.016  0.00595 **
segments                -26.547      4.156  -6.388  0.00777 **
log(segments)            14.067      1.957   7.189  0.00555 **
segments:log(segments)   10.384      1.852   5.606  0.01121 * 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.313 on 3 degrees of freedom
Multiple R-squared:  0.9782,	Adjusted R-squared:  0.9564 
F-statistic: 44.86 on 3 and 3 DF,  p-value: 0.005431

[1] "Total number of releases >= 0.2 & < 0.5 is 13"
inyears
1888 1897 1899 1934 1935 1938 1944 1947 1967 
   1    1    2    1    3    2    1    1    1 
[1] "Total number of releases >= 0.5 is 23"
inyears
1893 1896 1899 1903 1910 1935 1938 1939 1940 1941 1942 1943 1944 1978 1982 
   2    2    1    2    1    4    1    2    1    1    1    1    1    2    1 
[1] "## Splechtna analysis!"
[1] "Criteria 0.2 Criteria2 0.5 m1 10 m2 10 Buffer 4 Length 3 Segment 0.5 Segment2 0.5"
[1] "--Summary of y=a+bx fit."

Call:
lm(formula = tops ~ segments, data = boundaries)

Residuals:
      1       2       3       4       5       6       7 
-2.1637  1.7473  1.3473 -0.1650 -0.1749 -0.2988 -0.2922 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)  
(Intercept)   2.6631     1.0656   2.499   0.0545 .
segments     -0.7266     0.5287  -1.374   0.2277  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.399 on 5 degrees of freedom
Multiple R-squared:  0.2742,	Adjusted R-squared:  0.129 
F-statistic: 1.889 on 1 and 5 DF,  p-value: 0.2277

[1] "--Summary of y=a+bx+cx^2 fit."

Call:
lm(formula = tops ~ segments + I(segments^2), data = boundaries)

Residuals:
      1       2       3       4       5       6       7 
-1.2627  1.7473  0.8067 -0.8858 -0.7155 -0.2988  0.6088 

Coefficients:
              Estimate Std. Error t value Pr(>|t|)
(Intercept)     1.1766     1.5661   0.751    0.494
segments        1.7961     2.0898   0.859    0.439
I(segments^2)  -0.7208     0.5796  -1.244    0.282

Residual standard error: 1.328 on 4 degrees of freedom
Multiple R-squared:  0.4765,	Adjusted R-squared:  0.2148 
F-statistic: 1.821 on 2 and 4 DF,  p-value: 0.274

[1] "--Summary of y=ae^bx fit."

Formula: tops ~ a * exp(b * segments)

Parameters:
  Estimate Std. Error t value Pr(>|t|)
a   2.4721     1.4860   1.664    0.157
b  -0.3441     0.4231  -0.813    0.453

Residual standard error: 1.48 on 5 degrees of freedom

Number of iterations to convergence: 19 
Achieved convergence tolerance: 7.85e-06

[1] "y=c+ae^bx nls error: step factor 0.000488281 reduced below 'minFactor' of 0.000976562"
[1] "y=c+dx+ae^bx nls error: singular gradient"
[1] "y=ae^bx+ce^dx nls error: Missing value or an infinity produced when evaluating the model"
[1] "--Summary of y=a+blog(x) fit."

Formula: tops ~ a + b * log(segments)

Parameters:
  Estimate Std. Error t value Pr(>|t|)  
a   1.5195     0.6389   2.378   0.0633 .
b  -0.4241     0.7248  -0.585   0.5839  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.588 on 5 degrees of freedom

Number of iterations to convergence: 1 
Achieved convergence tolerance: 8.688e-09

[1] "--Summary of y=a+bx+clog(x)+dxlog(x) fit."

Call:
lm(formula = tops ~ segments + log(segments) + segments:log(segments), 
    data = boundaries)

Residuals:
        1         2         3         4         5         6         7 
-0.007628  0.001627  0.189574 -0.418157  0.170181  0.193449 -0.129045 

Coefficients:
                       Estimate Std. Error t value Pr(>|t|)   
(Intercept)              30.061      4.285   7.016  0.00595 **
segments                -26.547      4.156  -6.388  0.00777 **
log(segments)            14.067      1.957   7.189  0.00555 **
segments:log(segments)   10.384      1.852   5.606  0.01121 * 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.313 on 3 degrees of freedom
Multiple R-squared:  0.9782,	Adjusted R-squared:  0.9564 
F-statistic: 44.86 on 3 and 3 DF,  p-value: 0.005431

[1] "The fitted boundary line summary!"
[1] "Logarithmic model y=a+bx+clog(x)+dxlog(x) was the best!"

Call:
lm(formula = tops ~ segments + log(segments) + segments:log(segments), 
    data = boundaries)

Residuals:
        1         2         3         4         5         6         7 
-0.007628  0.001627  0.189574 -0.418157  0.170181  0.193449 -0.129045 

Coefficients:
                       Estimate Std. Error t value Pr(>|t|)   
(Intercept)              30.061      4.285   7.016  0.00595 **
segments                -26.547      4.156  -6.388  0.00777 **
log(segments)            14.067      1.957   7.189  0.00555 **
segments:log(segments)   10.384      1.852   5.606  0.01121 * 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.313 on 3 degrees of freedom
Multiple R-squared:  0.9782,	Adjusted R-squared:  0.9564 
F-statistic: 44.86 on 3 and 3 DF,  p-value: 0.005431

[1] "Total number of releases >= 0.2 & < 0.5 is 16"
inyears
1896 1927 1935 1936 1938 1941 1942 1978 1991 1993 
   1    1    4    3    1    1    1    2    1    1 
[1] "Total number of releases >= 0.5 is 9"
inyears
1896 1935 1936 1942 1947 1978 
   1    3    1    1    1    2 
                 Species Number.of.tree.rings
1             Abies alba              132 544
2             Abies alba               33 549
3  Betula alleghaniensis                4 491
4        Fagus sylvatica               94 649
5        Fagus sylvatica               53 324
6        Fagus sylvatica               80 539
7        Fagus sylvatica               19 833
8        Fagus sylvatica               20 670
9          Larix decidua                3 830
10           Picea abies              147 949
11           Picea abies                8 194
12           Picea abies              unknown
13           Picea abies              unknown
14          Picea glauca              102 306
15         Picea mariana               49 007
16        Pinus echinata               74 925
17       Pinus palustris               32 970
18       Pinus ponderosa              157 243
19         Pinus strobus               72 714
20 Pseudotsuga menziesii              172 372
21          Quercus alba              164 867
22    Quercus macrocarpa               92 092
23     Quercus mongolica               30 377
24       Quercus petraea               45 755
25        Quercus prinus               35 337
26      Quercus stellata              169 333
27      Tsuga canadensis              180 708
                               Boundary.line.equation
1           y = 131.8 + 1012.6exp(-1.603x) - 16.8078x
2        y = 266.138 + 2827.365exp(-3.259x) - 44.963x
3                               y = 1257.7exp(-1.16x)
4  y = 2801.0799exp(-5.4058x) + 488.6093exp(-0.7466x)
5          y = 10.089exp(-1.289x) + 1.959exp(-0.336x)
6          y = 18.040exp(-4.112x) + 4.797exp(-0.454x)
7                  y = 45.9429 + exp(7.58466-2.4772x)
8          y = 2242.78exp(-5.06x) + 418.24exp(-0.88x)
9                            Y = 204.78 - 153.16ln(x)
10 y = 130.8732 + 1399.4031exp(-2.4804x)  - 17.2694x 
11                           Y = 338.83 - 257.15ln(x)
12                            x = 530.69exp(-1.4626y)
13                            x = 308.49exp(-0.7713y)
14                            y = 649.97exp(-1.0798x)
15                            y = 407.92exp(-1.4679x)
16                            y = 998.65exp(-1.0237x)
17                            y = 1728.5exp(-0.9735x)
18                            y = 655.97exp(-0.9354x)
19                             y = 501.96exp(-0.664x0
20                             y = 569.80exp(-0.928x)
21                             y = 527.22exp(-0.787x)
22                            y = 511.27exp(-0.7018x)
23                              y = 195.73-153.9ln(x)
24                             y = 5.0067exp(-0.664x)
25                            y = 742.83exp(-0.9445x)
26                            y = 948.45exp(-1.6188x)
27                            y = 974.54exp(-1.1202x)
                                Source
1   (Splechtna,  Gratzer & Black 2005)
2       (Nagel,  Levanic & Diaci 2007)
3              (Webster & Jensen 2007)
4   (Splechtna,  Gratzer & Black 2005)
5                  (Ziaco et al. 2012)
6                  (Ziaco et al. 2012)
7                (Samonil et al. 2009)
8   (Trotsiuk,  Hobi & Commarmot 2012)
9               (Zielonka et al. 2010)
10  (Splechtna,  Gratzer & Black 2005)
11              (Zielonka et al. 2010)
12 (Szewczyk,  Szwagrzyk & Muter 2011)
13 (Szewczyk,  Szwagrzyk & Muter 2011)
14                 (Black et al. 2009)
15                 (Black et al. 2009)
16                 (Black et al. 2004)
17                 (Bhuta et al. 2008)
18                 (Black et al. 2004)
19               (Black & Abrams 2003)
20                 (Black et al. 2009)
21                 (Black et al. 2004)
22                 (Black et al. 2004)
23               (Altman et al. 2013a)
24               (Altman et al. 2013b)
25               (Black & Abrams 2003)
26                 (Black et al. 2009)
27               (Black & Abrams 2003)

TRADER documentation built on May 29, 2017, 11:20 p.m.