boundaryLineALL: Overal function for Black and Abrams 2003 method or "pure...

In TRADER: Tree Ring Analysis of Disturbance Events in R

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, prefix = "bl", drawing = TRUE, gfun = mean, 
  length = 2, notop = 10, notop2 = 10, storedev = pdf, ...)

Arguments

data	A data.frame with series as columns and years as rows such as that produced by read.* function of dplR .
releases	Optional parameter usable for precomputed releases.
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.
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.
criteria	Threshold for detection of moderate release
criteria2	Threshold for detection of major release.
segment	Determines length of the segment on which prior growth will be divided
segment2	Determines length of the segment on which first mm of prior growth will be divided.
prefix	Prefix of saved files.
drawing	If TRUE, graphical outputs for individual trees.
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.
...

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

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)} )

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
[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] "--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
1888 1897 1899 1934 1935 1938 1941 1944 1967 1969 
   1    1    2    1    2    4    2    1    1    1 
[1] "Total number of releases >= 0.5 is 37"
inyears
1890 1893 1895 1896 1899 1903 1910 1935 1936 1938 1939 1940 1941 1942 1943 1944 
   1    3    1    3    2    2    1    6    1    3    2    1    2    1    1    2 
1947 1978 1980 1982 
   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] "Total number of releases >= 0.2 & < 0.5 is 9"
inyears
1888 1896 1935 1936 1938 1940 1947 1986 
   1    1    1    2    1    1    1    1 
[1] "Total number of releases >= 0.5 is 17"
inyears
1895 1896 1903 1907 1935 1938 1939 1940 1942 1978 
   1    2    1    1    6    1    1    1    1    2 

TRADER documentation built on May 2, 2019, 9:02 a.m.