plotRelease: Plot releases according the given method.

In TRADER: Tree Ring Analysis of Disturbance Events in R

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, ...)

Arguments

data	A data.frame with series as columns and years as rows such as that produced by read.* function of dplR .
abs	Data frame with absolute increases.
rel	Data frame with releases.
treeno	Number of tree to plot.
method	Which method was used for releases.
type	type of plots (parameter type for plot).
xlab	Label of x-axis.
ylab	Label of y-axis.
main	Title of the figure.
col	List of colors for curves.
addHLinesCol	List of colors for horizontal lines.
addHLines	List values for horizontal lines.
addHLinesText	List texts for horizontal lines.
smallcex	cex for text.
plotfirst	If to plot first year of growth.
plotpoints	If to plot points on the top of releases.
...

Details

Complex plotting function of releases.

Value

Plot releases for given tree (treeno).

Note

Check the reference.

Author(s)

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

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))

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
[1] "## Nowacki & Abrams analysis!"
[1] "Criteria 0.25 Criteria2 0.5 m1 10 m2 10 Buffer 2 Length 2"
[1] "Total number of releases >= 0.25 & < 0.5 is 13"
inyears
1888 1899 1920 1936 1938 1971 1978 1979 1980 1986 1995 
   1    1    1    1    2    1    1    1    2    1    1 
[1] "Total number of releases >= 0.5 is 30"
inyears
1895 1896 1899 1903 1927 1935 1936 1938 1939 1942 1947 1978 1984 1986 1988 1990 
   1    3    1    1    1    5    5    3    1    1    1    2    1    1    1    1 
1993 
   1 
[1] "## Black & Abrams analysis!"
[1] "Criteria 0.25 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 >= 0.25 & < 0.5 is 14"
inyears
1888 1897 1899 1934 1935 1938 1941 1944 1967 1969 
   1    1    2    1    2    2    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 

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