maples {ade4}R Documentation

Phylogeny and quantitative traits of flowers

Description

This data set describes the phylogeny of 17 flowers as reported by Ackerly and Donoghue (1998). It also gives 31 traits corresponding to these 17 species.

Usage

data(maples)

Format

tithonia is a list containing the 2 following objects :

tre
is a character string giving the phylogenetic tree in Newick format.
tab
is a data frame with 17 species and 31 traits

Source

Data were obtained from the URL http://www.stanford.edu/~dackerly/acerdata.html.

References

Ackerly, D. D. and Donoghue, M.J. (1998) Leaf size, sappling allometry, and Corner's rules: phylogeny and correlated evolution in Maples (Acer). American Naturalist, 152, 767–791.

Examples

data(maples)
phy <- newick2phylog(maples$tre)
dom <- maples$tab$Dom
bif <- maples$tab$Bif
orthogram(dom, phylog = phy)
orthogram(bif, phylog = phy)
par(mfrow = c(1,2))
dotchart.phylog(phy, dom)
dotchart.phylog(phy, bif, clabel.nodes = 0.7)
par(mfrow = c(1,1))
plot(bif,dom,pch = 20)
abline(lm(dom~bif))
summary(lm(dom~bif))
if (require(ape, quiet = TRUE)){
cor.test(bif,dom)
phylo <- read.tree(text = maples$tre)
pic.bif <- pic(bif, phylo)
pic.dom <- pic(dom, phylo)
cor.test(pic.bif, pic.dom)}

Worked out examples


> library(ade4)
> ### Name: maples
> ### Title: Phylogeny and quantitative traits of flowers
> ### Aliases: maples
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(maples)
> phy <- newick2phylog(maples$tre)
> dom <- maples$tab$Dom
> bif <- maples$tab$Bif
> orthogram(dom, phylog = phy)
class: krandtest 
Monte-Carlo tests
Call: orthogram(x = dom, phylog = phy)

Test number:   4 
Permutation number:   999 
   Test       Obs   Std.Obs     Alter Pvalue
1 R2Max 0.6643853  8.152702   greater  0.001
2 SkR2k 2.9070512 -4.130821      less  0.001
3  Dmax 0.6494487  5.005252 two-sided  0.001
4   SCE 2.6758582 12.425942   greater  0.001

other elements: NULL
> orthogram(bif, phylog = phy)
class: krandtest 
Monte-Carlo tests
Call: orthogram(x = bif, phylog = phy)

Test number:   4 
Permutation number:   999 
   Test       Obs   Std.Obs     Alter Pvalue
1 R2Max 0.6063608  5.440499   greater  0.003
2 SkR2k 2.9620908 -3.806146      less  0.001
3  Dmax 0.6656148  4.810367 two-sided  0.002
4   SCE 2.5378741  9.627105   greater  0.001

other elements: NULL
> par(mfrow = c(1,2))
> dotchart.phylog(phy, dom)
> dotchart.phylog(phy, bif, clabel.nodes = 0.7)
> par(mfrow = c(1,1))
> plot(bif,dom,pch = 20)
> abline(lm(dom~bif))
> summary(lm(dom~bif))

Call:
lm(formula = dom ~ bif)

Residuals:
     Min       1Q   Median       3Q      Max 
-0.14842 -0.06725  0.00496  0.07620  0.11130 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)    
(Intercept)  1.259967   0.105927  11.895 4.88e-09 ***
bif         -0.008654   0.001699  -5.093 0.000132 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

Residual standard error: 0.08404 on 15 degrees of freedom
Multiple R-squared: 0.6336,	Adjusted R-squared: 0.6091 
F-statistic: 25.94 on 1 and 15 DF,  p-value: 0.0001324 

> if (require(ape, quiet = TRUE)){
+ cor.test(bif,dom)
+ phylo <- read.tree(text = maples$tre)
+ pic.bif <- pic(bif, phylo)
+ pic.dom <- pic(dom, phylo)
+ cor.test(pic.bif, pic.dom)}

	Pearson's product-moment correlation

data:  pic.bif and pic.dom 
t = -1.5823, df = 14, p-value = 0.1359
alternative hypothesis: true correlation is not equal to 0 
95 percent confidence interval:
 -0.7419510  0.1316186 
sample estimates:
       cor 
-0.3894993 

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[Package ade4 Index]