Dear R experts,

I hope this is the right list for my question.

As a newcomer in R, I am testing the R CAPER package, applying a simple
regression on a phylogeny tree with three binary traits: (t1, t2, t3).

My goal is to test the sensitivity to a correlation between t1 and t3. But
if a correlation of 100% is considered (i.e. t3 = t1). The pgls method of
CAPER seems to crash:

You can find there the code I used
http://iktp.tu-dresden.de/~prudent/Divers/R/toy.R
with the tree
http://iktp.tu-dresden.de/~prudent/Divers/R/toy3.tree
and the data
http://iktp.tu-dresden.de/~prudent/Divers/R/toy_cor100.data

just copy the .tree and .data files and run
> R
> source("toy.R")

(please find the outpt below)

Am I doing anything wrong?

Thanks in advance,

regards,

Xavier Prudent

==================================
>>>>>>> Regression #2


Call:
pgls(formula = t1 ~ t3, data = cdat)

Coefficients:
(Intercept)           t3
          0            1


Call:
pgls(formula = t1 ~ t3, data = cdat)

Residuals:
   Min     1Q Median     3Q    Max
     0      0      0      0      0

Branch length transformations:

kappa  [Fix]  : 1.000
lambda [Fix]  : 1.000
delta  [Fix]  : 1.000

Coefficients:
            Estimate Std. Error t value  Pr(>|t|)
(Intercept)        0          0      NA        NA
t3                 1          0     Inf < 2.2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0 on 8 degrees of freedom
Multiple R-squared:     1,      Adjusted R-squared:     1
F-statistic:   Inf on 2 and 8 DF,  p-value: < 2.2e-16
Error in density.default(res) : 'x' contains missing values
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