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 ======================= [[alternative HTML version deleted]]
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