To fit the brownian motion for independent evolution of traits i used below code:

rownames(carni)<-gsub("_",".",rownames(carni))  #Renaming to match the tip of tree
#Independent Evolution
brown_indepen <- mvBM(carni_tree,carni,param=list(constraint="diagonal"))

mvBM is the function from mvMORPH package. It seems by giving constraint="diagonal" would fit the model for traits to be evolved independently. I would like to know the idea behind it. Also, i got the below output after running the code. I would also like to know what below output means.

LogLikelihood:   -589.2373 
AIC:     1186.475 
AICc:    1186.771 
4 parameters 

Estimated rate matrix 
      size    range
size  73.70335  0.00000
range  0.00000 13.54524

Estimated root state 
       size    range
theta: 38.43947 13.78439

Size and range were the two traits.

  • 1
    $\begingroup$ This seems appropriate for the biology forum, but consider posting/migrating to statistics or bioinformatics--they may be more familiar with mvMORPH $\endgroup$ – julianstanley Dec 6 '18 at 3:42

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