Hi,
I tried to calculate a delta statistic and I got this message:
Error in ace(trait, tree, type = "discret", method = "ML", model = "ARD") :
object "phy" is not of class "phylo"
So I suppose that there is problem with the tree format but I could not identify the problem (I am starting with R). Could you help me?
SUB_TREEnewick.pdf
I have a second question:
I would like to run the analysis with k = 9, but looking at the R code I suppose that it is restricted for k = 2 to 5, right? I wonder if I add the text herebelow in the code whether it might work?
if(k==9){,,,,,,,,
pi[1]*0,pi[2]*rho[1],pi[3]*rho[2],pi[4]*rho[3],pi[5]*rho[4],pi[6]*rho[5],pi[7]*rho[6],pi[8]*rho[7],pi[9]*rho[8]
pi[1]*rho[1],pi[2]*0,pi[3]*rho[9],pi[4]*rho[10],pi[5]*rho[11],pi[6]*rho[12],pi[7]*rho[13],pi[8]*rho[14],pi[9]*rho[15]
pi[1]*rho[2],pi[2]*rho[9],pi[3]*0,pi[4]*rho[16],pi[5]*rho[17],pi[6]*rho[18],pi[7]*rho[19],pi[8]*rho[20],pi[9]*rho[21]
pi[1]*rho[3],pi[2]*rho[10],pi[3]*rho[16],pi[4]*0,pi[5]*rho[22],pi[6]*rho[23],pi[7]*rho[24],pi[8]*rho[25],pi[9]*rho[26]
pi[1]*rho[4],pi[2]*rho[11],pi[3]*rho[17],pi[4]*rho[22],pi[5]*0,pi[6]*rho[27],pi[7]*rho[28],pi[8]*rho[29],pi[9]*rho[30]
pi[1]*rho[5],pi[2]*rho[12],pi[3]*rho[18],pi[4]*rho[23],pi[5]*rho[27],pi[6]*0,pi[7]*rho[31],pi[8]*rho[32],pi[9]*rho[33]
pi[1]*rho[6],pi[2]*rho[13],pi[3]*rho[19],pi[4]*rho[24],pi[5]*rho[28],pi[6]*rho[31],pi[7]*0,pi[8]*rho[34],pi[9]*rho[35]
pi[1]*rho[7],pi[2]*rho[14],pi[3]*rho[20],pi[4]*rho[25],pi[5]*rho[29],pi[6]*rho[32],pi[7]*rho[34],pi[8]*0,pi[9]*rho[36]
pi[1]*rho[8],pi[2]*rho[15],pi[3]*rho[21],pi[4]*rho[26],pi[5]*rho[30],pi[6]*rho[33],pi[7]*rho[35],pi[8]*rho[36],pi[9]*0)
with best regards
Fabienne Van Rossum
Hi,
I tried to calculate a delta statistic and I got this message:
Error in ace(trait, tree, type = "discret", method = "ML", model = "ARD") :
object "phy" is not of class "phylo"
So I suppose that there is problem with the tree format but I could not identify the problem (I am starting with R). Could you help me?
SUB_TREEnewick.pdf
I have a second question:
I would like to run the analysis with k = 9, but looking at the R code I suppose that it is restricted for k = 2 to 5, right? I wonder if I add the text herebelow in the code whether it might work?
if(k==9){,,,,,,,,
pi[1]*0,pi[2]*rho[1],pi[3]*rho[2],pi[4]*rho[3],pi[5]*rho[4],pi[6]*rho[5],pi[7]*rho[6],pi[8]*rho[7],pi[9]*rho[8]
pi[1]*rho[1],pi[2]*0,pi[3]*rho[9],pi[4]*rho[10],pi[5]*rho[11],pi[6]*rho[12],pi[7]*rho[13],pi[8]*rho[14],pi[9]*rho[15]
pi[1]*rho[2],pi[2]*rho[9],pi[3]*0,pi[4]*rho[16],pi[5]*rho[17],pi[6]*rho[18],pi[7]*rho[19],pi[8]*rho[20],pi[9]*rho[21]
pi[1]*rho[3],pi[2]*rho[10],pi[3]*rho[16],pi[4]*0,pi[5]*rho[22],pi[6]*rho[23],pi[7]*rho[24],pi[8]*rho[25],pi[9]*rho[26]
pi[1]*rho[4],pi[2]*rho[11],pi[3]*rho[17],pi[4]*rho[22],pi[5]*0,pi[6]*rho[27],pi[7]*rho[28],pi[8]*rho[29],pi[9]*rho[30]
pi[1]*rho[5],pi[2]*rho[12],pi[3]*rho[18],pi[4]*rho[23],pi[5]*rho[27],pi[6]*0,pi[7]*rho[31],pi[8]*rho[32],pi[9]*rho[33]
pi[1]*rho[6],pi[2]*rho[13],pi[3]*rho[19],pi[4]*rho[24],pi[5]*rho[28],pi[6]*rho[31],pi[7]*0,pi[8]*rho[34],pi[9]*rho[35]
pi[1]*rho[7],pi[2]*rho[14],pi[3]*rho[20],pi[4]*rho[25],pi[5]*rho[29],pi[6]*rho[32],pi[7]*rho[34],pi[8]*0,pi[9]*rho[36]
pi[1]*rho[8],pi[2]*rho[15],pi[3]*rho[21],pi[4]*rho[26],pi[5]*rho[30],pi[6]*rho[33],pi[7]*rho[35],pi[8]*rho[36],pi[9]*0)
with best regards
Fabienne Van Rossum