[R] ace error because of missings?

Birgitle birgit.lemcke at systbot.uzh.ch
Thu Jul 10 17:21:37 CEST 2008


Hello RUser!

I try to use ace for an ancestral state reconstruction but got back an error
message.

     ace(FacVar,Tree, type="discrete")

Warning messages:
1: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE)
:
  NA/Inf durch größte positive Zahl ersetzt     (NA/Inf replaced by positive
number)
2: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE)
:
  NA/Inf durch größte positive Zahl ersetzt
3: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE)
:
  NA/Inf durch größte positive Zahl ersetzt
4: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE)
:
  NA/Inf durch größte positive Zahl ersetzt
5: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE)
:
  NA/Inf durch größte positive Zahl ersetzt
6: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE)
:
  NA/Inf durch größte positive Zahl ersetzt
7: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE)
:
  NA/Inf durch größte positive Zahl ersetzt
8: In nlm(function(p) dev(p), p = rep(ip, length.out = np), hessian = TRUE)
:
  NA/Inf durch größte positive Zahl ersetzt
9: In ace(SummaCharNAavoidOpt7$Spik_orient_Anth_Diff,
RestioTreeOoutgrBLrooted,  :
  The likelihood gradient seems flat in at least one dimension (gradient
null):
cannot compute the standard-errors of the transition rates.

I presume it is due to my missing values?

     na.pattern(dataframe)
    #dataframe contains 7 discrete characters. I get an error message with
all of them

pattern
0000000 0000001 0000100 0010000 0100000 1000000 1001000 1100100 1111111 
    274               5            1           3            7            2           
1            1            4 

Can I fix this somehow?

Thanks in advance

Birgit



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