[R] computationally singular and lack of variance parameters in SEM
Elizabeth Pringle
epringle at stanford.edu
Sat May 2 00:59:18 CEST 2009
Hi all,
I am trying to set up a simple path analysis in the SEM package, but I am
having some trouble. I keep getting the following error message or
something similar with my model, and I'm not sure what I'm doing wrong:
Error in solve.default(C) :
system is computationally singular: reciprocal condition number =
2.2449e-20
In addition: Warning message:
In sem.default(ram = ram, S = S, N = N, param.names = pars, var.names =
vars, :
The following variables have no variance or error-variance parameter
(double-headed arrow):
Ants, Herbivory
The model is almost surely misspecified; check also for missing covariances.
I have tried my data set with both a correlation (cor) and a variance (var)
matrix, but both produce the same error, and I'm not sure which one is
correct. The error message about the variables that have no variance or
error-variance parameters are for my exogenous variables (or those that I am
not listing as "fixed.x=" in the model). I have tried both single and
double arrows between ants and coccoids, but neither works. I am not sure
that I know what it means for the system to be computationally singular
(sometimes it says it is exactly singular). I am setting N=80 because I
have four observed variables with 20 observations each, I hope this is
correct. I have attached the path diagram for my model as a jpeg.
My R code is the following:
data<-read.table("ChamelaColonySize.csv",header=TRUE,sep=",")
attach(data)
cor(data,method="spearman")
CorMatrix<-matrix(c(
+ 1, 0, 0, 0,
+ -0.4974, 1, 0, 0,
+ -0.4403, 0.7965, 1, 0,
+ 0.1250, 0.2602, 0.1825, 1),ncol=4,byrow=T)
rownames(CorMatrix)<-colnames(CorMatrix)<-c('Herbivory','Ants','Coccoids',
'Space')
ramcor<-specify.model()
Coccoids<->Ants, gam12, NA
Space->Ants, gam12, NA
Ants->Herbivory,bet21, NA
?read.table
sem<-sem(ram=ramcor,S=CorMatrix,N=80,fixed.x=c('Coccoids','Space'))
var(data)
VarMatrix<-matrix(c(
+ 0.73, 0, 0, 0,
+ -86.11, 35877.52, 0, 0,
+ -23.46, 11569.9, 5620.26, 0,
+ 0.82, 346.83, 138.21, 34.81),ncol=4,byrow=T)
semVar<-sem(ram=ramcor,S=VarMatrix,N=80,fixed.x=c('Coccoids','Space'))
Many thanks for any help.
Beth
--
****************************************************
Elizabeth G. Pringle
Department of Biology
Stanford University
Stanford, CA 94305
(Tel): 650-725-6791
(Fax): 650-462-5968
****************************************************
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