It looks to me like Ken is correct.

I you read the help page for specify.model(), it says that when no input file is specified (as here), then input comes from the "standard input stream" (i.e., the keyboard) and is terminated by a blank line.

There is no blank line after input line #37

36: sodium <-> sodium, th16, NA
37: satfat <-> satfat, th17, NA
38: sem.model.KerryQ3 <- sem(model.KerryQ3, KerryQ3cov, 2123)
38: summary (sem.model.KerryQ3)


David, did you really type in all those lines of the form
   f1 ->
   f2 ->
and so on???

I'd have at least put them in a file, and then given the file name to specify.model() !

-Don

At 7:19 AM +1000 5/16/08, Ken Beath wrote:
Hi,

The problem is that specify.model() is not terminating its input and so is reading R commands, see line 38. I have only looked at sem, but maybe a blank line will work.

Ken

On 16/05/2008, at 6:15 AM, David Kaplan wrote:

Hi all,

I was asked to provide a bit more information. Here is the output to the problem. Note that I changed the data format to tab-delimited and also used read.table, but to no avail. The problem is exactly the same when I use .csv data and read.csv. The program I'm using is John Fox's SEM program within R for Mac. The 2123 is the sample size and there are no missing data values, or any other peculiarities as far as I can see. The data are clean.



 ## CFA for Kerry Data Set, Question 3
 ## load the sem package

 KerryQ3 <- read.table("~/Desktop/KerryQ3a.txt", header=TRUE)
 KerryQ3cov <- cov(KerryQ3)
 model.KerryQ3 <- specify.model()
1: f1 -> calcm, lam11, NA
2: f1 -> phytoc, lam21, NA    3: f1 -> soypro, lam31, NA
4: f1 -> antiox, lam41, NA
5: f1 -> fiber, lam51, NA
6: f1 -> vitmin, lam61, NA
7: f1 -> protn, lam71, NA
8: f1 -> monoft, lam81, NA
9: f1 -> omega3, lam91, NA
10: f2 -> chol, lam102, NA
11: f2 -> fat, lam112, NA
12: f2 -> sugar, lam122, NA
13: f2 -> calor, lam132, NA
14: f2 -> recarb, lam142, NA
15: f2 -> trnsft, lam152, NA
16: f2 -> sodium, lam162, NA
17: f2 -> satfat, lam172, NA
18: f1 <-> f1, NA, 1
19: f2 <-> f2, NA, 1
20: f1 <-> f2, ph21, NA
21: calcm <-> calcm, th1, NA
22: phytoc <-> phytoc, th2, NA
23: soypro <-> soypro, th3, NA
24: antiox <-> antiox, th4, NA
25: fiber <-> fiber, th5, NA
26: vitmin <-> vitmin, th6, NA
27: protn <-> protn, th7, NA
28: monoft <-> monoft, th8, NA
29: omega3 <-> omega3, th9, NA
30: chol <-> chol, th10, NA
31: fat <-> fat, th11, NA
32: sugar <-> sugar, th12, NA
33: calor <-> calor, th13, NA
34: recarb <-> recarb, th14, NA
35: trnsft <-> trnsft, th15, NA
36: sodium <-> sodium, th16, NA
37: satfat <-> satfat, th17, NA
38: sem.model.KerryQ3 <- sem(model.KerryQ3, KerryQ3cov, 2123)
38: summary (sem.model.KerryQ3)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
scan() expected 'a real', got '2123)'
 std.KerryQ3 <- standardized.coefficients(sem.model.KerryQ3)
Error in standardized.coefficients(sem.model.KerryQ3) :
object "sem.model.KerryQ3" not found


--
===============================================================
David Kaplan, Ph.D.
Professor
Department of Educational Psychology
University of Wisconsin - Madison
Educational Sciences, Room, 1061
1025 W. Johnson Street
Madison, WI 53706

email: dkaplan at education dot wisc dot edu
homepage:
http://www.education.wisc.edu/edpsych/facstaff/kaplan/kaplan.htm
Phone: 608-262-0836

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--
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062

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