Dear R Users,
I'm fitting non-linear models using nlme package.
How can I check models estimability?
Data were obtained using an incomplete factorial design:
effect 1 = 4 levels
effect 2 = 5 levels
effect 3 = 5 levels
effect 4 = 5 levels
Cross table example for effect 1 and effect 2:
4 5 6 7 8
55 58 0 16 0 59
57 0 84 25 78 0
60 18 24 167 24 16
62 0 80 22 89 0
Cheers,
Vasco
On 14/01/14 11:00, r-help-requ...@r-project.org wrote:
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Today's Topics:
1. To modify FMCD (Hock Ann Lim)
2. Re: computation (Lisa S)
3. Re: Find the package of a class given classname (Hadley Wickham)
4. Re. Confidence intervals for prediction with R2Bayesx (garth)
5. Re: HOW TO CREATE A SUBSET FROM A LARGE DATASET based on some
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12. Barplot not showing all labels (Jeff Johnson)
13. coxph with time-dependent covariates (Phil Stevenson)
14. Re: Barplot not showing all labels (Jim Lemon)
15. Re: coxph with time-dependent covariates (David Winsemius)
16. How to use ddply (Amitabh Dugar)
17. likelihood ratio test for mean difference assuming unequal
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18. Re: How to use ddply (arun)
19. Re: SE for R-squared (peter dalgaard)
20. Re: How to use ddply (David Winsemius)
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22. Plot only a portion of a record (Janet Choate)
23. Re: Plot only a portion of a record (Jim Lemon)
24. Re: Plot only a portion of a record (David Winsemius)
25. Re: Plot only a portion of a record (arun)
26. Re: likelihood ratio test for mean difference assuming
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27. Running multidimensional regressions (andrews Nikolaiv)
28. "squashed" domains when doing PCA with bio3d (Bianca Ihrig)
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----------------------------------------------------------------------
Message: 1
Date: Mon, 13 Jan 2014 03:52:30 -0800 (PST)
From: Hock Ann Lim <lim...@yahoo.com>
To: R-Help <r-help@r-project.org>
Subject: [R] To modify FMCD
Message-ID:
<1389613950.86125.yahoomail...@web160501.mail.bf1.yahoo.com>
Content-Type: text/plain
Dear R Experts,
Can anyone teach me how to modify the FMCD algorithm in R. If I wish to replace
the C-step in FMCD by the index set.
Let I(old)={pi(1)old,pi(2)old,...,p(h)old} and I(new)={pi(1)new,
pi(2)new,..,p(h)new} the index sets that correspond to the sample items in
H(old) and H(new) respectively.
The C-step is conducted as follow:
If I(new) not equal to I(old), H(old):=H(new). and calculate T and S based on
H(new). Otherwise, the process is stopped.
Thank you.
Regards,
Lim Hock Ann
[[alternative HTML version deleted]]
------------------------------
Message: 2
Date: Mon, 13 Jan 2014 16:01:31 +0800
From: Lisa S <lisha.sh...@gmail.com>
To: IZHAK shabsogh <ishaqb...@yahoo.com>
Cc: "r-help@r-project.org" <r-help@r-project.org>
Subject: Re: [R] computation
Message-ID:
<caospdsvnbwt6gbkdo88ftyxpssfaexa0guwqu-9wnwe94yl...@mail.gmail.com>
Content-Type: text/plain
In this calculation:
(dg0%*%t(dx0))
is
[,1] [,2]
[1,] 0 -0.75
[2,] 0 0.50
So: exp2 = NaN
It is extremely easy to find out the issue if you go back line by line,
this is a basic procedure of debugging. Please do it yourself next time.
On Mon, Jan 13, 2014 at 3:09 PM, IZHAK shabsogh <ishaqb...@yahoo.com> wrote:
kindly help me fine what is the mistake with following:
my aim is to compute those steps and obtain a vector with values (3,5)
but i am geting (NAN,NAN)
Q<-matrix(c(5,-3,-3,2),2,2)
b<-rbind(0,1)
H0<-diag(2)
x0<-rbind(0,0)
d0<-b
g0<--b
a0<--(t(g0)%*%d0)/(t(d0)%*%Q%*%d0)
x1<-x0+a0[,1]*d0
dx0<-x1-x0
g1<-Q%*%x1-b
dg0<-g1-g0
exp1<-(t(dg0)%*%H0%*%dg0)/(t(dg0)%*%dx0)
exp2<-(dx0%*%t(dx0))/(dg0%*%t(dx0))
exp3<-(dx0%*%t(dg0)%*%H0 +H0%*%dg0%*%t(dx0))/(dx0%*%t(dg0))
H1<-H0+(1+exp1[,1])*exp2-exp3
d1<--H1%*%g1
a2<-(t(g1)%*%d1)/(t(d1)%*%Q%*%d1)
x2<-x1+a2[,1]*d1
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------------------------------
Message: 3
Date: Mon, 13 Jan 2014 08:42:09 -0600
From: Hadley Wickham <h.wick...@gmail.com>
To: Herv? Pag?s <hpa...@fhcrc.org>
Cc: R-help <r-help@r-project.org>
Subject: Re: [R] Find the package of a class given classname
Message-ID:
<CABdHhvFtxOZY6Ghfw4o=c_rh9dexmg7k8mchgjgphgeroyc...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
How to find the package of a class given classname?
For example, there is a class called GAlignments, I want to do something
like
attr("GAlignments", "package") that gives you the package where the class
is defined? But of course, attr("GAlignments", "package") won't work...
You didn't say whether you wanted to be able to do this
programmatically.
If that's the case maybe you're lucky and the package where the class
is defined is already attached to your session. In that case:
> attr(class(new("GAlignments")), "package")
[1] "GenomicRanges"
Or maybe findClass?
Otherwise, if the package in question is installed but not attached
you can still do:
??`GAlignments-class`
Or class?GAlignments
Hadley
--
Vasco A. P. Cadavez, PhD
Departamento de Ciência Animal & Centro de Investigação de Montanha (CIMO)
Escola Superior Agrária do Instituto Politécnico de Bragança
Campus de Santa Apolónia, Apartado 1172
5301-854 Bragança Portugal
Telefone: (+351) 273 303 304
Fax: (+351) 273 325 405
e-mail: vcada...@ipb.pt
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