Re: Asreml_R help: Is the model wrong?

From: <Yutao.Li_at_CSIRO.AU>
Date: Fri, 4 Sep 2009 16:42:34 +1000

Thanks, Dave. It works now after using ASReml_R 3.0 version.

Regards

Yutao

*********************************************************
Dr Yutao Li
Senior Research Scientist
CSIRO Livestock Industries
Level 5, QBP, 306 Carmody Road
St Lucia, QLD 4067
AUSTRALIA
 
Tel: +61 7 3214 2465
Fax: +61 7 3214 2480
Email: Yutao.Li_at_csiro.au
 
**********************************************************
-----Original Message-----
From: ASReml users discussion group [mailto:ASREML-L_at_DPI.NSW.GOV.AU] On Behalf Of Butler, David
Sent: Friday, September 04, 2009 1:35 AM
To: ASREML-L_at_DPI.NSW.GOV.AU
Subject: Re: Asreml_R help: Is the model wrong?

Dear Li,

There was a (relatively) recent internal upgrade to asreml that broke the conditional F-tests and approximate stratum variance components of wald(). This has been corrected so all you may need is a later version than the one you have.

Dave.

-----Original Message-----
From: ASReml users discussion group on behalf of yutao
Sent: Thu 03-Sep-09 1:27 PM
To: ASREML-L_at_DPI.NSW.GOV.AU
Subject: Asreml_R help: Is the model wrong?
 
Dear Brian/Arthur,
I have a dataset (ecoli.txt) which contains the following information.
? 3 trials (trial1, trial2 and trial3)
? 2 treatments (trt1 vs trt2)
? Different sampling dates(sdate) were recorded for each treatment in each trial
trial1: 7, 14, 20, 34, 56, 69, 83, 112, 154, 181, 205
trial2: 14, 27, 48, 69, 97, 125, 153, 183
trial3: 14, 27, 55, 76, 97, 133, 153, 174
? Within each trial for each sampling date, logcount of ecoli were measured from sampling 3 different plates of 2 or 3 chambers of 3 blocks (A, B, C).
trial1: 3 chambers /block
trials 2 and 3: 2 chambers/block.
 
The aim of the analysis is to examine the difference between two treatments in each trial and across trials, and predict the relationship between sampling date (sdate) and logcount for each treatment.

I have used ASReml_R to fit the following model:
asreml(logcount~trial+trial/treatment+trial/(sdate+sd2)+trial/treatment:(sdate+sd2),data=ecoli,random=~(trial/sdate):block/chamber/plate)
The term sd2 is a quadratic of covariate sdate.

The program gives the results, but it does not give a denominator df when I ask for conditional wald tests.

Is my model wrong?

The ASreml_R code:
rm(list=ls())
ecoli=read.table("C:\\Documents and Settings\\li042\\Desktop\\ecoli.txt",sep="\t",header=T)
library(asreml)
ecoli$chamber <- as.factor(ecoli$chamber)
ecoli$plate <- as.factor(ecoli$plate)
ecoli$sd2<-ecoli$sdate^2
ecoli_m2.asr <- asreml(logcount~trial+trial/treatment+trial/(sdate+sd2)+trial/(treatment:(sdate+sd2)),data=ecoli,random=~(trial/sdate):block/chamber/plate)
wald.asreml(ecoli_m2.asr, denDF = "default", ssType = "conditional")$Wald

The data file is attached. Thanks in advance.
Yutao Li

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Received on Sat Sep 04 2009 - 16:42:34 EST

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