difficulty with predict statement

From: Holland, Jim <Jim.Holland_at_ARS.USDA.GOV>
Date: Mon, 14 Jan 2008 15:33:45 -0500

Dear ASREML listserv:


We have an experiment with 26 populations of corn, each with 200 lines,
plus two more populations with 212 and 281 lines. We have data from
three environments.


We are having serious problems getting the predict statement to give us
predictions for all of the lines that we have data on and excluding
lines we do not have data on.


We have effects coded as loc for location, pop for population, and
entry_num for the line code within each population (which runs 1 - 200
or to 281). We can fit a very simple model like:


Trait ~ mu !r loc pop loc.pop entry_num.pop,


And then try to predict as such:


predict entry_num pop !present entry_num pop


The prediction list excludes far too many lines (some 1000 of the ~5400
we have data on). Weirder still, it includes a few predictions on lines
that are not in the data set (entry_num > 200 for some of the pops). We
have fit much more complicated models to account for the GxE structure
and within-environment spatial variation, and of course the problem is
there as well.


We have tried different permutations of the predict statement, e.g.:


predict pop entry_num!present pop entry_num


Still, we have the same problem.


We have run a tabulate statement with !count and verified that we have
very little missing data relative to how many predictions are missing,
although we do not have the problem for all traits. The missing data
structure varies across traits, but is not much worse for the trait we
have the problem with than the others.


Any ideas how to fix this? Thanks - Jim



Jim Holland

USDA-ARS Plant Science Research Unit

Department of Crop Science

North Carolina State University

Phone: 919-513-4198

Fax: 919-515-7959

Web: http://www4.ncsu.edu/~jholland/homepage.htm

Received on Thu Jan 14 2008 - 15:33:45 EST

This webpage is part of the ASReml-l discussion list archives 2004-2010. More information on ASReml can be found at the VSN website. This discussion list is now deprecated - please use the VSN forum for discussion on ASReml. (These online archives were generated using the hypermail package.)