condense.dmmblockarray {dmm} | R Documentation |
Condense an object of type dmmblockarray
to an object of type dmm
Description
An object of class dmmblockarray
is a list containing two items called array
and blocks
. Item array
is an array of objects of type dmm
, with each array element representing the reult of a dmm()
analysis for one pair of blocks of traits. The function condense.dmmarray
will recombine these results into a single object of class dmm
with the variance component and genetic parameter estimates matrices being for all traits, and other elements of the dmm
object being appropriately pooled. Item blocks
is a list, each element of which is a list of the traits present in each block.
Usage
condense.dmmblockarray(da)
Arguments
da |
An object of class |
Details
In bringing together the results of several traitsblockwise
analyses into a single matrix of (for example) individual additive genetic variance/covariance components, one is putting together into one matrix elements estimated with different precisions due to differnt replication for each block of traits. The resulting matrix may not be positive definite even if all the contributing traitsblockwise
ni x nj matrices are forced positive definite.
If the argument da
contains results from a dmm
run with gls=T
then the GLS results for each traitblockpair will also be condensed. In this case the GLS results must be present for every traitblockpair. It can be quite difficult to get gls=T
runs to converge successfully for every pair of blocks.
Value
An object of class dmm
, containing the recombined results for all traits.
Note
An object of class dmmblockarray
can be manipulated as is without using the
condense.dmmblockarray
function. For example one element of the array can be printed with
print(objectname$array[[i,j]])
where i
and j
are subscripts indicating the row and column position of the element to be printed. The summary()
and gsummary()
functions are also available. It is necessary that the
library(dmm)
statement be made, otherwise one will get the standard print()
and summary()
functions instead of those appropriate for an object of class dmm
. The double square brackets are necessary because each element of the array is a list object, and you want its contents, not its name attribute.
Author(s)
Neville Jackson
See Also
Functions dmm()
, condense.dmmarray()
Examples
library(dmm)
# prepare the dataset sheep.df
data(sheep.df)
# add a matrix 'Ymat' to the dataframe,
# which is required for traitsblockwise
# keep=TRUE also required
sheep.mdf <- mdf(sheep.df,pedcols=c(1:3),factorcols=c(4:6),ycols=c(7:9),
sexcode=c("M","F"),keep=TRUE)
# make sheep.fit as a class dmmarray object
sheep.fit <- dmm(sheep.mdf, Ymat ~ 1 + Year + Sex,
components=c("VarE(I)","VarG(Ia)"),traitsblockwise=TRUE,
Block1=c("Cww","Diam"),Block2="Bwt")
# look at one element of the dmmblockarray
summary(sheep.fit$array[["Block1","Block2"]])
# condense the dmmblockarray to a class dmm object
sheep.condense <- condense.dmmblockarray(sheep.fit)
# compute a response to selection
sheep.resp <- gresponse(sheep.condense,
psd=list(dp=c(1,1,1)),effects=c("G(Ia)"))
# look at response object
summary(sheep.resp)
#cleanup
rm(sheep.df)
rm(sheep.mdf)
rm(sheep.fit)
rm(sheep.condense)
rm(sheep.resp)