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  3. What’s Changed Between Versions: ASReml-R 3 and ASReml-R 4

What’s Changed Between Versions: ASReml-R 3 and ASReml-R 4

As newer versions of ASReml-R have been developed it has become apparent that some terms can be named more appropriately, the naming of others can be simplified and in some cases the terms can be grouped together.

The table below is a list of terms (arguments, functions, objects, methods) in Version 3 that have been removed, deprecated or deleted, with their replacement and reason for replacement in Version 4.

The numbers in the Replacement in Version 4 table column refer to the PDF document sections Navigating from ASReml-R Version 3 to 4. These sections contain detailed descriptions of the changes.

Terms in Version 3 Status in Version 4 Action in Version 4 Replacement in Version 4 Reasons for change
asreml() arguments
as.multivariate removed terminates call asmv more succinct argument name
constraints removed terminates call vcc, vcm, 4.1 extended functionality
control removed terminates call use
asreml.options, 3.6
less frequently used options
dump.model removed terminates call obsolete
gammas.table removed terminates call use vparameters.table more appropriate name
ginverse removed terminates call use vm(), 4.2 more uni fied framework for specification of special variance models
maxiter deprecated honoured maxit can be set in asreml.options
model removed terminates call obsolete
na.method.X removed terminates call use na.action, 3.2 more unifi ed framework for related
arguments
na.method.Y removed terminates call use na.action, 3.2
rcov removed terminates call residual, 3.1.1 more appropriate name
asreml.argument removed terminates call asr_argument, 3.2 prefi x asreml. replaced by asr_
to simplify name and avoid confusion, eg. GLM family functions,
argument = gaussian, Gamma,
inverse.gaussian, binomial,
multinomial, negative.binomial,
poisson
predictpoints  deleted terminates call design.points, 3.2 more appropriate name
pwrpoints  deleted terminates call pwr.points, 3.2 more appropriate name
splinepoints  deleted terminates call knot.points, 3.2 more appropriate name
splinescale  deleted terminates call spline.scale, 3.6 more appropriate name
Mixed model functions
at() in rcov or residual removed terminates call use dsum, 4.2 avoid inconsistent use of at()
giv removed R error will be
generated
use vm(), 4.2 more unified framework for specification of special variance models
ped removed R error will be
generated
use vm(), 4.2 more unified framework for specification of special variance models
The asreml object
family removed reports NULL family sensible inclusion in the model
frame
gammas removed reports NULL vparameters more appropriate name
gammas.type removed reports NULL vparameters.type more appropriate name
gammas.con removed reports NULL vparameters.con more appropriate name
monitor removed reports NULL trace logical companion name to the
tr() method
fixed.formula removed reports NULL use formulae, 3.7 a list with components fixed,
random, sparse and residual;
more unified framework for related
components of the asreml object
random.formula removed reports NULL use formulae, 3.7 more unified framework for related
components of the asreml object
sparse.formula removed reports NULL use formulae, 3.7 more unified framework for related
components of the asreml object
Methods or functions
asreml.Ainverse() removed R error will be
generated
ainverse(), 3.6 more appropriate function name
asreml.control() removed R error will be
generated
asreml.options, 3.6 now a function that groups job control and less frequently used options
asreml.variogram() removed R error will be
generated
use asr_varioGram, 3.6 renamed to avoid conflict with similar naming in other R packages
variogram() removed R error will be
generated
varioGram(), 3.6 renamed to avoid conflict with similar naming in other R packages
variogram.asreml() removed R error will be
generated
varioGram.asreml(), 3.6 renamed to avoid conflict with similar naming in other R packages
Updated on July 31, 2018

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