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 |