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News for Package asremlPlus
asremlPlus Version 4.4.38 (2024-08-19
Add check that spatial variance is not bound whilst the nugget variance is positive when fitting correlation models in addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests. If it is, fix the nugget variance,
Add the argument
nugget.variance
to addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests to control the fitting of a nuggetvariance when fitting correlation models.Add
trace
argument addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests, primarily for tracking the fitting of correlation models.Add traps for errors resulting from singular information matrices when fitting correlation models in addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests.
Fix bug in addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests when fitting metric correlation functions.
Fix bug in newfit.asreml that occurred when change to random model results in no random terms.
asremlPlus Version 4.4.37 (2024-07-23
Modify the fitting of corb correlation models in addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests to make it more robust.
Fix a bug in infoCriteria.asreml and infoCriteria.list that caused an
incorrect-dimensions
error when computing the full likelihood.
asremlPlus Version 4.4.36 (2024-07-01
Make sure that, when
false.pos.wt
is used with pickLSDstatistics and there are several values with the same weighted sum, LSDstatisics with less false positives are favoured.
asremlPlus Version 4.4.35 (2024-06-19
Fix faulty links in manual.
asremlPlus Version 4.4.34 (2024-06-19
Add
EGLS.linTransform
to linTranform.alldiffs, predictPlus.asreml, predictPresent.asreml and pairdiffsTransform.alldiffs.Add S3 method function isCompoundSymmetric.matrix.
Modify print.alldiffs so that the diagonal elements of pairwise differences, sed and p-values are printed as blank spaces.
asremlPlus Version 4.4.33 (2024-06-10
Fix bug in checking loaded versions that occurs with R 4.4.0.
asremlPlus Version 4.4.32 (2024-04-11
Update for CRAN submission.
asremlPlus Version 4.4.31 (2024-03-15
Revise warning message in R2adj.asreml for when generalized inverse fails.
Add fix for bug in as.asrtests that caused a C stack overflow error when trying to update the
wald.tab
component of anasrtests.obj
.
asremlPlus Version 4.4.30 (2024-03-03
For chooseSpatialModelOnIC.asrtests, change the abbreviations for the two P-spline models from
TPPCS
andTPP1LS
toTPPSC2
andTPPSL1
. If the call to chooseSpatialModelOnIC.asrtests includes the former abbreviations, they will be converted to the new abbreviatons and all output will be labelled with the new abbreviations.Revise the deocumentation of the P-spline details for addSpatialModel.asrtests, addSpatialModelOnIC.asrtests or chooseSpatialModelOnIC.asrtests.
asremlPlus Version 4.4.29 (2024-02-26
For R2adj.asreml, correct the check that terms to be included in the random model for calculating
R2.adj
are in the fitted model so that a warning is no longer issued when a term for inclusion differs from a fitted term only in the order of the factors/variables comprising the terms.Trap errors issued by
svd
function from baseR
in computing generalized inverses for R2adj.asreml. Instead, issue a warning and returnNA
.
asremlPlus Version 4.4.28 (2024-02-13
Fix a bug in estimateV that meant that terms involving the asreml
at
function on other than the first variable in the term caused an error.Instead of producing an error when the number of columns in the design matrix does not equal the number of coefficients for the term, now add columns of zeros for missing design-matrix columns. An error may still occur when this does not work.
Add checks in estimateV.asreml and R2adj.asreml for when the design matrix for a term is not available. Rather than issue an error,
NA
is returned and an attributemissing.termmatrix
added that contains a list of the problematic terms. Also added an error to variofaces.asreml and bootREMLRT for when this problem occurs.Extend the the
include.which.fixed
andinclude.which.random
arguments of R2adj.asreml to process correctly formulae to update the existing fixed and random formula using a formula that includes the '.' and terms, typically a list of bracketed terms preceded by a '-' so that terms are removed from a formula.
asremlPlus Version 4.4.27 (2024-02-05
Spell check the manual.
Revise the detection of variance parameters involving
sections
in addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests.
asremlPlus Version 4.4.26 (2024-02-01
Implement bespoke strategy for fitting
corb
correlation models that first fits a random units length term and constrains the residual variance to one. Then, the corb models are fitted and, whencorr.orders
is set to 0, up to 10 correlation bands are fitted depending on whether additonal bands improve an information criterion.Fix a bug in estimateV when a
corb
function is involved in a variance term and asreml version 4.2 is being used.Minor corrections to documentation for makeTPPSplineMats.data.frame, addSpatialModel.asrtests, addSpatialModelOnIC.asrtests or chooseSpatialModelOnIC.asrtests.
Fixed bugs in passing the arguments for setvarianceterms.call via ... from addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests to changeTerms and changeModelOnIC.asrtests.
Minor revisions to documentation for R2adj.asreml.
asremlPlus Version 4.4.25 (2024-01-15
Add an error for a
NULL
vcov
component in thealldiffs.obj
supplied to the ratioTransform.alldiffs function.Add
printPlot
argument to plotPredictions.data.frame and change the function to return the plot.Add function R2adj.asreml to calculate an adjusted coefficient of determination for linear mixed models.
Fixed bugs in estimateV for
asr_str
terms with non-diagonal variance structures.Rectify a problem in extracting the correct columns of the design matrix for some terms that affected estimateV.
Update the vignettes.
Add link to GitHub issues page for BugReports in DESCRIPTION file.
asremlPlus Version 4.4.24 (2023-12-20
Fix a bug in plotLSDerrors so that the correct errors are now plotted.
Add argument
false.pos.wt
to pickLSDstatistics.alldiffs, which when it is notNULL
results in mininzing the weighted sum of the false.pos and false.neg comparisons of pairwise differences.
asremlPlus Version 4.4.23 (2023-12-12
Add the use of the R optimizer
nloptr::bobyqa
to search for the optimal angles for the rotation of the eigenvlues of the penalty matrix when fitting cubic P-splines using addSpatialModel.asrtests, addSpatialModelOnIC.asrtests or chooseSpatialModelOnIC.asrtests. This provides an alternative to searching over a two-dimensional grid of angles.Fix a bug in the fits used in searching for optimal rotation angles by doing the search before any spatial P-spline models are fitted.
There has been several changes to the arguments of makeTPPSplineMats.data.frame, addSpatialModel.asrtests, addSpatialModelOnIC.asrtests or chooseSpatialModelOnIC.asrtests as follows:
The default for
ngridangles
has changed toNULL
to provide for using an optimizer to search for the optimal rotation.The arguments
dropRowterm
anddropColterm
have been replaced with the more general argumentsdropFixed
anddropRandom
.The default for
asreml.option
has changed frommbf
togrp
. Whilegrp
requires more storage thatmbf
, it is easier to applyasreml
andasrtests
methods to fitted models whengrp
is used.
asremlPlus Version 4.4.22 (2023-11-14
Add the S3-method function convEffectNames2DataFrame.asreml.
asremlPlus Version 4.4.21 (2023-11-05
Increment version for resubmission to CRAN after fixing an S3 method declaration error.
asremlPlus Version 4.4.20 (2023-11-05
Revise manual pages to meet cran syntax requirements.
Add the argument
usRandLinCoeffs
to addSpatialModel.asrtests, addSpatialModelOnIC.asrtests or chooseSpatialModelOnIC.asrtests to control whether to attempt the fit of the unstructured variance model for the constant and linear terms in random interactions with smooth terms. Also, added code to reject the model if any of the variances or covariances are bound.
asremlPlus Version 4.4.19 (2023-10-30
Fix bug that prevented the fitting of unstructured variance model between the random constant and linear parameters in the interaction of these terms with the random smooth row and random column terms in a
TPPCS
model.
asremlPlus Version 4.4.18 (2023-10-29
For fitting in P-spline models using addSpatialModel.asrtests, addSpatialModelOnIC.asrtests or chooseSpatialModelOnIC.asrtests, change the function for fitting the covariance of the constant and the linear term from
us
tocorh
orcorgh
.
asremlPlus Version 4.4.17 (2023-10-26
Fix bug in investigating nugget variance for correlation models when there are
sections
.Further improve the handling of situations in which the residual variance or the spatial variance associated with a correlation term becomes singular or bound in fitting a spatial correlation model using addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests.
Add
allow.corrsJointFit
argument as a device for dealing with fits that hang when attempting to fit simultaneously both correlations for the two grid dimesnions.Internal recoding.
asremlPlus Version 4.4.16 (2023-10-18
Added the
maxit
option forasreml
to addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests, setting its default to 30 for thesefunctions
to increase the chances that the models will converge.Extensively revise the code to improve the handling of situations in which the residual variance or the spatial variance associated with a correlation term becomes singular or bound in fitting a spatial correlation model using addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests.
Revise checking for nugget variance when there are sections and the residual has a separate terms for each section.
Added a basic check for separate random and residual terms for sections and, if there are none, issue a warning that better fitting can result if they are included.
asremlPlus Version 4.4.15 (2023-10-02
Make the default number of cores (
ncores
) for parallel processing in bootREMLRT.asreml, simulate.asreml and variofaces.asreml.Add the function convAsremlobj.asreml that recreates an existing
asreml
object using the currently loadedasreml
version so that the object is compatible with this version.Made the following modifications to addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests:
Tweaked the code underlying these functions for fitting local spatial variation models to make it more robust.
Added reporting the optimal rotation angles to the test.summary when
rotateX
isTRUE
. Also, added theta(s) as an attribute to theasreml.object
.Added the
which.rotacriterion
so that one could choose between thedeviance
,likelihood
,AIC
andBIC
as the criterion to use in determining the optimal roation angle for rotating the eigenvectors of the penalty matrix.Add the capacity to parallel process, for each column angle, the search of the row angles. This option is only available for the
asreml.option
set togrp
.Removed the need to precede a call to these functions with a call makeTPPSplineMats.data.frame when
asreml.option
is set tombf
.Fix a bug in fitting natural cubic smoothing spines (
TPNCSS
) using these functions where only the first of thesections
had splines fitted to it.Change from ordinal numbers to levels in labelling the fitting of correlation
corr
spatial models when using these functions.
Modify makeTPPSplineMats.data.frame so that the default enviroment of the data.frames for the
mbf
option ofasreml.opt
is that of the function that calls makeTPPSplineMats.data.frame. Also, formbf.env
set toNULL
, do not assign thembf
data.frames; just include them in thelist
that is returned.Make the
data.plus
component of thelist
produced by makeTPPSplineMats.data.frame whenasreml.option
is set tombf
equivalent to that produced whenasreml.option
is set togrp
.Corrected bug in detecting
Fixed (F)
variance components in rmboundary.asrtests.Added to newfit.asreml, a test for bound and singular terms in a new model when
update
isTRUE
and, if there are any, added code to refit the model as ifupdate
wasFALSE
, to see if any bound terms become unbound terms.Clarified the dcoumentation of the
update
argument in all functions that include it.
asremlPlus Version 4.4.14 (2023-08-28)
Minor internal code changes.
asremlPlus Version 4.4.13 (2023-08-24)
Add arguments
rotateX
andtheta
to makeTPPSplineMats.data.frame so that the eigenvectors of the penalty matrix used in generating the design matrices for the random terms could be rotated by the angles intheta
.Add code to carry out a grid search to find the optimal angle by which to rotate the eigenvectors of the penalty matric when fitting P-splines. Add arguments
rotateX
andngridlines
to addSpatialModel.asrtests, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests to allow the use to request that grid seach be made for the optimal ritation angle and to control the size of the grid searched.Fix a bug in fitting a correlation model that occurs when addSpatialModel is used to fit the model.
There remains an svd bug with the oneMKL libraries version 2023.1.0 that is causing problems for
IClikelhood
set to"full"
.
asremlPlus Version 4.4.12 (2023-08-03)
Modifications to deal with classhes between multithreading and external linear algebra packages under Windows. The environmental variable OMP_NUM_THREADS needs to be set to 1 if parallel processing is to be undertaken on a Windows machine. This can be done for individual tasks by using
Sys.setenv("OMP_NUM_THREADS" = 1)
prior to running the task; otherwise, the environmental variable can be set for all tasks in the Windows system viaAdvanced system settings
>Envirnomental Variables
.There remains an svd bug with the oneMKL libraries version 2023.1.0 that is causing problems for
IClikelhood
set to"full"
.
asremlPlus Version 4.4.11 (2023-07-19)
This version has known issues when the Intel MKL libraries are installed in the R installation directories.
Modified makeTPPSplineMats.data.frame to implement the use of mbf in fitting P-spline models for local spatial variation.
asremlPlus Version 4.4.10 (2022-12-28)
Modifications for ASReml-R version 4.2. Those that may impact upon users include the following:
The names of the columns of the design matrix has changed, as has the order of the columns.
character codes are now stored in both
vparameters.type
andvparameters.con
, making vpt.char and vpc.char obsolete and so no longer available.For predict, the intercept-only classify and the name of the column in the
predictions.freame
, has changed from(Intercept)
toIntercept
.The designation of estmates on the boder of the parameter space has changed from fixed (
F
) to (B
) e.g. correlations.When the levels of a factor are being specified in terms with an
at
, as opposed to an ordinal number for the position of the level in the levels list, then the levels must be enclosed in single or double quotes. Further, the names of the terms will nclude single or double quotes.
asremlPlus Version 4.3.56 (2023-06-20)
Correct issue with alldiffs attributes not being retained when subsetting using subset.alldiffs.
asremlPlus Version 4.3.55 (2023-06-13)
Remove bloated system-generated testthat-problems.rds file so that the tarball to be submitted is less than 5 Mb.
asremlPlus Version 4.3.54 (2023-06-12)
Fix problem with deprecated function setvarianceterms.asreml when submitted to CRAN.
asremlPlus Version 4.3.53 (2023-06-12)
Add new vignette
WheatSpatialModels
that illustrates the fitting of models for local spatial variation.Generalize correlation spatial models to allow the independent specification of any asreml variance model for rows and columns. Improve the fitting of spatial correlation models, including changing the default correlation model to
ar1
and postpone removing bundary terms until after all components of the correlarion model have been fitted.Revised the spatial modelling to resolve several bugs associated with them when the residual specifies heterogeneous variance using eith
idh
ordsum
.Repurpose
row.factor
andcol.factor
arguments ofaddSpatialModel.asrtests
,addSpatialModelOnIC.asrtests
andchooseSpatialModelOnIC.asrtests
to specify the row and column factors for correlation model where required and add the argumentsdropRowterm
anddropColterm
to specify the main effect terms to be dropped in fitting spline models.Modified changeTerms.asrtests and changeModelOnIC.asrtests so that the
bounds
andinitial values
of terms specified usingset.terms
without changing any terms in the model.Fix problem detected during CRAN submission that found setvarianceterms.asreml was apparently an unregistered exported generic.
asremlPlus Version 4.3.52 (2023-05-18)
Fix bug in identifying residual terms for ASReml-R v. 4.x.
Fix bug in rmboundary.asrtests when removing a bound term results in no random terms.
asremlPlus Version 4.3.51 (2023-04-02)
Fix bug in fitting P-splines when difforder is one.
Change infoCriteria to use the deviance in calculating information criteria for
family
set to asr_binomial or asr_poisson.Add the argument
transform.function
to addBacktransforms.alldiffs, allDifferences.data.frame, predictPlus.asreml and predictPresent.asreml so thatpredictions
anderror.intervals
on the scale of thetransform.function
can be backtransformed.
asremlPlus Version 4.3.50 (2023-03-9)
Add
classify
argument to as.predictions.frame, checking that variables in theclassify
are in thepredictions.frame
and conversion of any variables in theclassify
that are not factor to factors.Update ggplot2 functions to use tidy evaluation.
Fix internal anomaly causing a Note on CRAN.
asremlPlus Version 4.3.49 (2023-03-3)
Add the argument
useIntervals
to plotLSDerror.alldiffs.Fix a bug in plotLSDerrors that resulted in not being able to determine which LSDs in the LSD component apply to the pairwise comparisons. It resulted in all comparisons being shown as
n.a.
.
asremlPlus Version 4.3.48 (2023-02-18)
Rename makeTPSPlineXZMats.data.frame to makeTPPSplineMats.data.frame.
asremlPlus Version 4.3.47 (2023-02-17)
Tidy up code for trySpatial = "none".
Revise makeTPSPlineXZMats.data.frame to cover
asreml.opt
set togrp
.Fix bug in plotLSDerrors when LSDs have beeen computed for
LSDtype
set tofactor.combinations
.
asremlPlus Version 4.3.46 (2023-02-05)
Fix bug in testing whether an ar1 fit has been achieved in addSpatialModel.asrtests and chooseSpatialModelOnIC.asrtests.
asremlPlus Version 4.3.45 (2023-01-24)
Modify system tests to cater for for M1Mac numerical accuracy.
Fix bug in which the setting of IClikelihood was not being passed to infoCriteria calls in chooseSpatialModelOnIC.asrtests, resulting in always reporting the
REML
likelihood.Change that
spatial.IC
component of thelist
returned by chooseSpatialModelOnIC.asrtests to contains the information criteria for each spatial model that is fitted. Also, rename the componentsbest
andbest.AIC
tobest.spatial.mod
andbest.spatial.IC
.Fix bug in reporting the likelihood when a TPNCSS model does not fit.
Add function addSpatialModel.asrtests that adds a spatial model to a supplied model without asessing the fit of the model.
asremlPlus Version 4.3.44 (2022-12-30)
Add arguments
nestorder
,degree
anddifforder
to functions addSpatialModelOnIC.asrtests and makeTPSPlineXZMats.data.frame, as well as argumentnestorder
to chooseSpatialModelOnIC.asrtests. Add the optionTPLV
to the argumenttrySpatial
from chooseSpatialModelOnIC.asrtests to allow a linear spatial model with first-order penalty to be fitted.Fix bug in testing for fixed correlations that meant they were not always detected.
Fix error in changeModelsonIC.asrtests in the action when the model is
Unswapped
- it was being reported asChanged random
.Stop crashing of changeTerms.asrtests and ChangeModelOnIC.asrtests when rmboundary.asrtests unable to remove singular terms.
asremlPlus Version 4.3.43 (2022-11-30)
Fix bugs in choosing the best spatial model in chooseSpatialModelOnIC.asrtests. Add components
best.spatial
andbest.spatial.AIC
to the value returned by chooseSpatialModelOnIC.asrtests.Add linear-row-by-linear-column-covariates interaction to the model fitted for TPNCSS option of addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests.
asremlPlus Version 4.3.42 (2022-11-23)
Add functions makeTPSPlineZMats.data.frame, addSpatialModelOnIC.asrtests and chooseSpatialModelOnIC.asrtests.
asremlPlus Version 4.3.41 (2022-11-16)
Revise test for fixed correlation so that allow.fixedcorrelation recognises any correlation term, rather than being restricted to ar1.
asremlPlus Version 4.3.40 (2022-11-16)
Compress pdf files and resubmit to CRAN.
asremlPlus Version 4.3.39 (2022-11-13)
Rebuild for R 4.2.2 and submission to CRAN.
asremlPlus Version 4.3.38 (2022-10-24)
Added function pickLSDstatistics.alldiffs.Rd.
Revise documentation for the arguments
LSDtype
,LSDsupplied
,LSDby
andLSDstatistic
.
asremlPlus Version 4.3.37 (2022-09-19)
Fix bugs in function newfit.asreml that involves making changes to models that involve the
at
function. This bug affected the functions changeTerms.asrtests, changeModelOnIC.asrtests, rmboundary.asrtests, testswapran.asrtests and testranfix.asrtests. In removing a term that involve a single lewvel of a factor in an at function, it is now possible to specify either the level or the level index.Modify rmboundary.asrtests to allow the removal of random term for a single level of an
at
function when the levels are specified singly in the random model.Add function addto.test.summary.
asremlPlus Version 4.3.36 (2022-08-17)
Minor correction for resubmitting to CRAN.
asremlPlus Version 4.3.35 (2022-08-16)
Rebuild under R 4.2.1 for new submission.
asremlPlus Version 4.3-34 (2022-04-20)
Add functions plotLSDerrors.alldiffs and plotLSDerrors.data.frame.
Replace the use of the package
reshape
with the use ofreshape2
.Replace
X1
andX2
withRows
andColumns
as the default names for the the first two columns of thedata.frame
produced by plotPvalues.alldiffs, plotLSDs.alldiffs and plotLSDerrors.alldiffs and provided as input to plotPvalues.data.frame, plotLSDs.data.frame and plotLSDerrors.data.frame.Change plotPvalues.alldiffs and plotLSDs.alldiffs to return a two component list, one component of which is a
data.frame
that contains the statistics to be plotted and the other of which is alist
containing the plots that have be produced asggplot
objects.
asremlPlus Version 4.3-33 (2022-04-09)
Add an error if all residual variances are bound.
asremlPlus Version 4.3-32 (2021-12-21)
Fix bug in chooseModelOnIC result from a change in as.vector for data.frames and lists in R 4.2.0.
asremlPlus Version 4.3-31 (2021-12-06)
Rebuild under R 4.1.2 for new submission.
asremlPlus Version 4.3-30 (2021-11-22)
Put in a trap for fixed-effects variances being inestimable when calculating the full likelihood.
asremlPlus Version 4.3-29 (2021-11-06)
Modify linTransform.alldiffs so that an intercept-only submodel can be fitted.
Revise the manual entry for exploreLSDs.alldiffs and for pairdiffsTransform.alldiffs.
asremlPlus Version 4.3-28 (2021-10-26)
Fix bug in newfit.asreml that re-orders the fixed model because of R limitations.
asremlPlus Version 4.3-27 (2021-10-24)
Fix problem in linTransform.alldiffs when the product of the numbers of levels in the classiify factors is large and not all combinations of the levels are observed.
Relax the requirement for
LSDby
variable to be in theclassify
to beng that they must be in thepredictions
component of thealldiffs.obj
.
asremlPlus Version 4.3-26 (2021-10-21)
Fix bug in false.pos and false.neg for
LSDtype
set tosupplied
whenLSDby
is notNULL
.Add quantiles 25 (
q25
) and 75 (q75
) to the values thatLSDstatistic
can take and the exploreLSDs.alldiffs investigates.Allow for multiple
LSDstatistic
values whenLSDtype
isfactor.combination
andLSDby
is set.
asremlPlus Version 4.3-25 (2021-10-15)
Add
sig.size
,sig.face
andsig.colour
arguments to plotPvalues.data.frame and plotPvalues.alldiffs.
asremlPlus Version 4.3-24 (2021-10-14)
Make sure that when
predicted.values
and the associatedvcov
andsed
in analldiffs.object
have values that are close to zero as a result of the limitations of real number calculations, they are set to zero so as to avoid further calculation problems.Add
zero.tolerance
argument to linTransform.alldiffs.
asremlPlus Version 4.3-23 (2021-10-03)
Modify the test for fixed correlation from a test for
Fixed
(F
) to cover also correlations that arebound
(B
) orsingular
(S
).Add tests on incoming fits for fixed correlation.
asremlPlus Version 4.3-22 (2021-10-01)
Support is no longer provided in asremlPlus for versions of ASReml-R prior to version 4.0.
Add a new argument
allow.fixedcorrelation
to changeModelOnIC.alldiffs, newfit.asreml, chooseModel.asrtests, changeTerms.asrtests, testranfix.asrtests, testresidual.asrtests, testswapran.asrtests and reparamSigDevn.asrtests so that a model with a fixed correlation parameter may be rejected.
asremlPlus Version 4.3-21 (2021-09-23)
Fix a bug in pairdiffsTransform.alldiffs where the factors indexing the predictions were not generated correctly.
In changeModelOnIC.alldiffs, add detection of absent terms to be dropped and do not change the model if one or more are detected.
asremlPlus Version 4.3-20 (2021-09-03)
Fix bug in the calculation of false positives and negatives in exploreLSDs.alldiffs for
LSDtype
set tooverall
.Change default for
plotHistogram
in exploreLSDs.alldiffs toFALSE
.
asremlPlus Version 4.3-19 (2021-09-01)
Rebuild under R 4.1.1 for new submission.
asremlPlus Version 4.3-18 (2021-08-31)
Change number of comparisons symbol in an
LSD.frame
fromn
toc
.
asremlPlus Version 4.3-17 (2021-08-30)
Add False positives and negatives counts to LSD statistics.
asremlPlus Version 4.3-16 (2021-08-24)
Fix bug in redoErrorIntervals when only one factor in
LSDby
.Add function print.LSDdata.
asremlPlus Version 4.3-15 (2021-08-19)
Fixed bug in
halfLeastSignificant.limit
whenLSDtype
isfactor.combination
and theassignedLSD
is zero to now ensure that the limit isNA
.Reinstated passing of parameters from linTransform.alldiffs to redoErrorIntervals.alldiffs.
asremlPlus Version 4.3-14 (2021-08-18)
Fix newly introduced bug for
LSDtype = "halfLeastSignificant"
when there is not a numeric covariate involved in theLSDby
argument.Stop extra frequency plot produced by exploreLSDs.
Minor internal modification.
asremlPlus Version 4.3-13 (2021-08-16)
Fix bug for
LSDtype = "halfLeastSignificant"
when there is a numeric covariate involved in theLSDby
argument.Minor internal modification.
asremlPlus Version 4.3-12 (2021-08-11)
Fix bug in pairdiffsTransform when only two factors in
classify
.Add function subset.list.
Add functions exploreLSDs, plotLSDs.alldiffs, plotLSDs.matrix and plotLSDs.data.frame.
Incorporate arguments
retain.zerLSDs
andzero.tolerance
into AllDifferences.data.frame, redoErrotIntervals.alldiffs amd exploreLSDs.alldiffs to allow control of the retention of the zero LSD values when calculating LSD summaries.
asremlPlus Version 4.3-11 (2021-07-28)
Deprecate the function asrtests, which has been replaced by the function as.asrtests.
There has been a substantial revision of the calculation and saving of the LSD component of an
alldiffs
object.The argument
meanLSD.type
has been changed toLSDtype
. All functions that are S3 methods foralldiffs
objects will check for themeanLSD.type
attribute and, if found, change it toLSDtype
.The option
supplied
has been added to the argumentLSDtype
so that the user can supply LSD values to replace those in theassignedLSD
column of theLSD
component.The two new arguments
LSDstatistic
andLSDaccuracy
have been added. The argumentLSDstatistic
allows a choice ofminimum
,mean
,median
ormaximum
. The values of the nominated LSD statistics are stored in a column of the LSD component namedassignedLSD
. The argumentLSDaccuracy
allows the specification of a statistic summarizing the differences between the the LSDs and the assigned LSD value for each row of the LSD component. The values of the chosen measure are stored in a column of theLSD
component namedaccuracyLSD
. These two arguments have been added to the functions allDifferences.data.frame, as.alldiffs.object, as.alldiffs, linTransform.alldiffs, pairdiffsTransform, predictPlus.asreml, predictPresent.asreml, ratioTransform.alldiffs, recalcLSD.alldiffs and redoErrorIntervals.alldiffs.The
LSD
component is always calculated and stored as a component whenpairwise
isTRUE
.
A new argument
accuracy.threshold
has been introduced to control the addition of a column namesLSDwarning
to thepredictions
of analldiffs
object. THis column indicates whether or not the anhalfLeastSignificant
error.interval
is reliable as determined using the supplied value ofaccuracy.threshold
.The attributes of an alldiffs object and of the
predictions
component have been modified. The argumentsLSDtype
,LSDstatistic
andLSDby
, if set, are attributes of analldiffs
object. They are also attributes of aprediction.frame
and thebacktransforms
component of analldiffs
object, as isLSDvalues
, whenhalfLeastSignificant
error.intervals
are specified. TheLSDvalues
attribute has the values used in calculating half-LSD intervals. ThemeanLSD
attribute has been removed.A separate entry for
LSD.frame
has been introduced into the manual to dedscribe thedata.frame
that is stored in theLSD
component of analldiffs
object.
asremlPlus Version 4.3-10 (2021-07-5)
Fix bug in facRecast that meant that the argument
levels.order
was being ignored.Fix a bug in facRecast where only the predictions component was appropriately re-ordered.
Add new functions ratioTransform.alldiffs and pairdiffsTransform.
Add new method to sort for a
predictions.frame
: function sort.predictions.frame.Change the argument
sortWithinVals
tosortParallelToCombo
in sort.alldiffs.Add the new argument
sortNestinFactor
to sort.alldiffs.Add new function getTestEntry.asrtests.
Fix bug in infoCriteria.asreml that resulted in values of
Inf
for thefull
likelihood.
asremlPlus Version 4.2-36 (2021-05-16)
Deprecate facRecode.alldiffs because it only make sense to redo the current levels or labels.
Tidy up function facRecast.alldiffs.
asremlPlus Version 4.2-35 (2021-05-16)
Add new function facRecast.alldiffs that supercedes facRecode.alldiffs.
Revise sort.alldiffs to use facRecast.alldiffs to reorder the alldiffs components. This fixed a bug when not all levels of the
saortFactor
are present in the subset on which the sort is based.Add argument
alpha
to plotPvalues.data.frame and plotPvalues.alldiffs.
asremlPlus Version 4.2-34 (2021-05-12)
Add argument
axis.text.size
to plotPvalues.data.frame and plotPvalues.alldiffs.
asremlPlus Version 4.2-33 (2021-05-06)
Modify testresidual to not change the variance model when there is no difference in the variance DF between the models being compared.
In as.asrtests, add variance DF to
test.summary
when forming anasrtests
object.
asremlPlus Version 4.2-32 (2021-03-19)
Rebuild vignerttes.
Modify more links to asreml.
asremlPlus Version 4.2-31 (2021-03-19)
Modify link to asreml.
asremlPlus Version 4.2-30 (2021-03-18)
Revise doi specification in a link to a reference in the manual.
Increment version number for resubmission.
asremlPlus Version 4.2-29 (2021-03-18)
Increment version number for resubmission.
asremlPlus Version 4.2-28 (2021-03-17)
Recompile for CRAN submission.
asremlPlus Version 4.2-27 (2021-03-13)
Fix bugs in redoErrorIntervals.alldiff concerning whether or not meanLSD.type and LSDby settings result in the LSD component being recalculated.
Add rowname
overall
to the LSD component whenmeanLSD.type
is set tooverall
.
asremlPlus Version 4.2-26 (2020-11-11)
Modify URLs for CRAN submission.
asremlPlus Version 4.2-25 (2020-11-11)
Try to neutralize problem that occurs with
colourise
in print.predictions.frame.Rebuild for R 4.0.3 and recompile vignettes for CRAN submission.
asremlPlus Version 4.2-24 (2020-09-25)
Include a
key
option in thewhich
that producesvparametersummary
rather than the fullasremlsummary
.Remove attributes from formuale when executing printFormulae.
Add the ChickpeaEnd data set.
asremlPlus Version 4.2-23 (2020-09-07)
Modify code so that error intervals are set to NA when the LSDs are zero.
asremlPlus Version 4.2-22 (2020-09-04)
Modify code for calculating LSDs so that all zero LSDs are allowed; this is needed when a linear transformation has resulted in predictions that are equal.
asremlPlus Version 4.2-21 (2020-07-11)
Rebuild the vignettes prior to CRAN submission.
Add
envir
argument to getFormulae.asreml and printFormulae.asreml to make them more robust to where the objects in theasreml.obj
have been defined.
asremlPlus Version 4.2-20 (2020-06-29)
Fix bug in getFormulae.asreml and printFormulae.asreml that occurs when formula(e) have been supplied to asreml in an object.
asremlPlus Version 4.2-19 (2020-04-02)
Change the Maintainer email address.
Add ellipsis to as.asrtests call within an rmboundary.asrtests call so that arguments in the calling routine are passed through.
Add a trap in recalcWaldTab.asrtests for a
NULL
wald.tab
before dealing withdenDF
so that recalcWaldTab.asrtests throws a warning rather than an error.Modify recalcWaldTab.asrtests to deal with a Wald table that has Chi-square instead of F statistics (this happens when
denDF = "none"
.)
asremlPlus Version 4.2-18 (2020-03-16)
Increment version number for resubmission to CRAN.
asremlPlus Version 4.2-17 (2020-03-16)
Fix bug in changeTerms when both
addFixed
anddropFixed
areNULL
.
asremlPlus Version 4.2-16 (2020-02-25)
Revisions to the manual.
Fix bug in forming test.summary.
asremlPlus Version 4.2-15 (2020-02-17)
Added the
IClikelihood
argument to chooseModel.asrtests, reparamSigDevn.asrtests, rmboundary.asrtests, testranfix.asrtests, testresidual.asrtests, and testswapran.asrtests.Fix bug in printFormulae when the formula is long.
Various bug fixes associated with asreml-R version 3.
asremlPlus Version 4.2-14 (2020-02-14)
Fix bug in processing a formula that includes an
at
function.
asremlPlus Version 4.2-13 (2020-02-11)
Removed the
material.diff
argument and theboth
option from thewhich.IC
argument of changeModelOnIC.
asremlPlus Version 4.2-12 (2020-02-09)
Change
likelihood
in infoCriteria toIClikelihood
to make it consistent with other functions.Replace
tol.diff
withmaterial.diff
and set the default to 0.5 in changeModelOnIC.Revise all vignettes.
asremlPlus Version 4.2-11 (2020-02-08)
Add a new vignette for the use of information criteria with the wheat experiment.
Fixed bugs in changeModelOnIC associated with
addFixed
anddropFixed
and with dealing with unconverged models.
asremlPlus Version 4.2-10 (2020-02-07)
This version represents a major revision in that the facilities for employing information criteria (AIC and BIC) have been considerabley expanded. The infoCriteria method has been modified to add the possibility of calculating not only the the information criteria based on the REML likelihood, but those based on the full likelihood instead. There are now two infoCriteria methods, one for
asreml
objects and the other forlist
s ofasreml
objects. An alternative is to use changeTerms.asrtests wiithIClikelihood
set toREML
orfull
and the information criteria will be included in the Thetest.summary
of theasrtest
object. A new function changeModelOnIC has been included to allow model selection to be based on the information criteria, rather than on hypothesis tests. However, the two methods of selecting models can be interweaved.Add argument
omit.columns
to print.test.summary that allows the specification of columns to be omitted from the printout.Various modifications to the internal code for the handling of the
test.summary
component of anasrtest.object
to allow more flexibility in the make up oftest.summary
.Add function iterate.asrtests to execute additional iterations of the fit stored in an
asreml.obj
within anasrtests
object; the model itself cannot be changed.Add functions getFormulae.asreml and printFormulae.asreml to extract and print the
formula
e stored in thecall
of anasreml
object.Add
trace
argument to newfit.asreml and activated it for asreml-R version 4.Made R >= 3.5.0 a requirement for asremlPlus.