news R Documentation

News for Package asremlPlus

asremlPlus Version 4.3.50 (2023-03-9)

• Add classify argument to as.predictions.frame, checking that variables in the classify are in the predictions.frame and conversion of any variables in the classify that are not factor to factors.

• Update ggplot2 functions to use tidy evaluation.

• Fix internal anomaly causing a Note on CRAN.

asremlPlus Version 4.3.48 (2023-02-18)

• Rename makeTPSPlineXZMats.data.frame to makeTPPSplineMats.data.frame.

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 to grp.

• Fix bug in plotLSDerrors when LSDs have beeen computed for LSDtype set to factor.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 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 the list returned by chooseSpatialModelOnIC.asrtests to contains the information criteria for each spatial model that is fitted. Also, rename the components best and best.AIC to best.spatial.mod and best.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 (2022-12-31)

• Add arguments nestorder, degree and difforder to functions addSpatialModelOnIC.asrtests and makeTPSPlineXZMats.data.frame, as well as argument nestorder to chooseSpatialModelOnIC.asrtests. Add the option TPLV to the argument trySpatial 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 as Changed 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 and best.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 4.3.41 (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)

• Revise documentation for the arguments LSDtype, LSDsupplied, LSDby and LSDstatistic .

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.

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 of reshape2.

• Replace X1 and X2 with Rows and Columns as the default names for the the first two columns of the data.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 a list containing the plots that have be produced as ggplot 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 the classify to being that they must be in the predictions component of the alldiffs.obj.

asremlPlus Version 4.3-26 (2021-10-21)

• Fix bug in false.pos and false.neg for LSDtype set to supplied when LSDby is not NULL.

• Add quantiles 25 (q25) and 75 (q75) to the values that LSDstatistic can take and the exploreLSDs.alldiffs investigates.

• Allow for multiple LSDstatistic values when LSDtype is factor.combination and LSDby is set.

asremlPlus Version 4.3-25 (2021-10-15)

• Add sig.size, sig.face and sig.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 associated vcov and sed in an alldiffs.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 are bound (B) or singular (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 to overall.

• Change default for plotHistogram in exploreLSDs.alldiffs to FALSE.

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 from n to c.

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.

asremlPlus Version 4.3-15 (2021-08-19)

• Fixed bug in halfLeastSignificant.limit when LSDtype is factor.combination and the assignedLSD is zero to now ensure that the limit is NA.

• 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 the LSDby 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 the LSDby argument.

• Minor internal modification.

asremlPlus Version 4.3-12 (2021-08-11)

• Fix bug in pairdiffsTransform when only two factors in classify.

• Add functions exploreLSDs, plotLSDs.alldiffs, plotLSDs.matrix and plotLSDs.data.frame.

• Incorporate arguments retain.zerLSDs and zero.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 to LSDtype. All functions that are S3 methods for alldiffs objects will check for the meanLSD.type attribute and, if found, change it to LSDtype.

• The option supplied has been added to the argument LSDtype so that the user can supply LSD values to replace those in the assignedLSD column of the LSD component.

• The two new arguments LSDstatistic and LSDaccuracy have been added. The argument LSDstatistic allows a choice of minimum, mean, median or maximum. The values of the nominated LSD statistics are stored in a column of the LSD component named assignedLSD. The argument LSDaccuracy 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 the LSD component named accuracyLSD. 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 when pairwise is TRUE.

• A new argument accuracy.threshold has been introduced to control the addition of a column names LSDwarning to the predictions of an alldiffs object. THis column indicates whether or not the an halfLeastSignificant error.interval is reliable as determined using the supplied value of accuracy.threshold.

• The attributes of an alldiffs object and of the predictions component have been modified. The arguments LSDtype, LSDstatistic and LSDby, if set, are attributes of an alldiffs object. They are also attributes of a prediction.frame and the backtransforms component of an alldiffs object, as is LSDvalues, when halfLeastSignificant error.intervals are specified. The LSDvalues attribute has the values used in calculating half-LSD intervals. The meanLSD attribute has been removed.

• A separate entry for LSD.frame has been introduced into the manual to dedscribe the data.frame that is stored in the LSD component of an alldiffs 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 to sortParallelToCombo in sort.alldiffs.

• Add the new argument sortNestinFactor to sort.alldiffs.

• Fix bug in infoCriteria.asreml that resulted in values of Inf for the full 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 an asrtests object.

asremlPlus Version 4.2-32 (2021-03-19)

• Rebuild vignerttes.

• Modify more links 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 when meanLSD.type is set to overall

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 the which that produces vparametersummary rather than the full asremlsummary.

• 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 the asreml.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 with denDF 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 and dropFixed are NULL.

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 the both option from the which.IC argument of changeModelOnIC.

asremlPlus Version 4.2-12 (2020-02-09)

• Change likelihood in infoCriteria to IClikelihood to make it consistent with other functions.

• Replace tol.diff with material.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 and dropFixed 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 for lists of asreml objects. An alternative is to use changeTerms.asrtests wiith IClikelihood set to REML or full and the information criteria will be included in the The test.summary of the asrtest 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 an asrtest.object to allow more flexibility in the make up of test.summary.

• Add function iterate.asrtests to execute additional iterations of the fit stored in an asreml.obj within an asrtests object; the model itself cannot be changed.

• Add functions getFormulae.asreml and printFormulae.asreml to extract and print the formulae stored in the call of an asreml object.

• Add trace argument to newfit.asreml and activated it for asreml-R version 4.

• Made R >= 3.5.0 a requirement for asremlPlus.

asremlPlus Version 4.1-37 (2020-01-27)

• Modify linTransform.alldiffs so that submodels involving covariates are possible.

• Split Ladybird vignette into two, one based on asreml and the other on lm, lmerTest and emmeans.

• Modified newfit to circumvent problems in the test functions in dealing with terms that include the at function and modified testranfix to improve its detection of multiple terms.

asremlPlus Version 4.1-36 (2020-01-12)

• Correct date in DESCRIPTION for CRAN rsubmission.

asremlPlus Version 4.1-35 (2020-01-11)

• Rebuild for CRAN submission.

asremlPlus Version 4.1-34 (2019-12-14)

• Change default for subset argument in subset.alldiffs so that the complete set of predictions is returned. Also, change check on the resulting classify so that it checks whether the variables in the classify uniquely index the predictions.

• Include in renewClassify.alldiffs a check that the newclassify uniquely indexes the predictions.

asremlPlus Version 4.1-33 (2019-11-08)

• Add printPlot = FALSE to both plotPvalues.data.frame and plotPvalues.alldiffs. Change return for plotPvalues.data.frame from nothing to the plot produced using ggplot.

asremlPlus Version 4.1-32 (2019-09-30)

• Fix bug in check for predict.asreml returning sed and/or vcov when requested.

asremlPlus Version 4.1-31 (2019-09-19)

• Add new functions facRecode.alldiffs and facRename.alldiffs.

asremlPlus Version 4.1-30 (2019-09-05)

• Implement a check that predict.asreml has returned sed and/or vcov when requested.

asremlPlus Version 4.1-29 (2019-07-08)

• Allow for calculation of notional LSDs when LSDs for a single observation are specified.

• Removed restriction that overall LSD is always used when the range of the SEDs divided by the average of the SEDs is less than the avsed.tolerance.

• A bug in detecting valid wald.tab objects was fixed.

asremlPlus Version 4.1-28 (2019-07-04)

• Modify testranfix.asrtests, as.asrtests, recalcWaldTab.asrtests and chooseModel.asrtests to allow for p-values based on a conditional Wald F-statistic if one is present in the wald.tab.

• Allow for 6-column wald.tab such as is obtained for ssType set to "conditional".

asremlPlus Version 4.1-27 (2019-06-01)

• Revise Wheat vignette to use qqplotr for Normal Probability Plots.

• Revise test for tilde (~) in formula supplied to changeTerms so that only a leading tilde causes an error.

asremlPlus Version 4.1-26 (2019-05-12)

• Rebuild for R 3.6.0.

asremlPlus Version 4.1-25 (2019-04-18)

• Fix a bug in changeTerms.asrtests that reset the residual model to the default when changing fixed or random terms.

• Check for NULL wald.tab when setting its class prior to storing it in an asrtests.object.

asremlPlus Version 4.1-24 (2019-04-11)

• Allow numerics, in addition to factors, in LSDby argument of predictPlus.

• Rename reorderClassify to renewClassify.

• Fix a bug in retention of attributes of the alldiffs.object in renewClassify.

• Add transform.power, offset and scale as attributes of the backtransforms component of an alldiffs.object.

• Rework the storage of the backtransforms component of an alldiffs.object to ensure that it is retained when manipulating alldiffs.object.

asremlPlus Version 4.1-23 (2019-04-03)

• Build in R version 3.5.3.

• Update the Author field of the DESCRIPTION to include an ORCID.

• Allow backtransformed halfLSD intervals in the backtransforms component of an alldiffs.object.

asremlPlus Version 4.1-22 (2019-03-04)

• Build in R version 3.5.2.

• Update the license to remove blank line and resubmit to CRAN.

asremlPlus Version 4.1-21 (2019-03-01)

• Build in R version 3.5.2.

• Update the license to include 2019.

asremlPlus Version 4.1-20 (2019-02-23)

• Add print.predictions.frame and print.wald.tab as S3 methods to give more control over the printing of objects of class wald.tab and predictions.frame.

• Made sure that class wald.tab is associated with a wald.tab and classes asreml.predict and predictions.frame are associated with a predictions.frame when these are produced by asreml.

asremlPlus Version 4.1-19 (2019-02-22)

• Add colourise argument to print.alldiffs so that the default is FALSE and it overrides the asreml.options setting.

asremlPlus Version 4.1-18 (2019-02-21)

• Use R.rsp to install vignettes so that hyperlinks are active.

• Add colourise argument to print.asrtests so that the default is FALSE and it overrides the asreml.options setting.

asremlPlus Version 4.1-17 (2019-02-16)

• Fix bug in infoCriteria.asreml when DF supplied. For both infoCriteria.asreml and REMLRT.asreml, calculate the bound terms and if appropriate give arning messages.

asremlPlus Version 4.1-16 (2019-02-07)

• More vignettes changes, including adding manual to vignettes.

• Fix accidental reordering of alldiffs object when meanLSD.type is factor combinatons.

asremlPlus Version 4.1-15 (2019-02-05)

• Make vignettes visible.

• Modify estimateV in response to correction of corb naming in latest build.

asremlPlus Version 4.1-14 (2019-02-02)

• Revise Wheat vignette and entry in asremlPlus-package documentation.

• Modify printing of wald.tab by print.asrtests to remove colouring because it causes problems with knitr.

asremlPlus Version 4.1-13 (2019-01-30)

• Add a check to plotPredictions.data.frame to warn when linear.transformation is supplied.

• Also remove zero LSDs when calculating overall LSD and sed.range.

• Add a check to linTransform.alldiffs that factors in LSDby are in the submodel.

• Add the Wheat example as a vignette.

asremlPlus Version 4.1-12 (2019-01-26)

• Remove LSDs for which sed is effectively zero from the calculation of LSD statistics, provided not all are zero.

asremlPlus Version 4.1-11 (2019-01-21)

• Fix bug in test of the range of SEDs against avsed.tolerance when caclulating LSDs.

• Add attributes meanLSD.type and LSDby to alldiffs objects so that redoErrorIntervals.alldiffs can determine these attributes when its meanLSD.type argument is not set.

• Minor documentation changes.

asremlPlus Version 4.1-10 (2019-01-08)

• Add entries for predictions.frame, alldiffs.object and asrtests.object and made changes to the documentation to provide links to these pages.

• Defined classes alldiffs, asrtests and predictions.frame.

• Added the functions is.alldiffs, validAlldiffs, is.asrtests, validAsrtests, is.predictions.frame and validPredictionsFrame for validating the objects.

• Added tests for the validity of objects to methods functions.

• Provided as.asrtests function, while retaining asrtests function as a pseudonym for as.asrtests. Added an as.prediction.frame function.

• Add examples for alldiffs and data.frame methods functions that use lme4 to show how to use asremlPlus with packages othere than asreml.

asremlPlus Version 4.1-08 (2018-12-10)

• Correct predictPlus, plotPredictions and allDifferences.dat.frame to deal with a classify equal to "(Intercept)".

• Implement fix of R.param and G.param in supplied object for corb in estimateV function.

• Make documentation changes for asreml-R4.1.

asremlPlus Version 4.1-06 (2018-09-03)

• Fix minor bugs in redoErrorIntervals.alldiffs.

asremlPlus Version 4.1-05 (2018-08-29)

• Allow no Vmatrix in linTransform.alldiffs when error.intervals is none and allow transformation of predicted.value only when vcov component of alldiffs object is not available.

• Allow no sed in allDifferences.data.frame when not pairwise is TRUE.

asremlPlus Version 4.1-04 (2018-08-16)

• Modify legend size and position in plotPvalues.alldiffs.

asremlPlus Version 4.1-03 (2018-08-12)

• Add rmClassifyVars to subset.alldiffs.

asremlPlus Version 4.1-02 (2018-06-13)

• Rebuild under latest version of R 3.5.0 with requirement for R >= 3.1.0.

• Fix bug in bootREMLRT.

asremlPlus Version 4.1-01 (2018-06-03)

• Changes to make asremlPlus with the release version of asreml version 4.1.

• Fixed bug in predictPlus that meant the denominator degrees of freedom could not be obtained from wald.tab when error.intervals was set to "none" or "StandardError".

• Fixed bug in LSDby option that meant the correct subsets were not being identified when the levels of one factor in the predictions are subset of another factor.

asremlPlus Version 4.0-28 (2018-04-18)

• Fix minor bug in plotPvalues.alldiffs associated with factors.per.grid when there ais more than one factor indexing the different grids.

asremlPlus Version 4.0-27 (2018-03-23)

• Add factors.per.grid plotPvalues.alldiffs to allow automatic calculation of grid spacing.

asremlPlus Version 4.0-26 (2018-03-16)

• Add argument linear.transformation to predictPresent.

asremlPlus Version 4.0-25 (2018-03-15)

• Minor bug fix in print.alldiffs.

asremlPlus Version 4.0-24 (2018-03-15)

• Add argument vcov to allDifferences.data.frame and as.alldiffs and modify print.alldiffs, recalcLSD.alldiffs, sort.alldiffs and subset.alldiffs to process the vcov component of an alldiffs object.

• Add argument linear.transformation to predictPlus to enable a linear transformation of the predictiions as specified by a matrix or a model formula.

• Add function linTransform.alldiffs that effects a linear transformation of the predictions stored in an alldiffs object.

• Fixed bug in backtransforming predictions in predictPlus when offset is nonzero and scale is not one.

asremlPlus Version 4.0-23 (2018-02-19)

• Fix bug in gridline in plotPvalues whentriangles is set to upper or lower.

asremlPlus Version 4.0-22 (2018-02-01)

• Fix bug in reordering components of an alldiffs object.

asremlPlus Version 4.0-20 (2017-12-28)

• Modifications to checking of options for function arguments.

• Add tip for installing asremlPlus from github.

• Modifications to internals.

asremlPlus Version 4.0-19 (2017-12-18)

• Fix bug in redoErrorIntervals.alldiffs to make sure status or est.status is the last column in the predictions component of the alldiffs object.

• Modifications to internals.

asremlPlus Version 4.0-18 (2017-12-11)

• Add colours argument to plotPvalues.data.frame and to plotPvalues.alldiffs and add triangles argument to plotPvalues.alldiffs. In plotPvalues.data.frame, move legend.position to bottom of plot and increase legend.width to 2 cm. Also, remove panel.grid from plot and enforce an aspect.ratio of one.

• Fix bug in subset.asreml that did not reduce the levels of the in the prediction component of an alldiffs object to those remaining after subsetting.

asremlPlus Version 4.0-16 (2017-11-20)

• Add code to allDifferences.data.frame that ensures that the order of the predictions, and associated compoenents are in standard order for the classify on which the predictions are based.

asremlPlus Version 4.0-15 (2017-11-17)

• Fix bug in REMLRT.asreml related to bound.exclusions with asreml3.

asremlPlus Version 4.0-14 (2017-10-26)

• Have modified testresidual.asrtests, testranfix.asrtests and testswapran.asrtests to fit the new random/residual model when the old random/residual model has not converged and allow.unconverged is set to FALSE. In such cases the value of p will be NA. For these functions, when airthe the new or the old model has failed to converge, an indication of failure to converge will be added to the action reported in test.summary.

asremlPlus Version 4.0-13 (2017-10-22)

• Modified meanLSD.type argument in allDifferences.data.frame, predictPlus.asreml and predictPresent.asreml to include a factor.combinations option that obtains the mean LSD for each combinaton of the levels of one or more factors.

• Added functions recalcLSD.alldiffs and redoErrorIntervals.alldiffs to enable recalculations on alldiffs objects.

• (Added call to asreml.options with keep.order = TRUE in newfit.asreml when asreml4 is loaded, because asreml4 requires it.)

asremlPlus Version 4.0-12 (2017-10-09)

• Modified recalcWaldTab.asrtests to pass empty wald.tab when wald.asreml has failed.

• Made minor changes to testresidual.asrtests to make clear the still use rcov in asreml3.

asremlPlus Version 4.0-11 (2017-07-13)

• Fixed bug in REMLRT.asreml and rmboundary.asrtests.

asremlPlus Version 4.0-10 (2017-07-06)

• Fixed bugs in allDifferences.data.frame and plotPvalues.alldiffs.

• Some internal recoding to replace calls to summary.asreml.

asremlPlus Version 4.0-09 (2017-05-14)

• Added gridspacing option to plotPvalues.alldiffs and plotPvalues.data.frame so that a grid could be formed over groups of rows and columns“.

• Added function sort.alldiffs to sort the components of an alldiffs object according to the predicted values. Add arguments and a call to it to predictPlus.asreml, predictPresent.asreml and plotPvalues.alldiffs.

• Added attributes sortFactor and sortOrder to an alldiffs object so that this is accessible to users for use in other calls.

• Added the oats split-plot design from Yates (1937).

asremlPlus Version 4.0-08 (2017-05-4)

• Minor change to as.alldiffs to make sure that using standard.error and est.status rather than std.error and status in the predictions data.frame.

asremlPlus Version 4.0-07 (2017-4-12)

• Added which.matrix argument to estimateV so that could estimate the varaince, random or residual matrix.

• Incorporate newresidual.asrtests into changeTerms.asrtests and added check for boundary and singular terms.

asremlPlus Version 4.0-06 (2017-3-25)

• Added checkboundaryonly argument to rmboundary.asrtest and all functions that call it so that could control removal of boundary and singular terms.

• Incorporate newresidual.asrtests into changeTerms.asrtests and added check for boundary and singular terms.

asremlPlus Version 4.0-05 (2017-3-19)

• Change full.asreml.obj and reduced.asreml.obj to h1.asreml.obj and h0.asreml.obj in REMLRT.asreml and reordered them.

asremlPlus Version 4.0-03 (2017-2-26)

• Make the default in variofaces.asreml for V be NULL, in which case V is obtained using estimateV.asreml.

asremlPlus Version 4.0-02 (2017-2-19)

• Fix bug in plotPvalues arising from asreml not always returning factors in the predicted values.

asremlPlus Version 4.0-01 (2017-2-12)

• Modify varofaces.asreml and simulate.asreml to perform the simulations and analysis of data sets using parallel processng.

• Add recalcWaldTab to asrtests so that wald.tab options for denominator degrees of freedom are taken into account whenever wald.tab is recalculated.

• Add arguments DF and bound.exclusions to REMLRT.asreml and infoCriteria.asreml to allow more control over how the DF are determined. The number of bound parameters was added to the data.frame produced by these methods. Also, the arguments bound.exclusions and REMLDF were added to the methods testranfix.asrtests, testresidual.asrtests and testswapran.asrtests.

• Added meanLSD.type to allDifferences.data.frame, predictPlus.asreml and predictPresent.asreml to provide for an overall or per-prediction meanLSD. Allow avsed.tolerance in predictPlus to be set to NA which forces the calculation of LSDs for the overall mean LSD and set calculations of per-prediction LSDs whatever the value of codeavsed.tolerance. Changed to calculate the mean SED to be used for an LSD as the square root of the mean(s) of the variances of pairwise differences.

• Added functions plotPvalues.data.frame and plotPvalues.alldiffs to plot heat maps of p-values for pairwise differences between predictions.

• Added function estimateV.asreml to form the estimated variance matrix for the observations. However, this function is not available in ASReml-R version 3.

Changes in asremlPlus Version 4.0-0 (2017-1-1)

The asremlPlus version 4.x package represents a major revamp of asremlPlus to make it compatible with ASReml-R version 4 and, at the same time, to make the functions that operate on asreml, asrtests and alldiffs objects into S3 methods for these S3 objects. This means that

• The function names have been modified so that the only period (‘.’) in the name is that before the object type for which the function is a method;

• The object part of the function name is no longer needed when calling the function;

• The arguments had to be reordered for some functions so that the argument for the object for which it is a method is the first argument; this may cause problems if matching of arguments by position has been used in calling functions;

• The names of some arguments have been changed because of changes in ASReml-R version 4; for example, rcov has been changed to residual throughout.

The full set of changes to function names is detailed in the asremlPlus manual and can be accessed using ?asremlPlus-deprecated.

In spite of th changes, the new version still works with ASReml-R version 3, although with changes. A particularly problematic change for version 3 is that testrcov.asrtests becomes testresidual.asrtests even though rcov is still used in calls to asreml.

asremlPlus Version 3.0-0 (2016-11-19)

• Version 3 of asremlPlus was skipped in order to line up the version numbers of asreml and asremlPlus.

Changes in asremlPlus Version 2.0-13 (2016-09-26)

• Add argument allow.unconverged in addrm.terms.asrtests, choose.model.asrtests, newfit.asreml, newrcov.asrtests, sig.devn.reparam.asrtests, testranfix.asreml, testrcov.asrtests, testswapran.asrtests. It allows control over whether an unconverged analysis is to be abandoned.

Changes in asremlPlus Version 2.0-12 (2016-09-16)

• Rebuild under R 3.4.0.

Changes in asremlPlus Version 2.0-11 (2016-08-13)

• Added check that wald.tab is a four-column data.frame to predictionplot.asreml and pred.present.asreml.

Changes in asremlPlus Version 2.0-10 (2016-06-08)

• Added ggplotFuncs argument to predictionplot.asreml and pred.present.asreml.

• Added bound.test.parameters to reml.lrt.asreml, choose.model.asartests, testranfix.asrtests, testrcov.asrtests. testwapran.asrtests.

Changes in asremlPlus Version 2.0-9 (2016-05-15)

• Revised some documentation.

Changes in asremlPlus Version 2.0-8 (2016-04-18)

• Fixed a minor bug in rmboundary.asrtests.

Changes in asremlPlus Version 2.0-7 (2016-04-06)

• Fixed some minor bugs in testswapran.asrtests.

Changes in asremlPlus Version 2.0-6 (2016-02-16)

• Fixed some minor bugs.

Changes in asremlPlus Version 2.0-5 (2016-01-24)

• Added WaterRunoff.dat data set and modified examples based on this data set so that the examples would run.

• Fixed some minor bugs.

Changes in asremlPlus Version 2.0-4 (2015-11-12)

• Added means argument to variofaces.asreml.

Changes in asremlPlus Version 2.0-3 (2015-11-11)

• Modifications to predictionplot.asreml and pred.present.asreml as a result of changes made to ggplot2 version 1.0.1.

Changes in asremlPlus Version 2.0-1 (2015-09-14)

• Added graphics.device argument to variofaces.asreml and changed default for this argument to NULL in pred.present.asreml and predictionplot.asreml.

Changes in asremlPlus Version 2.0-0 (2015-06-24)

• The following functions were deprecated and replaced with functions that have the suffix asrtests instead of asreml, to signify that they operate on asrtests objects: addrm.terms.asreml, choose.model.asreml, recalc.wald.tab.asreml, rmboundary.asreml, sig.devn.reparam.asreml, testranfix.asreml, testrcov.asreml and testswapran.asreml.

• The following functions were deprecated info.crit and reml.lrt; they are replaced by info.crit.asreml and reml.lrt.asreml, repsectively.

• NEWS and documentation of deprecated functions added.

Changes in asremlPlus Version 1.10-16 (2015-06-06)

• First version placed on CRAN.