News for Package dae

Changes in dae version 3.2.28 (2024-06-12)

• Update for submission to CRAN.

Changes in dae version 3.2.27 (2024-05-27)

• Add the variable daeRNGkind to the daeEnv, with default Mersenne-Twister, and the functions set.daeRNGkind and get.RNGkind. This ensures tha the random number generator used by dae has to be explicitly changed by the user.

Changes in dae version 3.2.26 (2024-04-21)

• Fixed bugs in testing whether projectors are symmetric or idempotent caused by unimportant differences in attributes of objects involved in the testing.

Changes in dae version 3.2.25 (2024-04-09)

• Update for submission to CRAN.

Changes in dae version 3.2.24 (2024-03-19)

• Fixed bug in pstructure, also affecting designAnatomy, that resulted aliasing of two terms going undetected, nesting of sources was not being correctly determined when aliasing was present, and computed marginality relationships not being transitive.

Changes in dae version 3.2.23 (2024-02-25)

• Added trap for svd error so that only a warning will be given and an NA returned.

Changes in dae version 3.2.22 (2024-02-13)

• Add link to GitHub issues page for BugReports in DESCRIPTION file.

• Fixed problem in mat.ginv for inverting matrices of rank one that led to a conformability error caused by R returning a single column matrix as a vector.

Changes in dae version 3.2.21 (2024-01-14)

• Corrects some minor issues in the manual.

Changes in dae version 3.2.20 (2024-01-14)

• Update the DesignNotes vignette.

• Add the function porthogonalize.list to orthogonalize a sequence of projectors. It externalizes the process for othogonalizing projectors previously performed within pstructure.formula.

• Add the function mat.ginv for computing generalized inverses.

• Add the functions mat.cor and mat.corg for forming correlation matrices.

Changes in dae version 3.2.19 (2023-08-08)

• Fix CRAN errors and increment version number.

Changes in dae version 3.2.18 (2023-08-07)

• Correct the DesignNotes vignette.

• Add facetstrips.switch argument to designGGPlot and the facetstrips.placement argument to designGGPlot and designBlocksGGPlot.

Changes in dae version 3.2.17 (2023-03-30)

• Correct the DesignNotes vignette.

• Add a check for a term that is equivalent to the grand mean term in designAnatomy.

Changes in dae version 3.2.16 (2023-03-26)

• Revise the DesignNotes vignette.

Changes in dae version 3.2.15 (2023-03-10)

• Update ggplot2 functions to use tidy evaluation.

Changes in dae version 3.2-14 (2023-01-13)

• Update DesignNotes vignette.

• Add a replications argument to designAmeasures and implement the calculation of weighted average pairwise variances using the replications.

Changes in dae version 3.2-13 (2021-11-15)

• Rebuild for R version 4.1.2.

Changes in dae version 3.2-12 (2021-11-05)

• Fix bug in the function fac.multinested that resulted in the order of the levels for each new nested factor, when each has the same levels, depending on the order that they occurred within the level of the nesting.fac.

Changes in dae version 3.2-11 (2021-09-01)

• Add the function fac.uncombine.

Changes in dae version 3.2-10 (2021-08-6)

• Add the functions fac.split and fac.genfactors.

• Modify fac.gen so that the number of levels for each recipient factor is the number of observed levels of that factor.

• Fix bug in finding marginal terms in pstructure.formula when there is partial aliasing amongst terms.

Changes in dae version 3.1-41 (2021-06-07)

• Add the function fac.recast, a function that replaces and extends fac.recode.

Changes in dae version 3.1-40 (2021-05-12)

• Fix bug in pstructure that resulted in errors in aliasing reporting.

Changes in dae version 3.1-39 (2021-04-10)

• Add scales.free argument to allow the axis scales to vary between facets in designGGPlot.

Changes in dae version 3.1-38 (2021-03-19)

• Rebuild vignette

Changes in dae version 3.1-37 (2021-03-17)

• Recompile for submission to CRAN

Changes in dae version 3.1-36 (2021-03-04)

• Fix bug in pstructure for parenthesizing terms that consist of generalized or combined factors.

Changes in dae version 3.1-35 (2021-02-25)

• Fix bug in the aliasing table, where "## Information remaining" not printed for pstructure.

• Add ... argument to print.aliasing call in print.structure.

• Allow multiple values for which argument in print.pstructure.

Changes in dae version 3.1-34 (2021-02-16)

• Minor refinements of the the tables of aliasing generated by pstructure.formula, projs.2canon and designAnatomy.

Changes in dae version 3.1-33 (2021-02-15)

• Tidy up print.pstructure by removing the ineffective which.criteria option and adding a which option to control which components are printed.

• Change the tables of aliasing generated by pstructure.formula, projs.2canon and designAnatomy so that the amount of information that is confounded is reported, instead of the amount of information that remains. The amount that remains is reported in the decomposition table.

Changes in dae version 3.1-32 (2020-11-11)

• Rebuild vignettes and and package for R 4.0.3 and CRAN submission.

Changes in dae version 3.1-31 (2020-09-21)

• Fix a bug in print.summary.pcanon that resulted in incorrect consecutive repetitions of sources within a column.

Changes in dae version 3.1-30 (2020-09-15)

• Check that at least one of labels and cellfillcolour.column is set in a call to designGGPlot.

Changes in dae version 3.1-29 (2020-08-05)

• Add label.size and labeller arguments to designGGPlot.

Changes in dae version 3.1-28 (2020-07-20)

• Re-implement fac.nested so that it is much more efficient.

Changes in dae version 3.1-27 (2020-07-09)

• Rebuild vignettes and and package for R 4.0.2 and CRAN submission.

Changes in dae version 3.1-26 (2020-06-15)

• Add x.axis.position argument to designGGPlot, making top the default.

Changes in dae version 3.1-25 (2020-05-12)

• Rebuild for R version 4.0.0.

• Minor revisions to DesignNotes vignette.

Changes in dae version 3.1-24 (2020-03-23)

• Change the Maintainer email address.

• Add function mat.vcomp.

Changes in dae version 3.1-23 (2020-03-16)

• Add the function rep.data.frame.

• Rename the design species for which designTwoPhaseAnatomies produces anatomies. Also, allow the overriding of the default titles for each anatomy.

Changes in dae version 3.1-22 (2020-01-16)

• Add the function fac.uselogical.

Changes in dae version 3.1-21 (2020-01-12)

• Reduce example for fac.multinested and build for CRAN resubmission.

Changes in dae version 3.1-20 (2020-01-11)

• Rebuild for CRAN submission.

Changes in dae version 3.1-19 (2019-12-30)

• Add names of countries to Countries factor in Casuarina.dat.

• Make additions to the DesignNotes vignette.

Changes in dae version 3.1-18 (2019-12-27)

• Add names of missing factor/covariate to error message in pstructure.

• Add function fac.multinested

Changes in dae version 3.1-17 (2019-11-23)

• Revise the DesignNotes vignette.

• Further debug designRandomize for some data.frames not in standard order.

Changes in dae version 3.1-16 (2019-11-07)

• Correct typo and re-upload to CRAN.

Changes in dae version 3.1-15 (2019-11-07)

• Prepare for upload to CRAN.

Changes in dae version 3.1-14 (2019-10-29)

• Add the capability to mat.Vpredicts to return either the variance or the information matrix. Also, add the rank of the matrix as an attribute of the matrix.

Changes in dae version 3.1-13 (2019-10-27)

• Revise DesignNotes vignette.

• Further debug designRandomize for either data.frame not in standard order or column order inconsistencies.

• Rename name of data set Exp249.mplot.des to Exp249.munit.des.

Changes in dae version 3.1-12 (2019-10-20)

• Include check for names supplied in nested.recipients are in the names in recipients.

Changes in dae version 3.1-11 (2019-10-10)

• Fix bug in designRandomize that occurs when a supplied data.frame is not in standard order.

• Deprecate fac.layout

• Update the DesignNotes vignette.

Changes in dae version 3.1-10 (2019-09-29)

• Merge features of designPlot and designPlotlabels into a new function designGGPlot and replace blockboundaryPlot with designBlocksGGPlot. The functions designPlot, blockboundaryPlot and designPlotlabels have been marked for future deprecation.

• Update the DesignNotes vignette.

Changes in dae version 3.0-32 (2019-05-15)

• Rebuild under version 3.6.0 prior to resubmission to CRAN.

Changes in dae version 3.0-31 (2019-04-04)

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

• Add new function designTwophaseAnatomies.

Changes in dae version 3.0-30 (2019-03-29)

• Add reverse.x and reverse.y arguments to designPlotlabels.

Changes in dae version 3.0-29 (2019-03-23)

• Dcoumentation revisions.

Changes in dae version 3.0-28 (2019-03-12)

• Fix bug in mat.Vpredicts when there are no random effects.

Changes in dae version 3.0-27 (2019-02-21)

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

Changes in dae version 3.0-26 (2019-02-18)

• Deal with a mean only formula (~1) in pstructure.formula.

Changes in dae version 3.0-25 (2019-02-07)

• Reorganize vignette and include manual as a vignette.

Changes in dae version 3.0-24 (2019-02-01)

• Minor updates to the daeDesignNotes vignette and move to a vignettes subdirectory.

Changes in dae version 3.0-23 (2018-10-17)

• Add diagnostic message to mat.Vpredicts.

• Fix a bug in setValidity of class "projector".

Changes in dae version 3.0-22 (2018-10-01)

• Fix bug in mat.Vpredicts when have a a single random term for a single factor.

Changes in dae version 3.0-21 (2018-09-29)

• Add the new function mat.Vpredicts that has renamed arguments and the capability of using formulae in generating the required matrices.

Changes in dae version 3.0-20 (2018-09-02)

• Add eliminate argument to mat.Vpred.

Changes in dae version 3.0-19 (2018-08-25)

• Fix bug in summary.pcanon for a single formula when projectors are saved.

Changes in dae version 3.0-18 (2018-08-09)

• Small documentation edits.

Changes in dae version 3.0-17 (2018-6-12)

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

Changes in dae version 3.0-16 (2018-6-11)

• Rebuild under latest version of R 3.6.0.

Changes in dae version 3.0-15 (2018-04-06)

• Fix bugs in designAnatomy when there is only one structure.

• Fix bugs in print.summary.pcanon when there are no entries in a column of the table.

• Add a warning to print.summary.canon when the sum of sources' dimensions is less than the number of rows in data.

Changes in dae version 3.0-14 (2017-12-24)

• Modified checking of options for function arguments.

Changes in dae version 3.0-13 (2017-12-08)

• Modified mat.Vpred so that the Moore-Penrose inverse, which is unique, is always used for matrix inverses.

Changes in dae version 3.0-12 (2017-12-04)

• Rebuild under latest version of R.

Changes in dae version 3.0-11 (2017-10-22)

• Minor editing of documentation.

Changes in dae version 3.0-10 (2017-10-08)

• Changed designRandomize so that, if allocated is NULL, then a random permutation of the recipient factors is produced.

Changes in dae version 3.0-09 (2017-09-28)

• Adjust caption of summary.pcanon.

• Added new function designPlotlabels that uses ggplot to plot labels on a grid.

Changes in dae version 3.0-08 (2017-09-20)

• Correct bug in axis labelling in interaction.ABC.plot.

Changes in dae version 3.0-07 (2017-07-31)

• Reinstate ability to form and print a summary from old pcannon objects (pre version 3.0-0).

Changes in dae version 3.0-06 (2017-07-26)

• Fixed a bug in summary.pcanon so that aliasing table is printed when required.

Changes in dae version 3.0-05 (2017-07-13)

• Put in a check that factors/covariates in a formula are in data.

• Formatted the aliasing table to be similar to the decomposition table.

Changes in dae version 3.0-04 (2017-07-05)

• Apply David Stern's fix to fac.nested so that it deals with missing values in the nesting factor.

Changes in dae version 3.0-02 (2017-06-30)

• Added links to documentation.

Changes in dae version 3.0-01 (2017-06-29)

• Added a component named aliasing to pstructure.object that stores the information about (partial) aliasing between sources derived a single formula. Added a component named aliasing to pcanon.object that collects all the aliasing that has occured in the decomposition.

• Added the function print.aliasing to print a data.frame of class aliasing that contains aliasing information.

• Renamed Ameasures to designAmeasures

• Replaced the vignette for randomzing designs with a vignette that discusses the facilities for designing experiments that includes the use of designRandomize and designAnatomy.

Changes in dae version 3.0-0 (2017-06-11)

• Added the new function designRandomize with the intention that it will eventaully replace fac.layout. The new function replaces the arguments unrandomized and randomized with recipients and allocated, respectively, and nested.factors with nested.recipients. Also, it changes the default for unit.permutation to FALSE.

• Deprecated projs.structure, replacing it with pstructure.formula, creating a pstructure.object that stores the projectors, the lists of their term names and source names, and the marginality matrix for the terms. Added arguments marginality and check.marginality to allow the marginality matrix to be supplied, overwriting any that is produced by pstructure.formula. The argument check.marginality allows one to decide if the supplied and calculated marginality matrices are the same. Methods for as.data.frame, marginality and print were added for objects of class pstructure.

• Deprecated projs.canon, it being replaced by designAnatomy.

• Modified the function designAnatomy to accomodate the changes to pstructure. Added new argument labels to designAnatomy, which has option sources that will result in sources indicating whether they represent interactions and/or nested effects. Added argument marginality that allows a list of marginality matrices to be supplied. Added the argument check.marginality allows one to decide if the supplied and calculated marginality matrices are the same.

• Added argument labelswap to summary.pcanon so that can swap between terms and sources in the output.

• Added new method marginality.pcannon to extract the list of marginality matrices corresponding to the formulae in the call to designAnatomy. Added the argument labelswap to the summary.pcanon method so that either terms or sources can be output.

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

Changes in dae version 2.7-26 (2017-05-04)

• Converted projs.canon to designAnatomy, changing the position of data to be second in the argument list and changing meanTerm to grandMean. Retained projs.canon as a synonym with the same arguments as before. Also changed meanTerm to grandMean in projs.structure.

• Added new functions mat.ncssvar and Zspline that calculate the varaince matrix of the random spline effects and the design matrix for fitting random spline effects, respectively.

Changes in dae version 2.7-25 (2017-04-12)

• In designPlot, have the whole designMatrix plotted if labels is NULL.

Changes in dae version 2.7-24 (2017-02-10)

• Add the more general hybrid option to projs.structure and projs.canon and made it the default option.

• Changed fac.combine so that a single factor would pass through without generating an error message.

• Revise interaction.ABC.plot to account for ggplot deprecation.

• Add functions mat.sar, to form the correlation matrix from an SAR parameter, and mat.gau, to form a correlation function based on the square of the distance between coordinates.

Changes in dae version 2.7-23 (2017-01-05)

• Fix a bug in tukey.1df when there is no Error function in the model.

• Add tips.

Changes in dae version 2.7-22 (2016-10-03)

• Fix bug in no.reps when the number of reps to achieve the desired power is less than 2.

Changes in dae version 2.7-21 (2016-09-19)

• Fix bug in fac.combine that can introduce a level equal to NA when none of the factors has such a level.

Changes in dae version 2.7-20 (2016-09-16)

• Rebuild under R 3.4.0.

Changes in dae version 2.7-19 (2016-09-07)

• Include the argument meanTerm in projs.structure and projs.canon to allow the option to include the grand mean term.

Changes in dae version 2.7-18 (2016-08-07)

• Fixed a bug for aliased terms in projs.jandw.

Changes in dae version 2.7-17 (2016-05-18)

• Extended Ameasures to include a groups argument that allows explicit specification of the elements of groups for which A values are required.

Changes in dae version 2.7-16 (2016-05-16)

• Fixed a bug in fac.gen when there is a factor with a single character value.

Changes in dae version 2.7-15 (2016-05-14)

• Revised fac.recode and fac.divide to deal with factors with both numeric and character levels and to improve efficiency.

Changes in dae version 2.7-14 (2016-05-10)

• Added designLatinSqrSys.

• Revised some documentation.

Changes in dae version 2.7-13 (2016-04-25)

• Added functions mat.Vpred and Ameasures.

• Fixed bugs in fac.vcmat.

Changes in dae version 2.7-12 (2016-03-10)

• Reversed order of parameters in mat.ar1 and mat.exp.

• Added functions mat.ar2, mat.ar3, mat.ma1, mat.ma2, mat.arma and mat.sar2.

Changes in dae version 2.7-11 (2016-02-11)

• Added xefficiency, the maximum efficiency factor projector-based functions.

Changes in dae version 2.7-10 (2016-01-19)

• Improved the code for analyzing the relationships between pairs of projectors.

Changes in dae version 2.7-9 (2015-01-03)

• Include new functions designPlot and blockboundaryPlot, that are the same as design.plot and blockboundary.plot, except that they have less cryptic argument names and some arguments have been modified. It is envisaged that the new functions will supersede the old functions with the old functions being deprecated in due course.

• Fixed bug in projs.structure to ensure that arguments, including keep.order, are passed to the terms function.

Changes in dae version 2.7-8 (2015-12-16)

• Add arguments rchtdiv and cchtdiv to design.plot so that can size row and column labels independetly of the cell labels.

Changes in dae version 2.7-7 (2015-11-15)

• Improved the documentation of efficiency criteria in a number of functions.

Changes in dae version 2.7-6 (2015-11-02)

• Allow a single formula to be specified in formula of projs.canon.

• Improved proj2.combine to equate Qconf to Q1 when all of Q1 is confounded by Q2.

Changes in dae version 2.7-5 (2015-10-29)

• Fix bug in mat.banded in which the elements were being placed starting with the first subdiagonal instead of the diagonal.

Changes in dae version 2.7-4 (2015-10-01)

• Add arrgument ggplotFuncs to interaction.ABC.plot to allow ggplot functions to be used to modify the plot.

• Add detect.diff to allow the calculation of the detectable difference for given replication, power, delta and alpha.

Changes in dae version 2.7-3 (2015-08-23)

• Change option differencingfirst to differencing in projs.structure and projs.canon. Code modified so that differencing only orthogonalizes by subtracting from a projector those projectors whose factors are a subset of its factors.

• Added new criteria dforth to efficiency.criteria.

• Added order to the default setting of which.criteria in all functions that have this argument.

• NEWS added.

Changes in dae version 2.7-2 (2015-06-24)

• minor reprogramming.

• documentation of deprecated functions added.

• NEWS added.

Changes in dae Version 2.7-1 (2015-05-26)

• An except argument added to fac.layout so that nominated unrandomized factors are not permuted.

Changes in dae Version 2.7-0 (2015-04-29)

• Added functions to perform an eigenalysis of the projection matrices for an experimental design to produce the decomposition or skeleton-anova table. These functions include projs.combine.p2canon, projs.structure, projs.2canon, projs.canon, summary.p2canon, summary.pcanon, print.summary.p2canon, print.summary.pcanon. The top-level functions are those with the suffix 'pcanon'.

• This version uploaded to CRAN.