# dae v3.0-32

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## Functions Useful in the Design and ANOVA of Experiments

The content falls into the following groupings: (i) Data, (ii) Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions, (vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions. There is a vignette describing how to use the design functions for randomizing and assessing designs available as a vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of information when the 'Error' function has been used in the call to 'aov'. The package 'dae' can also be installed from <http://chris.brien.name/rpackages/>.

## Functions in dae

 Name Description dae-package dae ABC.Interact.dat Randomly generated set of values indexed by three factors BIBDWheat.dat Data for a balanced incomplete block experiment correct.degfree Check the degrees of freedom in an object of class projector designLatinSqrSys Generate a systematic plan for a Latin Square design designPlot A graphical representation of an experimental design using labels stored in a matrix. Casuarina.dat Data for an experiment with rows and columns from Williams (2002) dae-deprecated Deprecated Functions in Package dae fac.layout Generate a randomized layout for an experiment fac.match Match, for each combination of a set of columns in x, the row that has the same combination in table harmonic.mean Calcuates the harmonic mean. fac.recode Recodes factor levels using values in a vector. The values in the vector do not have to be unique. McIntyreTMV.dat The design and data from McIntyre's (1955) two-phase experiment fac.sumop computes the summation matrix that produces sums corresponding to a (generalized) factor mpone Converts the first two levels of a factor into the numeric values -1 and +1 Exp249.mplot.des Systematic, main-plot design for an experiment to be run in a greenhouse interaction.ABC.plot Plots an interaction plot for three factors mat.arma Forms an arma correlation matrix Oats.dat Data for an experiment to investigate nitrogen response of 3 oats varieties mat.banded Form a banded matrix from a vector of values efficiencies Extracts the canonical efficiency factors from a pcanon.object or a p2canon.object. mat.exp Forms an exponential correlation matrix efficiency.criteria Computes efficiency criteria from a set of efficiency factors no.reps Computes the number of replicates for an experiment fac.meanop computes the projection matrix that produces means resid.errors Extract the residuals for a fitted model mat.gau Forms an exponential correlation matrix Zncsspline Calculates the design matrix for fitting the random component of a natural cubic smoothing spline Fac4Proc.dat Data for a 2^4 factorial experiment as.data.frame.pstructure Coerces a pstructure.object to a data.frame. designAmeasures Calculates the average variance of pairwise differences from the variance matrix for predictions that can be obtained using mat.Vpredicts residuals.aovlist Extract the residuals from an aovlist object p2canon.object Description of a p2canon object fac.nested creates a factor whose values are generated within those of the factor nesting.fac LatticeSquare_t49.des A Lattice square design for 49 treatments decomp.relate Examines the relationship between the eigenvectors for two decompositions pcanon.object Description of a pcanon object pstructure.object Description of a pstructure object is.allzero Tests whether all elements are approximately zero is.projector Tests whether an object is a valid object of class projector degfree Degrees of freedom extraction and replacement designAnatomy Given the layout for a design, obtain its anatomy via the canonical analysis of its projectors to show the confounding and aliasing inherent in the design. designTwophaseAnatomies Given the layout for a design and three structure formulae, obtain the anatomies for the two-phase, first-phase, cross-phase and second-phase designs. detect.diff Computes the detectable difference for an experiment fac.divide Divides a factor into several individual factors fac.gen Generate all combinations of several factors and, optionally, replicate them fitted.errors Extract the fitted values for a fitted model mat.J Forms a square matrix of ones fac.ar1mat forms the ar1 correlation matrix for a (generalized) factor mat.Vpred Calculates the variances of a set of predicted effects from a mixed model qqyeffects Half or full normal plot of Yates effects mat.dirprod Forms the direct product of two matrices get.daeTolerance Gets the value of daeTolerance for the package dae mat.dirsum Forms the direct sum of a list of matrices projs.combine.p2canon Extract, from a p2canon object, the projectors that give the combined canonical decomposition mat.ar2 Forms an ar2 correlation matrix pstructure.formula Takes a formula and constructs a pstructure.object that includes the orthogonalized projectors for the terms in a formula rmvnorm generates a vector of random values from a multivariate normal distribution set.daeTolerance Sets the values of daeTolerance for the package dae fac.combine Combines several factors into one SPLGrass.dat Data for an experiment to investigate the effects of grazing patterns on pasture composition marginality Extracts the marginality matrix (matrices) from a pstructure.object or a pcanon.object. Sensory3Phase.dat Data for the three-phase sensory evaluation experiment in Brien, C.J. and Payne, R.W. (1999) mat.I Forms a unit matrix mat.ar3 Forms an ar3 correlation matrix mat.sar2 Forms an sar2 correlation matrix mat.ncssvar Calculates the variance matrix of the random effects for a natural cubic smoothing spline meanop computes the projection matrix that produces means as.numfac Convert a factor to a numeric vector print.projector Print projectors blockboundaryPlot This function plots a block boundary on a plot produced by designPlot. mat.sar Forms an sar correlation matrix print.summary.p2canon Prints the values in an summary.p2canon object print.pstructure Prints a pstructure.object proj2.combine Compute the projection and Residual operators for two, possibly nonorthogonal, projectors designPlotlabels Plots labels on a two-way grid using ggplot2 proj2.efficiency Computes the canonical efficiency factors for the joint decomposition of two projectors print.summary.pcanon Prints the values in an summary.pcanon object designRandomize Randomize allocated to recipient factors to produce a layout for an experiment proj2.eigen Canonical efficiency factors and eigenvectors in joint decomposition of two projectors tukey.1df Performs Tukey's one-degree-of-freedom-test-for-nonadditivity projector-class Class projector summary.p2canon Summarize a canonical analysis of the relationships between two sets of projectors yates.effects Extract Yates effects elements Extract the elements of an array specified by the subscripts summary.pcanon Summarizes the anatomy of a design, being the decomposition of the sample space based on its canonical analysis, as produced by designAnatomy extab Expands the values in table to a vector fac.vcmat forms the variance matrix for the variance component of a (generalized) factor fitted.aovlist Extract the fitted values for a fitted model from an aovlist object mat.Vpredicts Calculates the variances of a set of predicted effects from a mixed model, based on supplied matrices or formulae. mat.ar1 Forms an ar1 correlation matrix mat.ma1 Forms an ma1 correlation matrix mat.ma2 Forms an ma2 correlation matrix power.exp Computes the power for an experiment print.aliasing Print an aliasing data.frame projector Create projectors projs.2canon A canonical analysis of the relationships between two sets of projectors show-methods Methods for Function show in Package dae strength Generate paper strength values daeTips The intermittent, randomly-presented, startup tips. 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## Vignettes of dae

 Name DesignNotes.pdf.asis dae-manual.pdf.asis No Results!

## Details

 Date 2019-05-15 VignetteBuilder R.rsp License GPL (>= 2) URL http://chris.brien.name RoxygenNote 5.0.1 NeedsCompilation no Packaged 2019-05-15 05:16:50 UTC; briencj Repository CRAN Date/Publication 2019-05-15 08:30:02 UTC
 depends ggplot2 , R (>= 3.1.0) imports graphics , methods , plyr , stats suggests R.rsp , testthat Contributors