dae-package {dae} R Documentation

## Functions Useful in the Design and ANOVA of Experiments

### Description

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/>.

Version: 3.2-13

Date: 2021-11-15

### Index

 (i) Data ABC.Interact.dat Randomly generated set of values indexed by three factors BIBDWheat.dat Data for a balanced incomplete block experiment Casuarina.dat Data for an experiment with rows and columns from Williams (2002) Exp249.munit.des Systematic, main-plot design for an experiment to be run in a greenhouse Fac4Proc.dat Data for a 2^4 factorial experiment LatticeSquare_t49.des A Lattice square design for 49 treatments McIntyreTMV.dat The design and data from McIntyre (1955) two-phase experiment Oats.dat Data for an experiment to investigate nitrogen response of 3 oats varieties Sensory3Phase.dat Data for the three-phahse sensory evaluation experiment in Brien, C.J. and Payne, R.W. (1999) Sensory3PhaseShort.dat Data for the three-phase sensory evaluation experiment in Brien, C.J. and Payne, R.W. (1999), but with short factor names SPLGrass.dat Data for an experiment to investigate the effects of grazing patterns on pasture composition (ii) Factor manipulation functions as.numfac Convert a factor to a numeric vector fac.combine Combines several factors into one fac.divide Divides a factor into several individual factors fac.gen Generate all combinations of several factors and, optionally, replicate them fac.gen Generate all combinations of the levels of the supplied factors, without replication fac.match Match, for each combination of a set of columns in 'x', the row that has the same combination in 'table' fac.multinested Creates several factors, one for each level of a nesting.fac and each of whose values are either generated within those of the level of nesting.fac or using the values of a nested.fac fac.nested Creates a factor, the nested factor, whose values are generated within those of a nesting factor fac.recast Recasts a factor by modifying the values in the factor vector and/or the levels attribute, possibly combining some levels into a single level. fac.recode Recodes factor 'levels' using possibly nonunique values in a vector. (May be deprecated in future.) fac.split Splits a factor whose levels consist of several delimited strings into several factors. fac.uncombine Cleaves a single factor, each of whose levels has delimited strings, into several factors using the separated strings. fac.uselogical Forms a two-level factor from a logical object mpone Converts the first two levels of a factor into the numeric values -1 and +1 (iii) Design functions blockboundaryPlot This function plots a block boundary on a plot produced by 'designPlot'. It supersedes blockboundary.plot. designAmeasures Calculates the A-optimality measures from the variance matrix for predictions. 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. designBlocksGGPlot Adds block boundaries to a plot produced by designGGPlot. designGGPlot Plots labels on a two-way grid of coloured cells using ggplot2. designLatinSqrSys Generate a systematic plan for a Latin Square design. designPlot A graphical representation of an experimental design using labels stored in a matrix. It superseded design.plot. designPlotlabels Plots labels on a two-way grid using ggplot2. designRandomize Randomize allocated to recipient factors to produce a layout for an experiment. It supersedes fac.layout. designTwophaseAnatomies Given the layout for a design and three structure formulae, obtain the anatomies for the (i) two-phase, (ii) first-phase, (iii) cross-phase, treatments, and (iv) combined-units designs. marginality.pstructure Extracts the marginality matrix from a pstructure.object marginality.pstructure Extracts a list containing the marginality matrices from a pcanon.object print.aliasing Prints an aliasing data.frame no.reps Computes the number of replicates for an experiment detect.diff Computes the detectable difference for an experiment power.exp Computes the power for an experiment summary.pcanon Summarizes the anatomy of a design, being the decomposition of the sample space based on its canonical analysis (iv) ANOVA functions fitted.aovlist Extract the fitted values for a fitted model from an aovlist object fitted.errors Extract the fitted values for a fitted model interaction.ABC.plot Plots an interaction plot for three factors qqyeffects Half or full normal plot of Yates effects resid.errors Extract the residuals for a fitted model residuals.aovlist Extract the residuals from an aovlist object strength Generate paper strength values tukey.1df Performs Tukey's one-degree-of-freedom-test-for-nonadditivity yates.effects Extract Yates effects (v) Matrix functions elements Extract the elements of an array specified by the subscripts fac.ar1mat Forms the ar1 correlation matrix for a (generalized) factor fac.sumop Computes the summation matrix that produces sums corresponding to a (generalized) factor fac.vcmat Forms the variance matrix for the variance component of a (generalized) factor mat.I Forms a unit matrix mat.J Forms a square matrix of ones mat.ar1 Forms an ar1 correlation matrix mat.ar2 Forms an ar2 correlation matrix mat.ar3 Forms an ar3 correlation matrix mat.arma Forms an arma correlation matrix mat.banded Forms a banded matrix mat.exp Forms an exponential correlation matrix mat.gau Forms a gaussian correlation matrix mat.ma1 Forms an ma1 correlation matrix mat.ma2 Forms an ma2 correlation matrix mat.ncssvar Forms a variance matrix for random cubic smoothing spline effects mat.sar Forms an sar correlation matrix mat.sar2 Forms an sar2 correlation matrix mat.dirprod Forms the direct product of two matrices mat.dirsum Forms the direct sum of a list of matrices mat.random Calculates the variance matrix for the random effects from a mixed model, based on a formula or a supplied matrix mat.Vpred Forms the variance matrix of predictions mat.Vpredicts Forms the variance matrix of predictions, based on supplied matrices or formulae. Zncsspline Forms the design matrix for fitting the random effects for a natural cubic smoothing spline. (vi) Projector and canonical efficiency functions Projector class: projector Create projectors projector-class Class projector is.projector Tests whether an object is a valid object of class projector print.projector Print projectors correct.degfree Check the degrees of freedom in an object of class projector degfree Degrees of freedom extraction and replacement Accepts two or more formulae: designAnatomy An anatomy of a design, obtained from a canonical analysis of the relationships between sets of projectors. summary.pcanon Summarizes the anatomy of a design, being the decomposition of the sample space based on its canonical analysis print.summary.pcanon Prints the values in an 'summary.pcanon' object efficiencies.pcanon Extracts the canonical efficiency factors from a list of class 'pcanon' Accepts exactly two formulae: projs.2canon A canonical analysis of the relationships between two sets of projectors projs.combine.p2canon Extract, from a p2canon object, the projectors summary.p2canon A summary of the results of an analysis of the relationships between two sets of projectors print.summary.p2canon Prints the values in an 'summary.p2canon' object that give the combined decomposition efficiencies.p2canon Extracts the canonical efficiency factors from a list of class 'p2canon' Accepts a single formula: as.data.frame.pstructure Coerces a pstructure.object to a data.frame print.pstructure Prints a pstructure.object pstructure.formula Takes a formula and constructs a pstructure.object that includes the orthogonalized projectors for the terms in a formula Others: decomp.relate Examines the relationship between the eigenvectors for two decompositions efficiency.criteria Computes efficiency criteria from a set of efficiency factors fac.meanop Computes the projection matrix that produces means proj2.eigen Canonical efficiency factors and eigenvectors in joint decomposition of two projectors proj2.efficiency Computes the canonical efficiency factors for the joint decomposition of two projectors proj2.combine Compute the projection and Residual operators for two, possibly nonorthogonal, projectors show-methods Methods for Function 'show' in Package dae (vii) Miscellaneous functions extab Expands the values in table to a vector get.daeTolerance Gets the value of daeTolerance for the package dae harmonic.mean Calcuates the harmonic mean. is.allzero Tests whether all elements are approximately zero rep.data.frame Replicate the rows of a data.frame by repeating each row consecutively and/or repeating all rows as a group. rmvnorm Generates a vector of random values from a multivariate normal distribution set.daeTolerance Sets the value of daeTolerance for the package dae

### Author(s)

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Maintainer: NA

[Package dae version 3.2-13 Index]