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dae (version 3.2.32)

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 .

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Install

install.packages('dae')

Monthly Downloads

1,306

Version

3.2.32

License

GPL (>= 2)

Maintainer

Chris Brien

Last Published

August 20th, 2025

Functions in dae (3.2.32)

dae-deprecated

Deprecated Functions in Package dae
Sensory3Phase.dat

Data for the three-phase sensory evaluation experiment in Brien, C.J. and Payne, R.W. (1999)
dae-package

tools:::Rd_package_title("dae")
daeTips

The intermittent, randomly-presented, startup tips.
blockboundaryPlot

This function plots a block boundary on a plot produced by designPlot.
decomp.relate

Examines the relationship between the eigenvectors for two decompositions
as.numfac

Convert a factor to a numeric vector, possibly centering or scaling the values
as.data.frame.pstructure

Coerces a pstructure.object to a data.frame.
Zncsspline

Calculates the design matrix for fitting the random component of a natural cubic smoothing spline
correct.degfree

Check the degrees of freedom in an object of class projector
designBlocksGGPlot

Adds block boundaries to a plot produced by designGGPlot.
designAmeasures

Calculates the average variance of pairwise differences from the variance matrix for predictions
designLatinSqrSys

Generate a systematic plan for a Latin Square design
designPlotlabels

Plots labels on a two-way grid using ggplot2
degfree

Degrees of freedom extraction and replacement
designGGPlot

Plots labels on two-way grids of coloured cells using ggplot2 to represent an experimental design
designRandomize

Randomize allocated to recipient factors to produce a layout for an experiment
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 (i) two-phase, (ii) first-phase, (iii) cross-phase, treatments, and (iv) combined-units designs.
designPlot

A graphical representation of an experimental design using labels stored in a matrix.
fac.ar1mat

forms the ar1 correlation matrix for a (generalized) factor
detect.diff

Computes the detectable difference for an experiment
extab

Expands the values in table to a vector
efficiency.criteria

Computes efficiency criteria from a set of efficiency factors
fac.genfactors

Generate all combinations of the levels of the supplied factors, without replication
fac.gen

Generate all combinations of several factors and, optionally, replicate them
fac.combine

Combines several factors into one
efficiencies

Extracts the canonical efficiency factors from a pcanon.object or a p2canon.object.
elements

Extract the elements of an array specified by the subscripts
fac.divide

Divides a factor into several separate factors
fac.sumop

computes the summation matrix that produces sums corresponding to a (generalized) factor
fac.split

Splits a factor whose levels consist of several delimited strings into several factors
fac.multinested

Creates several factors, one for each level of the nesting factor and each of whose values are either generated within those of a level of the nesting factor or using the values of the nested factor within the levels of the 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.uselogical

Forms a two-level factor from a logical object.
fac.meanop

computes the projection matrix that produces means
fac.recode

Recodes factor levels using values in a vector. The values in the vector do not have to be unique.
fac.uncombine

Cleaves a single factor, each of whose levels has delimited strings, into several factors using the separated strings.
fac.nested

creates a factor, the nested factor, whose values are generated within those of the factor nesting.fac
is.projector

Tests whether an object is a valid object of class projector
fac.vcmat

forms the variance matrix for the variance component of a (generalized) factor
fac.match

Match, for each combination of a set of columns in x, the row that has the same combination in table
marginality

Extracts the marginality matrix (matrices) from a pstructure.object or a pcanon.object.
fitted.errors

Extract the fitted values for a fitted model
interaction.ABC.plot

Plots an interaction plot for three factors
get.daeRNGkind

Gets the value of daeRNGkind for the package dae from the daeEnv environment
is.allzero

Tests whether all elements are approximately zero
harmonic.mean

Calcuates the harmonic mean.
get.daeTolerance

Gets the value of daeTolerance for the package dae
fitted.aovlist

Extract the fitted values for a fitted model from an aovlist object
mat.I

Forms a unit matrix
mat.banded

Form a banded matrix from a vector of values
mat.Vpred

Calculates the variances of a set of predicted effects from a mixed model
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.ar2

Forms an ar2 correlation matrix
mat.corg

Forms a general correlation matrix
mat.ar3

Forms an ar3 correlation matrix
mat.dirsum

Forms the direct sum of a list of matrices
mat.arma

Forms an arma correlation matrix
mat.ma2

Forms an ma2 correlation matrix
mat.ma1

Forms an ma1 correlation matrix
mat.exp

Forms an exponential correlation matrix
mat.cor

Forms a correlation matrix in which all correlations have the same value.
mat.ginv

Computes the generalized inverse of a matrix
mat.ncssvar

Calculates the variance matrix of the random effects for a natural cubic smoothing spline
mat.J

Forms a square matrix of ones
mat.gau

Forms an exponential correlation matrix
mat.dirprod

Forms the direct product of two matrices
meanop

computes the projection matrix that produces means
power.exp

Computes the power for an experiment
pcanon.object

Description of a pcanon object
porthogonalize.list

Takes a list of projectors and constructs a pstructure.object that includes projectors, each of which has been orthogonalized to all projectors preceding it in the list.
print.aliasing

Print an aliasing data.frame
mat.random

Calculates the variance matrix for the random effects from a mixed model, based on a supplied formula or a matrix.
no.reps

Computes the number of replicates for an experiment
p2canon.object

Description of a p2canon object
mat.sar

Forms an sar correlation matrix
mat.sar2

Forms an sar2 correlation matrix
mpone

Converts the first two levels of a factor into the numeric values -1 and +1
projs.2canon

A canonical analysis of the relationships between two sets of projectors
print.projector

Print projectors
projector-class

Class projector
print.pstructure

Prints a pstructure.object
projector

Create projectors
proj2.eigen

Canonical efficiency factors and eigenvectors in joint decomposition of two projectors
print.summary.p2canon

Prints the values in an summary.p2canon object
print.summary.pcanon

Prints the values in an summary.pcanon object
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
rep.data.frame

Replicate the rows of a data.frame by repeating each row consecutively and/or repeating all rows as a group
residuals.aovlist

Extract the residuals from an aovlist object
projs.combine.p2canon

Extract, from a p2canon object, the projectors that give the combined canonical decomposition
set.daeRNGkind

Sets the values of daeRNGkind for the package dae in the daeEnv environment
pstructure.object

Description of a pstructure object
qqyeffects

Half or full normal plot of Yates effects
set.daeTolerance

Sets the values of daeTolerance for the package dae
rmvnorm

generates a vector of random values from a multivariate normal distribution
resid.errors

Extract the residuals for a fitted model
pstructure.formula

Takes a formula and constructs a pstructure.object that includes the orthogonalized projectors for the terms in a formula
strength

Generate paper strength values
tukey.1df

Performs Tukey's one-degree-of-freedom-test-for-nonadditivity
yates.effects

Extract Yates effects
show-methods

Methods for Function show in Package dae
summary.pcanon

Summarizes the anatomy of a design, being the decomposition of the sample space based on its canonical analysis, as produced by designAnatomy
summary.p2canon

Summarize a canonical analysis of the relationships between two sets of projectors
BIBDWheat.dat

Data for a balanced incomplete block experiment
Exp249.munit.des

Systematic, main-unit design for an experiment to be run in a greenhouse
McIntyreTMV.dat

The design and data from McIntyre's (1955) two-phase experiment
Cabinet1.des

A design for one of the growth cabinets in an experiment with 50 lines and 4 harvests
Oats.dat

Data for an experiment to investigate nitrogen response of 3 oats varieties
Casuarina.dat

Data for an experiment with rows and columns from Williams (2002)
ABC.Interact.dat

Randomly generated set of values indexed by three factors
SPLGrass.dat

Data for an experiment to investigate the effects of grazing patterns on pasture composition
LatticeSquare_t49.des

A Lattice square design for 49 treatments
Fac4Proc.dat

Data for a 2^4 factorial experiment