dae v3.0-32

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by Chris Brien View Source

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
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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