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
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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

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