dae (version 3.0-32)

dae-package: dae

Description

dae

Version: NA

Date: NA

Arguments

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.mplot.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.match
Match, for each combination of a set of columns
in 'x', the row that has the same combination
in 'table' fac.nested
Creates a factor whose values are generated
within those of the factor nesting.fac fac.recode
Recodes factor 'levels' using possibly nonunique
values in a vector. 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 that can be obtained
using mat.Vpredicts
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.
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It superseded design.plot.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 two-phase, first-phase,
cross-phase and second-phase 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.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
rmvnorm Generates a vector of random values from a
multivariate normal distribution
set.daeTolerance Sets the value of daeTolerance for the package dae