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dae (version 3.0-04)

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 in the file 'daeDesignNotes.pdf'. The ANOVA functions facilitate the extraction of information when the 'Error' function has been used in the call to 'aov'.

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Version

Install

install.packages('dae')

Monthly Downloads

1,095

Version

3.0-04

License

GPL (>= 2)

Maintainer

Chris Brien

Last Published

July 5th, 2017

Functions in dae (3.0-04)

Fac4Proc.dat

Data for a 2^4 factorial experiment
LatticeSquare_t49.des

A Lattice square design for 49 treatments
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
correct.degfree

Check the degrees of freedom in an object of class projector
dae-deprecated

Deprecated Functions in Package dae
ABC.Interact.dat

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

Data for a balanced incomplete block experiment
Zncsspline

Calculates the design matrix for fitting the random component of a natural cubic smoothing spline
as.data.frame.pstructure

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

Randomize allocated to recipient factors to produce a layout for an experiment
detect.diff

Computes the detectable difference for an experiment
SPLGrass.dat

Data for an experiment to investigate the effects of grazing patterns on pasture composition
Sensory3Phase.dat

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

dae
daeTips

The intermittent, randomly-presented, startup tips.
extab

Expands the values in table to a vector
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
Oats.dat

Data for an experiment to investigate nitrogen response of 3 oats varieties
as.numfac

Convert a factor to a numeric vector
efficiencies

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

Computes efficiency criteria from a set of efficiency factors
fac.ar1mat

forms the ar1 correlation matrix for a (generalized) factor
fac.combine

Combines several factors into one
elements

Extract the elements of an array specified by the subscripts
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
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
blockboundaryPlot

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

Calculates the A-optimality measures from the variance matrix for predictions
designAnatomy

An anatomy of a design showing the confounding and aliasing inherent in the design that is obtained via a canonical analysis of its projectors.
fac.meanop

computes the projection matrix that produces means
fac.nested

creates a factor whose values are generated within those of the factor nesting.fac
fitted.errors

Extract the fitted values for a fitted model
get.daeTolerance

Gets the value of daeTolerance for the package dae
fac.sumop

computes the summation matrix that produces sums corresponding to a (generalized) factor
is.allzero

Tests whether all elements are approximately zero
is.projector

Tests whether an object is a valid object of class projector
mat.banded

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

Forms the direct product of two matrices
no.reps

Computes the number of replicates for an experiment
mat.J

Forms a square matrix of ones
mat.Vpred

Calculates the variances of a set of predicted effects from a mixed model
meanop

computes the projection matrix that produces means
mat.ar3

Forms an ar3 correlation matrix
mat.arma

Forms an arma correlation matrix
mat.gau

Forms an exponential correlation matrix
mpone

Converts the first two levels of a factor into the numeric values -1 and +1
proj2.efficiency

Computes the canonical efficiency factors for the joint decomposition of two projectors
proj2.eigen

Canonical efficiency factors and eigenvectors in joint decomposition of two projectors
projs.2canon

A canonical analysis of the relationships between two sets of projectors
mat.ma1

Forms an ma1 correlation matrix
print.aliasing

Print an aliasing data.frame
print.projector

Print projectors
projector-class

Class projector
projector

Create projectors
p2canon.object

Description of a p2canon object
print.summary.pcanon

Prints the values in an summary.pcanon object
proj2.combine

Compute the projection and Residual operators for two, possibly nonorthogonal, projectors
pstructure.formula

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

Extracts the marginality matrix (matrices) from a pstructure.object or a pcanon.object.
mat.I

Forms a unit matrix
mat.dirsum

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

Forms an exponential correlation matrix
decomp.relate

Examines the relationship between the eigenvectors for two decompositions
degfree

Degrees of freedom extraction and replacement
designLatinSqrSys

Generate a systematic plan for a Latin Square design
designPlot

A graphical representation of an experimental design using labels stored in a matrix.
set.daeTolerance

Sets the values of daeTolerance for the package dae
show-methods

Methods for Function show in Package dae
projs.combine.p2canon

Extract, from a p2canon object, the projectors that give the combined canonical decomposition
yates.effects

Extract Yates effects
mat.sar

Forms an sar correlation matrix
mat.sar2

Forms an sar2 correlation matrix
pcanon.object

Description of a pcanon object
power.exp

Computes the power for an experiment
pstructure.object

Description of a pstructure object
qqyeffects

Half or full normal plot of Yates effects
resid.errors

Extract the residuals for a fitted model
strength

Generate paper strength values
summary.p2canon

Summarize a canonical analysis of the relationships between two sets of projectors
fac.divide

Divides a factor into several individual factors
fac.gen

Generate all combinations of several factors
harmonic.mean

Calcuates the harmonic mean.
interaction.ABC.plot

Plots an interaction plot for three factors
mat.ar1

Forms an ar1 correlation matrix
mat.ar2

Forms an ar2 correlation matrix
mat.ma2

Forms an ma2 correlation matrix
mat.ncssvar

Calculates the variance matrix of the random effects for a natural cubic smoothing spline
print.pstructure

Prints a pstructure.object
print.summary.p2canon

Prints the values in an summary.p2canon object
residuals.aovlist

Extract the residuals from an aovlist object
rmvnorm

generates a vector of random values from a multivariate normal distribution
summary.pcanon

Summarizes the anatomy of a design, being the decomposition of the sample space based on its canonical analysis
tukey.1df

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