# Functions Useful in the Design and ANOVA of Experiments

## Documentation for package ‘dae’ version 3.2.30

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P Q R S T Y Z

dae-package | Functions Useful in the Design and ANOVA of Experiments

## -- A --

ABC.Interact.dat | Randomly generated set of values indexed by three factors
Ameasures | Deprecated Functions in Package dae
as.data.frame.pstructure | Coerces a pstructure.object to a data.frame.
as.numfac | Convert a factor to a numeric vector, possibly centering or scaling the values

## -- B --

BIBDWheat.dat | Data for a balanced incomplete block experiment
blockboundary.plot | Deprecated Functions in Package dae
blockboundaryPlot | This function plots a block boundary on a plot produced by 'designPlot'.

## -- C --

Cabinet1.des | A design for one of the growth cabinets in an experiment with 50 lines and 4 harvests
Casuarina.dat | Data for an experiment with rows and columns from Williams (2002)
coerce-method | Class projector
coerce<--method | Class projector
correct.degfree | Check the degrees of freedom in an object of class projector

## -- D --

dae | Functions Useful in the Design and ANOVA of Experiments
dae-deprecated | Deprecated Functions in Package dae
daeTips | The intermittent, randomly-presented, startup tips.
decomp.relate | Examines the relationship between the eigenvectors for two decompositions
degfree | Degrees of freedom extraction and replacement
degfree<- | Degrees of freedom extraction and replacement
design.plot | Deprecated Functions in Package dae
designAmeasures | Calculates the average variance of pairwise differences from the variance matrix for predictions
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.
designBlocksGGPlot | Adds block boundaries to a plot produced by 'designGGPlot'.
designGGPlot | Plots labels on two-way grids of coloured cells using 'ggplot2' to represent an experimental 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.
designPlotlabels | Plots labels on a two-way grid using 'ggplot2'
designRandomize | Randomize allocated to recipient factors to produce a layout for an experiment
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.
detect.diff | Computes the detectable difference for an experiment

## -- E --

efficiencies | Extracts the canonical efficiency factors from a 'pcanon.object' or a 'p2canon.object'.
efficiencies.p2canon | Extracts the canonical efficiency factors from a 'pcanon.object' or a 'p2canon.object'.
efficiencies.pcanon | Extracts the canonical efficiency factors from a 'pcanon.object' or a 'p2canon.object'.
efficiency.criteria | Computes efficiency criteria from a set of efficiency factors
elements | Extract the elements of an array specified by the subscripts
Exp249.munit.des | Systematic, main-unit design for an experiment to be run in a greenhouse
extab | Expands the values in table to a vector

## -- F --

fac.ar1mat | forms the ar1 correlation matrix for a (generalized) factor
fac.combine | Combines several factors into one
fac.divide | Divides a factor into several separate factors
fac.gen | Generate all combinations of several factors and, optionally, replicate them
fac.genfactors | Generate all combinations of the levels of the supplied factors, without replication
fac.match | Match, for each combination of a set of columns in 'x', the row that has the same combination in 'table'
fac.meanop | computes the projection matrix that produces means
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.nested | creates a factor, the nested factor, whose values are generated within those of the factor nesting.fac
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.recode | Recodes factor 'levels' using values in a vector. The values in the vector do not have to be unique.
fac.split | Splits a factor whose levels consist of several delimited strings into several factors
fac.sumop | computes the summation matrix that produces sums corresponding to a (generalized) factor
fac.uncombine | Cleaves a single factor, each of whose levels has delimited strings, into several factors using the separated strings.
fac.uselogical | Forms a two-level 'factor' from a 'logical' object.
fac.vcmat | forms the variance matrix for the variance component of a (generalized) factor
Fac4Proc.dat | Data for a 2^4 factorial experiment
fitted | Extract the fitted values for a fitted model from an aovlist object
fitted.aovlist | Extract the fitted values for a fitted model from an aovlist object
fitted.errors | Extract the fitted values for a fitted model

## -- G --

get.daeRNGkind | Gets the value of daeRNGkind for the package dae from the daeEnv environment
get.daeTolerance | Gets the value of daeTolerance for the package dae

## -- H --

harmonic.mean | Calcuates the harmonic mean.

## -- I --

interaction.ABC.plot | Plots an interaction plot for three factors
is.allzero | Tests whether all elements are approximately zero
is.projector | Tests whether an object is a valid object of class projector

## -- L --

LatticeSquare_t49.des | A Lattice square design for 49 treatments

## -- M --

marginality | Extracts the marginality matrix (matrices) from a 'pstructure.object' or a 'pcanon.object'.
marginality.pcanon | Extracts the marginality matrix (matrices) from a 'pstructure.object' or a 'pcanon.object'.
marginality.pstructure | Extracts the marginality matrix (matrices) from a 'pstructure.object' or a 'pcanon.object'.
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 | Form a banded matrix from a vector of values
mat.cor | Forms a correlation matrix in which all correlations have the same value.
mat.corg | Forms a general correlation matrix
mat.dirprod | Forms the direct product of two matrices
mat.dirsum | Forms the direct sum of a list of matrices
mat.exp | Forms an exponential correlation matrix
mat.gau | Forms an exponential correlation matrix
mat.ginv | Computes the generalized inverse of a matrix
mat.I | Forms a unit matrix
mat.J | Forms a square matrix of ones
mat.ma1 | Forms an ma1 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
mat.random | Calculates the variance matrix for the random effects from a mixed model, based on a supplied formula or a matrix.
mat.sar | Forms an sar correlation matrix
mat.sar2 | Forms an sar2 correlation matrix
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.
McIntyreTMV.dat | The design and data from McIntyre's (1955) two-phase experiment
meanop | computes the projection matrix that produces means
mpone | Converts the first two levels of a factor into the numeric values -1 and +1

## -- N --

no.reps | Computes the number of replicates for an experiment

## -- O --

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

## -- P --

p2canon.object | Description of a p2canon object
pcanon.object | Description of a pcanon object
porthogonalize | 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.
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.
power.exp | Computes the power for an experiment
print-method | Print projectors
print.aliasing | Print an aliasing data.frame
print.projector | Print projectors
print.pstructure | Prints a pstructure.object
print.summary.p2canon | Prints the values in an 'summary.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
proj2.decomp | Deprecated Functions in Package dae
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
proj2.ops | Deprecated Functions in Package dae
projector | Create projectors
projector-class | Class projector
projs.2canon | A canonical analysis of the relationships between two sets of projectors
projs.canon | Deprecated Functions in Package dae
projs.combine.p2canon | Extract, from a p2canon object, the projectors that give the combined canonical decomposition
projs.structure | Deprecated Functions in Package dae
pstructure | Takes a formula and constructs a 'pstructure.object' that includes the orthogonalized projectors for the terms in a formula
pstructure.formula | Takes a formula and constructs a 'pstructure.object' that includes the orthogonalized projectors for the terms in a formula
pstructure.object | Description of a pstructure object

## -- Q --

qqyeffects | Half or full normal plot of Yates effects

## -- R --

rep.data.frame | Replicate the rows of a data.frame by repeating each row consecutively and/or repeating all rows as a group
resid.errors | Extract the residuals for a fitted model
residuals | Extract the residuals from an aovlist object
residuals.aovlist | Extract the residuals from an aovlist object
rmvnorm | generates a vector of random values from a multivariate normal distribution

## -- S --

Sensory3Phase.dat | Data for the three-phase 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)
set.daeRNGkind | Sets the values of daeRNGkind for the package dae in the daeEnv environment
set.daeTolerance | Sets the values of daeTolerance for the package dae
show-method | Methods for Function show in Package dae
show-methods | Methods for Function show in Package dae
SPLGrass.dat | Data for an experiment to investigate the effects of grazing patterns on pasture composition
strength | Generate paper strength values
summary-method | Summarize a canonical analysis of the relationships between two sets of projectors
summary-method | 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
summary.pcanon | Summarizes the anatomy of a design, being the decomposition of the sample space based on its canonical analysis, as produced by designAnatomy

## -- T --

tukey.1df | Performs Tukey's one-degree-of-freedom-test-for-nonadditivity

## -- Y --

yates.effects | Extract Yates effects

## -- Z --

Zncsspline | Calculates the design matrix for fitting the random component of a natural cubic smoothing spline