# 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. | |

No Results! |

## Vignettes of dae

Name | ||

DesignNotes.pdf.asis | ||

dae-manual.pdf.asis | ||

No Results! |

## Last month downloads

## 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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