# dae v3.1-23

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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 | |

LatticeSquare_t49.des | A Lattice square design for 49 treatments | |

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

McIntyreTMV.dat | The design and data from McIntyre's (1955) two-phase experiment | |

Exp249.munit.des | Systematic, main-unit design for an experiment to be run in a greenhouse | |

dae-deprecated | Deprecated Functions in Package dae | |

BIBDWheat.dat | Data for a balanced incomplete block experiment | |

Fac4Proc.dat | Data for a 2^4 factorial experiment | |

dae-package | dae | |

as.numfac | Convert a factor to a numeric vector | |

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

designPlot | A graphical representation of an experimental design using labels stored in a matrix. | |

Sensory3Phase.dat | Data for the three-phase sensory evaluation experiment in Brien, C.J. and Payne, R.W. (1999) | |

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 | |

designPlotlabels | Plots labels on a two-way grid using ggplot2 | |

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. | |

fac.combine | Combines several factors into one | |

fac.divide | Divides a factor into several individual factors | |

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. | |

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

Casuarina.dat | Data for an experiment with rows and columns from Williams (2002) | |

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

designBlocksGGPlot | Adds block boundaries to a plot produced by designGGPlot. | |

fac.vcmat | forms the variance matrix for the variance component of a (generalized) factor | |

extab | Expands the values in table to a vector | |

daeTips | The intermittent, randomly-presented, startup tips. | |

designGGPlot | Plots labels on two-way grids of coloured cells using ggplot2 | |

fitted.aovlist | Extract the fitted values for a fitted model from an aovlist object | |

degfree | Degrees of freedom extraction and replacement | |

decomp.relate | Examines the relationship between the eigenvectors for two decompositions | |

mat.ar1 | Forms an ar1 correlation matrix | |

designLatinSqrSys | Generate a systematic plan for a Latin Square design | |

detect.diff | Computes the detectable difference for an experiment | |

correct.degfree | Check the degrees of freedom in an object of class projector | |

designAmeasures | Calculates the average variance of pairwise differences from the variance matrix for predictions that can be obtained using mat.Vpredicts | |

fac.match | Match, for each combination of a set of columns in x, the row that has the same combination in table | |

mat.Vpredicts | Calculates the variances of a set of predicted effects from a mixed model, based on supplied matrices or formulae. | |

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

mat.J | Forms a square matrix of ones | |

efficiency.criteria | Computes efficiency criteria from a set of efficiency factors | |

fac.nested | creates a factor, the nested factor, whose values are generated within those of the factor nesting.fac | |

fac.gen | Generate all combinations of several factors and, optionally, replicate them | |

elements | Extract the elements of an array specified by the subscripts | |

fitted.errors | Extract the fitted values for a fitted model | |

is.allzero | Tests whether all elements are approximately zero | |

fac.meanop | computes the projection matrix that produces means | |

interaction.ABC.plot | Plots an interaction plot for three factors | |

fac.sumop | computes the summation matrix that produces sums corresponding to a (generalized) factor | |

harmonic.mean | Calcuates the harmonic mean. | |

mat.exp | Forms an exponential correlation matrix | |

fac.uselogical | Forms a two-level factor from a logical object. | |

fac.ar1mat | forms the ar1 correlation matrix for a (generalized) factor | |

fac.multinested | Creates several factors, one for each level of nesting.fac and each of whose values are either generated within those of a level of nesting.fac or using the values of nested.fac within a levels of nesting.fac. | |

fac.recode | Recodes factor levels using values in a vector. The values in the vector do not have to be unique. | |

get.daeTolerance | Gets the value of daeTolerance for the package dae | |

mat.arma | Forms an arma correlation matrix | |

mat.dirprod | Forms the direct product of two matrices | |

mat.Vpred | Calculates the variances of a set of predicted effects from a mixed model | |

mat.dirsum | Forms the direct sum of a list of matrices | |

is.projector | Tests whether an object is a valid object of class projector | |

mat.ma1 | Forms an ma1 correlation matrix | |

p2canon.object | Description of a p2canon object | |

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

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

mat.I | Forms a unit matrix | |

pcanon.object | Description of a pcanon object | |

mat.ncssvar | Calculates the variance matrix of the random effects for a natural cubic smoothing spline | |

print.summary.p2canon | Prints the values in an summary.p2canon object | |

mat.gau | Forms an exponential correlation matrix | |

mat.ar2 | Forms an ar2 correlation matrix | |

mat.sar | Forms an sar correlation matrix | |

power.exp | Computes the power for an experiment | |

pstructure.object | Description of a pstructure object | |

print.summary.pcanon | Prints the values in an summary.pcanon object | |

mat.ma2 | Forms an ma2 correlation matrix | |

proj2.eigen | Canonical efficiency factors and eigenvectors in joint decomposition of two projectors | |

mat.ar3 | Forms an ar3 correlation matrix | |

mpone | Converts the first two levels of a factor into the numeric values -1 and +1 | |

meanop | computes the projection matrix that produces means | |

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

projector | Create projectors | |

projector-class | Class projector | |

qqyeffects | Half or full normal plot of Yates effects | |

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

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 | |

mat.sar2 | Forms an sar2 correlation matrix | |

residuals.aovlist | Extract the residuals from an aovlist object | |

yates.effects | Extract Yates effects | |

print.projector | Print projectors | |

print.pstructure | Prints a pstructure.object | |

print.aliasing | Print an aliasing data.frame | |

projs.2canon | A canonical analysis of the relationships between two sets of projectors | |

projs.combine.p2canon | Extract, from a p2canon object, the projectors that give the combined canonical decomposition | |

set.daeTolerance | Sets the values of daeTolerance for the package dae | |

show-methods | Methods for Function show in Package dae | |

rmvnorm | generates a vector of random values from a multivariate normal distribution | |

summary.p2canon | Summarize a canonical analysis of the relationships between two sets of projectors | |

proj2.combine | Compute the projection and Residual operators for two, possibly nonorthogonal, 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 | |

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

strength | Generate paper strength values | |

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

ABC.Interact.dat | Randomly generated set of values indexed by three factors | |

Cabinet1.des | A design for one of the growth cabinets in an experiment with 50 lines and 4 harvests | |

No Results! |

## Vignettes of dae

Name | ||

DesignNotes.pdf.asis | ||

dae-manual.pdf.asis | ||

No Results! |

## Last month downloads

## Details

Date | 2020-03-16 |

VignetteBuilder | R.rsp |

License | GPL (>= 2) |

URL | http://chris.brien.name |

RoxygenNote | 5.0.1 |

NeedsCompilation | no |

Packaged | 2020-03-15 22:51:04 UTC; briencj |

Repository | CRAN |

Date/Publication | 2020-03-16 12:00:02 UTC |

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