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dae (version 3.1-27)

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 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 .

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Install

install.packages('dae')

Monthly Downloads

1,095

Version

3.1-27

License

GPL (>= 2)

Maintainer

Chris Brien

Last Published

July 9th, 2020

Functions in dae (3.1-27)

Deprecated Functions in Package dae

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.

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

Description of a pcanon object

Computes the power for an experiment

Forms a two-level factor from a logical object.

LatticeSquare_t49.des

A Lattice square design for 49 treatments

proj2.efficiency

Computes the canonical efficiency factors for the joint decomposition of two projectors

Canonical efficiency factors and eigenvectors in joint decomposition of two projectors

residuals.aovlist

Extract the residuals from an aovlist object

Extract the residuals for a fitted model

McIntyreTMV.dat

The design and data from McIntyre's (1955) two-phase experiment

Examines the relationship between the eigenvectors for two decompositions

The intermittent, randomly-presented, startup tips.

Extract Yates effects

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

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

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

designLatinSqrSys

Generate a systematic plan for a Latin Square design

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

Degrees of freedom extraction and replacement

designAmeasures

Calculates the average variance of pairwise differences from the variance matrix for predictions

Generate all combinations of several factors and, optionally, replicate them

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

forms the variance matrix for the variance component of a (generalized) factor

Combines several factors into one

Exp249.munit.des

Systematic, main-unit design for an experiment to be run in a greenhouse

blockboundaryPlot

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

computes the projection matrix that produces means

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

correct.degfree

Check the degrees of freedom in an object of class projector

designRandomize

Randomize allocated to recipient factors to produce a layout for an experiment

Divides a factor into several individual factors

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.

Data for a 2^4 factorial 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.

Forms a square matrix of ones

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

Forms an exponential correlation matrix

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

Forms an exponential correlation matrix

generates a vector of random values from a multivariate normal distribution

Calculates the variance matrix for the random effects from a mixed model, based on a supplied formula or a matrix.

Calcuates the harmonic mean.

Forms an ar2 correlation matrix

Forms an ar3 correlation matrix

set.daeTolerance

Sets the values of daeTolerance for the package dae

interaction.ABC.plot

Plots an interaction plot for three factors

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

Data for an experiment with rows and columns from Williams (2002)

Computes the number of replicates for an experiment

Description of a p2canon object

print.summary.pcanon

Prints the values in an summary.pcanon object

Computes the detectable difference for an experiment

summary.p2canon

Summarize a canonical analysis of the relationships between two sets of projectors

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

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

Replicate the rows of a data.frame by repeating each row consecutively and/or repeating all rows as a group

Half or full normal plot of Yates effects

Summarizes the anatomy of a design, being the decomposition of the sample space based on its canonical analysis, as produced by designAnatomy

Extract the fitted values for a fitted model

get.daeTolerance

Gets the value of daeTolerance for the package dae

Forms a unit matrix

as.data.frame.pstructure

Coerces a pstructure.object to a data.frame.

Convert a factor to a numeric vector

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

Forms an ma2 correlation matrix

Forms an ma1 correlation matrix

projector-class

Class projector

Create projectors

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

Data for a balanced incomplete block experiment

A canonical analysis of the relationships between two sets of projectors

Expands the values in table to a vector

projs.combine.p2canon

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

ABC.Interact.dat

Randomly generated set of values indexed by three factors

Sensory3Phase.dat

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

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

forms the ar1 correlation matrix for a (generalized) factor

efficiency.criteria

Computes efficiency criteria from a set of efficiency factors

designPlotlabels

Plots labels on a two-way grid using ggplot2

Forms an ar1 correlation matrix

computes the projection matrix that produces means

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

Extract the elements of an array specified by the subscripts

Forms an arma correlation matrix

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

Form a banded matrix from a vector of values

print.summary.p2canon

Prints the values in an summary.p2canon object

Tests whether all elements are approximately zero

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

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

Tests whether an object is a valid object of class projector

print.pstructure

Prints a pstructure.object

Generate paper strength values

Methods for Function show in Package dae

Forms the direct product of two matrices

Forms the direct sum of a list of matrices

Forms an sar2 correlation matrix

Forms an sar correlation matrix

Print an aliasing data.frame

pstructure.object

Description of a pstructure object

pstructure.formula

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

print.projector

Print projectors