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dae (version 3.2.30)

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

1,289

Version

3.2.30

License

GPL (>= 2)

Maintainer

Chris Brien

Last Published

December 1st, 2024

Functions in dae (3.2.30)

The intermittent, randomly-presented, startup tips.

Deprecated Functions in Package dae

correct.degfree

Check the degrees of freedom in an object of class projector

tools:::Rd_package_title("dae")

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.

blockboundaryPlot

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

Convert a factor to a numeric vector, possibly centering or scaling the values

Examines the relationship between the eigenvectors for two decompositions

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

designRandomize

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

Plots labels on two-way grids of coloured cells using ggplot2 to represent an experimental design

Divides a factor into several separate factors

Combines several factors into one

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.

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.

Expands the values in table to a vector

forms the ar1 correlation matrix for a (generalized) factor

designLatinSqrSys

Generate a systematic plan for a Latin Square design

Cleaves a single factor, each of whose levels has delimited strings, into several factors using the separated strings.

designBlocksGGPlot

Adds block boundaries to a plot produced by designGGPlot.

Degrees of freedom extraction and replacement

Splits a factor whose levels consist of several delimited strings into several factors

Forms a two-level factor from a logical object.

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

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

efficiency.criteria

Computes efficiency criteria from a set of efficiency factors

Recasts a factor by modifying the values in the factor vector and/or the levels attribute, possibly combining some levels into a single level.

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

designPlotlabels

Plots labels on a two-way grid using ggplot2

Computes the detectable difference for an experiment

Extract the elements of an array specified by the subscripts

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

designAmeasures

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

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

Generate all combinations of the levels of the supplied factors, without replication

computes the projection matrix that produces means

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

interaction.ABC.plot

Plots an interaction plot for three factors

get.daeTolerance

Gets the value of daeTolerance for the package dae

Extract the fitted values for a fitted model

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.

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

Gets the value of daeRNGkind for the package dae from the daeEnv environment

Calcuates the harmonic mean.

Tests whether all elements are approximately zero

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

Forms an ar1 correlation matrix

Forms a unit matrix

Forms an ar2 correlation matrix

Form a banded matrix from a vector of values

Forms a square matrix of ones

Forms an ma1 correlation matrix

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

Tests whether an object is a valid object of class projector

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

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

Forms a correlation matrix in which all correlations have the same value.

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

Forms an sar correlation matrix

Forms an ma2 correlation matrix

Forms an ar3 correlation matrix

Forms an arma correlation matrix

Forms an exponential correlation matrix

Computes the generalized inverse of a matrix

Forms a general correlation matrix

Forms the direct sum of a list of matrices

Forms an sar2 correlation matrix

Forms the direct product of two matrices

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

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

Computes the power for an experiment

Forms an exponential correlation matrix

Computes the number of replicates for an experiment

Description of a p2canon object

Print an aliasing data.frame

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

Description of a pcanon object

Extract Yates effects

Create projectors

computes the projection matrix that produces means

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

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

Canonical efficiency factors and eigenvectors in joint decomposition of two projectors

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.

projector-class

Class projector

A canonical analysis of the relationships between two sets of projectors

Sets the values of daeRNGkind for the package dae in the daeEnv environment

pstructure.object

Description of a pstructure object

projs.combine.p2canon

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

pstructure.formula

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

print.summary.p2canon

Prints the values in an summary.p2canon object

set.daeTolerance

Sets the values of daeTolerance for the package dae

print.projector

Print projectors

summary.p2canon

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

Half or full normal plot of Yates effects

print.summary.pcanon

Prints the values in an summary.pcanon object

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

residuals.aovlist

Extract the residuals from an aovlist object

generates a vector of random values from a multivariate normal distribution

print.pstructure

Prints a pstructure.object

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

Extract the residuals for a fitted model

Methods for Function show in Package dae

Generate paper strength values

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

McIntyreTMV.dat

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

ABC.Interact.dat

Randomly generated set of values indexed by three factors

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

Exp249.munit.des

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

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

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

LatticeSquare_t49.des

A Lattice square design for 49 treatments

Data for a 2^4 factorial experiment

Data for a balanced incomplete block experiment