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dae (version 3.1-23)

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

1,033

Version

3.1-23

License

GPL (>= 2)

Maintainer

Chris Brien

Last Published

March 16th, 2020

Functions in dae (3.1-23)

LatticeSquare_t49.des

A Lattice square design for 49 treatments

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

Deprecated Functions in Package dae

Data for a balanced incomplete block experiment

Data for a 2^4 factorial experiment

Convert a factor to a numeric vector

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

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.

Combines several factors into one

Divides a factor into several individual factors

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.

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

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

designBlocksGGPlot

Adds block boundaries to a plot produced by designGGPlot.

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

Expands the values in table to a vector

The intermittent, randomly-presented, startup tips.

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

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

Degrees of freedom extraction and replacement

Examines the relationship between the eigenvectors for two decompositions

Forms an ar1 correlation matrix

designLatinSqrSys

Generate a systematic plan for a Latin Square design

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

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

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

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

Forms a square matrix of ones

efficiency.criteria

Computes efficiency criteria from a set of efficiency factors

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

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

Extract the elements of an array specified by the subscripts

Extract the fitted values for a fitted model

Tests whether all elements are approximately zero

computes the projection matrix that produces means

interaction.ABC.plot

Plots an interaction plot for three factors

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

Calcuates the harmonic mean.

Forms an exponential correlation matrix

Forms a two-level factor from a logical object.

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.

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

Forms an arma correlation matrix

Forms the direct product of two matrices

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

Forms the direct sum of a list of matrices

Tests whether an object is a valid object of class projector

Forms an ma1 correlation matrix

Description of a p2canon object

Form a banded matrix from a vector of values

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

Forms a unit matrix

Description of a pcanon object

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

Forms an exponential correlation matrix

Forms an ar2 correlation matrix

Forms an sar correlation matrix

Computes the power for an experiment

pstructure.object

Description of a pstructure object

print.summary.pcanon

Prints the values in an summary.pcanon object

Forms an ma2 correlation matrix

Canonical efficiency factors and eigenvectors in joint decomposition of two projectors

Forms an ar3 correlation matrix

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

computes the projection matrix that produces means

Computes the number of replicates for an experiment

Create projectors

projector-class

Class projector

Half or full normal plot of Yates effects

proj2.efficiency

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

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

Forms an sar2 correlation matrix

residuals.aovlist

Extract the residuals from an aovlist object

Extract Yates effects

print.projector

Print projectors

print.pstructure

Prints a pstructure.object

Print an aliasing data.frame

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

Methods for Function show in Package dae

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

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

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

Generate paper strength values

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

ABC.Interact.dat

Randomly generated set of values indexed by three factors

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