dae v3.1-23

Monthly downloads

by Chris Brien View Source

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

depends	ggplot2 , R (>= 3.5.0)
imports	graphics , methods , plyr , stats
suggests	R.rsp , testthat
Contributors