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
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Vignettes of dae

Name
DesignNotes.pdf.asis
dae-manual.pdf.asis
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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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