Package: dae 3.2.33

dae: 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/>.

Authors:Chris Brien [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dae/json (API)

# Install 'dae' in R:

install.packages('dae', repos = c('https://briencj.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/briencj/dae/issues

Datasets:

ABC.Interact.dat - Randomly generated set of values indexed by three factors
BIBDWheat.dat - Data for a balanced incomplete block experiment
Cabinet1.des - A design for one of the growth cabinets in an experiment with 50 lines and 4 harvests
Casuarina.dat - Data for an experiment with rows and columns from Williams
Exp249.munit.des - Systematic, main-unit design for an experiment to be run in a greenhouse
Fac4Proc.dat - Data for a 2^4 factorial experiment
LatticeSquare_t49.des - A Lattice square design for 49 treatments
McIntyreTMV.dat - The design and data from McIntyre's (1955) two-phase experiment
Oats.dat - Data for an experiment to investigate nitrogen response of 3 oats varieties
Sensory3Phase.dat - Data for the three-phase sensory evaluation experiment in Brien, C.J. and Payne, R.W.
Sensory3PhaseShort.dat - Data for the three-phase sensory evaluation experiment in Brien, C.J. and Payne, R.W.
SPLGrass.dat - Data for an experiment to investigate the effects of grazing patterns on pasture composition

On CRAN:

8.35 score 2 stars 9 packages 308 scripts 1.1k downloads 4 mentions 111 exports 78 dependencies

Last updated from:14383312bb. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	180
source / vignettes	OK	215
linux-release-x86_64	OK	182
macos-release-arm64	OK	107
macos-oldrel-arm64	OK	181
windows-devel	OK	121
windows-release	OK	175
windows-oldrel	OK	118
wasm-release	OK	153

Exports:Ameasures as.data.frame.pstructure as.numfac blockboundary.plot blockboundaryPlot correct.degfree decomp.relate degfree degfree<-design.plot designAmeasures designAnatomy designBlocksGGPlot designGGPlot designLatinSqrSys designPlot designPlotlabels designRandomize designTwophaseAnatomies detect.diff efficiencies efficiencies.p2canon efficiencies.pcanon efficiency.criteria elements extab fac.ar1mat fac.combine fac.divide fac.gen fac.genfactors fac.match fac.meanop fac.multinested fac.nested fac.recast fac.recode fac.split fac.sumop fac.uncombine fac.uselogical fac.vcmat fitted.aovlist fitted.errors get.daeRNGkind get.daeTolerance harmonic.mean interaction.ABC.plot is.allzero is.projector makeLevsPadNums marginality marginality.pcanon marginality.pstructure mat.ar1 mat.ar2 mat.ar3 mat.arma mat.banded mat.cor mat.corg mat.dirprod mat.dirsum mat.exp mat.gau mat.ginv mat.I mat.J mat.ma1 mat.ma2 mat.ncssvar mat.random mat.sar mat.sar2 mat.Vpred mat.Vpredicts mpone no.reps porthogonalize porthogonalize.list power.exp print.aliasing print.projector print.pstructure print.summary.p2canon print.summary.pcanon proj2.combine proj2.decomp proj2.efficiency proj2.eigen proj2.ops projector projs.2canon projs.canon projs.combine.p2canon projs.structure pstructure pstructure.formula qqyeffects rep.data.frame resid.errors residuals.aovlist rmvnorm set.daeRNGkind set.daeTolerance strength summary.p2canon summary.pcanon tukey.1df yates.effects Zncsspline

Dependencies:abind backports boot broom car carData cli colorspace corrplot cowplot cpp11 Deriv doBy dplyr farver forecast Formula fracdiff generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable isoband labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mgcv minqa modelr nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig plyr polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rstatix S7 scales SparseM stringi stringr survival tibble tidyr tidyselect timeDate tryCatchLog urca utf8 vctrs viridisLite withr zoo

DesignNotes

Introduction | Single-allocation orthogonal design in R | Single-allocation, nonorthogonal design in R | Miscellaneous experimental design topics in R | Multiphase experiments in R

Rendered fromDesignNotes.pdf.asisusingR.rsp::asis

Last update: 2019-04-03
Started: 2019-04-03

Manual

Rendered fromdae-manual.pdf.asisusingR.rsp::asis

Last update: 2019-04-03
Started: 2019-04-03

Help page	Topics
Functions Useful in the Design and ANOVA of Experiments	dae-package dae
Randomly generated set of values indexed by three factors	ABC.Interact.dat
Coerces a pstructure.object to a data.frame.	as.data.frame.pstructure
Convert a factor to a numeric vector, possibly centering or scaling the values	as.numfac
Data for a balanced incomplete block experiment	BIBDWheat.dat
This function plots a block boundary on a plot produced by 'designPlot'.	blockboundaryPlot
A design for one of the growth cabinets in an experiment with 50 lines and 4 harvests	Cabinet1.des
Data for an experiment with rows and columns from Williams (2002)	Casuarina.dat
Check the degrees of freedom in an object of class projector	correct.degfree
Deprecated Functions in Package dae	Ameasures blockboundary.plot dae-deprecated design.plot proj2.decomp proj2.ops projs.canon projs.structure
The intermittent, randomly-presented, startup tips.	daeTips
Examines the relationship between the eigenvectors for two decompositions	decomp.relate
Degrees of freedom extraction and replacement	degfree degfree<-
Calculates the average variance of pairwise differences from the variance matrix for predictions	designAmeasures
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.	designAnatomy
Adds block boundaries to a plot produced by 'designGGPlot'.	designBlocksGGPlot
Plots labels on two-way grids of coloured cells using 'ggplot2' to represent an experimental design	designGGPlot
Generate a systematic plan for a Latin Square design	designLatinSqrSys
A graphical representation of an experimental design using labels stored in a matrix.	designPlot
Plots labels on a two-way grid using 'ggplot2'	designPlotlabels
Randomize allocated to recipient factors to produce a layout for an experiment	designRandomize
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.	designTwophaseAnatomies
Computes the detectable difference for an experiment	detect.diff
Extracts the canonical efficiency factors from a 'pcanon.object' or a 'p2canon.object'.	efficiencies efficiencies.p2canon efficiencies.pcanon
Computes efficiency criteria from a set of efficiency factors	efficiency.criteria
Extract the elements of an array specified by the subscripts	elements
Systematic, main-unit design for an experiment to be run in a greenhouse	Exp249.munit.des
Expands the values in table to a vector	extab
forms the ar1 correlation matrix for a (generalized) factor	fac.ar1mat
Combines several factors into one	fac.combine
Divides a factor into several separate factors	fac.divide
Generate all combinations of several factors and, optionally, replicate them	fac.gen
Generate all combinations of the levels of the supplied factors, without replication	fac.genfactors
Match, for each combination of a set of columns in 'x', the row that has the same combination in 'table'	fac.match
computes the projection matrix that produces means	fac.meanop
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.	fac.multinested
creates a factor, the nested factor, whose values are generated within those of the factor nesting.fac	fac.nested
Recasts a factor by modifying the values in the factor vector and/or the levels attribute, possibly combining some levels into a single level.	fac.recast
Recodes factor 'levels' using values in a vector. The values in the vector do not have to be unique.	fac.recode
Splits a factor whose levels consist of several delimited strings into several factors	fac.split
computes the summation matrix that produces sums corresponding to a (generalized) factor	fac.sumop
Cleaves a single factor, each of whose levels has delimited strings, into several factors using the separated strings.	fac.uncombine
Forms a two-level 'factor' from a 'logical' object.	fac.uselogical
forms the variance matrix for the variance component of a (generalized) factor	fac.vcmat
Data for a 2^4 factorial experiment	Fac4Proc.dat
Extract the fitted values for a fitted model from an aovlist object	fitted fitted.aovlist
Extract the fitted values for a fitted model	fitted.errors
Gets the value of daeRNGkind for the package dae from the daeEnv environment	get.daeRNGkind
Gets the value of daeTolerance for the package dae	get.daeTolerance
Calcuates the harmonic mean.	harmonic.mean
Plots an interaction plot for three factors	interaction.ABC.plot
Tests whether all elements are approximately zero	is.allzero
Tests whether an object is a valid object of class projector	is.projector
A Lattice square design for 49 treatments	LatticeSquare_t49.des
make a set of levels that consist of a prefix combined with padded numeric values	makeLevsPadNums
Extracts the marginality matrix (matrices) from a 'pstructure.object' or a 'pcanon.object'.	marginality marginality.pcanon marginality.pstructure
Forms an ar1 correlation matrix	mat.ar1
Forms an ar2 correlation matrix	mat.ar2
Forms an ar3 correlation matrix	mat.ar3
Forms an arma correlation matrix	mat.arma
Form a banded matrix from a vector of values	mat.banded
Forms a correlation matrix in which all correlations have the same value.	mat.cor
Forms a general correlation matrix	mat.corg
Forms the direct product of two matrices	mat.dirprod
Forms the direct sum of a list of matrices	mat.dirsum
Forms an exponential correlation matrix	mat.exp
Forms an exponential correlation matrix	mat.gau
Computes the generalized inverse of a matrix	mat.ginv
Forms a unit matrix	mat.I
Forms a square matrix of ones	mat.J
Forms an ma1 correlation matrix	mat.ma1
Forms an ma2 correlation matrix	mat.ma2
Calculates the variance matrix of the random effects for a natural cubic smoothing spline	mat.ncssvar
Calculates the variance matrix for the random effects from a mixed model, based on a supplied formula or a matrix.	mat.random
Forms an sar correlation matrix	mat.sar
Forms an sar2 correlation matrix	mat.sar2
Calculates the variances of a set of predicted effects from a mixed model	mat.Vpred
Calculates the variances of a set of predicted effects from a mixed model, based on supplied matrices or formulae.	mat.Vpredicts
The design and data from McIntyre's (1955) two-phase experiment	McIntyreTMV.dat
computes the projection matrix that produces means	meanop
Converts the first two levels of a factor into the numeric values -1 and +1	mpone
Computes the number of replicates for an experiment	no.reps
Data for an experiment to investigate nitrogen response of 3 oats varieties	Oats.dat
Description of a p2canon object	p2canon.object
Description of a pcanon object	pcanon.object
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.	porthogonalize porthogonalize.list
Computes the power for an experiment	power.exp
Print an aliasing data.frame	print.aliasing
Print projectors	print,projector-method print.projector
Prints a pstructure.object	print.pstructure
Prints the values in an 'summary.p2canon' object	print.summary.p2canon
Prints the values in an 'summary.pcanon' object	print.summary.pcanon
Compute the projection and Residual operators for two, possibly nonorthogonal, projectors	proj2.combine
Computes the canonical efficiency factors for the joint decomposition of two projectors	proj2.efficiency
Canonical efficiency factors and eigenvectors in joint decomposition of two projectors	proj2.eigen
Create projectors	projector
Class projector	coerce,projector,matrix-method coerce<-,projector,matrix-method projector-class
A canonical analysis of the relationships between two sets of projectors	projs.2canon
Extract, from a p2canon object, the projectors that give the combined canonical decomposition	projs.combine.p2canon
Takes a formula and constructs a 'pstructure.object' that includes the orthogonalized projectors for the terms in a formula	pstructure pstructure.formula
Description of a pstructure object	pstructure.object
Half or full normal plot of Yates effects	qqyeffects
Replicate the rows of a data.frame by repeating each row consecutively and/or repeating all rows as a group	rep.data.frame
Extract the residuals for a fitted model	resid.errors
Extract the residuals from an aovlist object	residuals residuals.aovlist
generates a vector of random values from a multivariate normal distribution	rmvnorm
Data for the three-phase sensory evaluation experiment in Brien, C.J. and Payne, R.W. (1999)	Sensory3Phase.dat Sensory3PhaseShort.dat
Sets the values of daeRNGkind for the package dae in the daeEnv environment	set.daeRNGkind
Sets the values of daeTolerance for the package dae	set.daeTolerance
Methods for Function show in Package dae	show,ANY-method show,classRepresentation-method show,genericFunction-method show,MethodDefinition-method show,MethodSelectionReport-method show,MethodWithNext-method show,ObjectsWithPackage-method show,oldClass-method show,projector-method show,signature-method show,traceable-method show-methods
Data for an experiment to investigate the effects of grazing patterns on pasture composition	SPLGrass.dat
Generate paper strength values	strength
Summarize a canonical analysis of the relationships between two sets of projectors	summary,p2canon-method summary.p2canon
Summarizes the anatomy of a design, being the decomposition of the sample space based on its canonical analysis, as produced by designAnatomy	summary,pcanon-method summary.pcanon
Performs Tukey's one-degree-of-freedom-test-for-nonadditivity	tukey.1df
Extract Yates effects	yates.effects
Calculates the design matrix for fitting the random component of a natural cubic smoothing spline	Zncsspline

Package: dae 3.2.33

dae: Functions Useful in the Design and ANOVA of Experiments

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