Description Usage Arguments Details Value Warning Note Author(s) References See Also Examples

Functions length2, length3, length4 and length5 calculate the numbers of generalized words of lengths 2, 3, 4, and 5 respectively, lengths calculates them all. Functions P3.3 and P4.4 calculate projection frequency tables, functions oa.min3, oa.min4, oa.min34, oa.maxGR (deprecated), oa.minRelProjAberr, oa.max3 and oa.max4 determine column allocations with minimum or maximum aliasing. Function nchoosek is an auxiliary function for calculating all subsets without replacement.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ```
length2(design, with.blocks = FALSE, J = FALSE)
length3(design, with.blocks = FALSE, J = FALSE, rela = FALSE)
length4(design, with.blocks = FALSE, separate = FALSE, J = FALSE, rela = FALSE)
length5(design, with.blocks = FALSE, J = FALSE, rela = FALSE)
lengths(design, ...)
## Default S3 method:
lengths(design, ...)
## S3 method for class 'design'
lengths(design, ...)
## S3 method for class 'matrix'
lengths(design, ...)
contr.XuWu(n, contrasts=TRUE)
contr.XuWuPoly(n, contrasts=TRUE)
oa.min3(ID, nlevels, all, rela = FALSE, variants = NULL, crit = "total")
oa.min4(ID, nlevels, all, rela = FALSE, variants = NULL, crit = "total")
oa.min34(ID, nlevels, variants = NULL, min3=NULL, all = FALSE, rela = FALSE)
oa.max3(ID, nlevels, rela = FALSE)
oa.max4(ID, nlevels, rela = FALSE)
oa.maxGR(ID, nlevels, variants = NULL)
oa.minRelProjAberr(ID, nlevels, maxGR = NULL)
P2.2(ID, digits = 4, rela=FALSE, parft=FALSE, parftdf=FALSE, detailed=FALSE)
P3.3(ID, digits = 4, rela=FALSE, parft=FALSE, parftdf=FALSE, detailed=FALSE)
P4.4(ID, digits = 4, rela=FALSE, parft=FALSE, parftdf=FALSE, detailed=FALSE)
nchoosek(n, k)
tupleSel(design, type="complete", selprop=0.25, ...)
## S3 method for class 'design'
tupleSel(design, type="complete", selprop=0.25, ...)
## Default S3 method:
tupleSel(design, type="complete", selprop=0.25, ...)
``` |

`design` |
an experimental design. This can either be a matrix or a data frame
in which all columns are experimental factors, or a special data frame
of class |

`with.blocks` |
a logical, indicating whether or not an existing block factor
is to be included into word counting. This option is ignored if |

`J` |
a logical, indicating whether or not a vector of contributions from
individual degrees of freedom is produced. If |

`rela` |
logical indicating whether the word lengths are to be calculated in
absolute terms (as usual) or relative to the maximum possible word length in case of
complete aliasing; if |

`separate` |
a logical, indicating whether or not separate (and overlapping)
sums are requested for each two-factor interaction;
the idea is to be able to identify clear two-factor interactions;
this may be useful for a design for which |

`n` |
integer; |

`contrasts` |
must always be |

`ID` |
an orthogonal array, either a matrix or a data frame; need not be of class |

`nlevels` |
a vector of requested level informations (vector with an entry for each factor) |

`all` |
logical; if |

`variants` |
matrix of integer column number entries; each row gives the column numbers
for one variant to be compared; the matrix columns must correspond to the entries of the |

`crit` |
character string that requests |

`min3` |
the outcome of a call to |

`maxGR` |
the outcome of a call to |

`digits` |
number of decimal points to which to round the result |

`parft` |
logical indicating whether to tabulate projection averaged $R^2$
values (see Groemping 2013) instead of word lengths;
if |

`parftdf` |
logical indicating whether to tabulate averaged $R^2$
values, where averaging is over individual degrees of freedom; this variant
is not explicitly described in Groemping (2013, 2017) and usually yields very similar
results as |

`detailed` |
logical indicating whether the vector of all (relative) tuple word lengths
is to become an attribute of the output object (attribute |

`k` |
number of elements to be chosen, integer from 0 to n |

`type` |
character string with type of worst case to consider; |

`selprop` |
(approximate) proportion of worst case tuples to be selected (see |

`...` |
further arguments; for the |

These functions work for factors only and are not intended for quantitative variables.
Nevertheless it is possible to apply them to class `design`

plans with quantitative
variables in them in some situations.

The generalized word length pattern as introduced in Xu and Wu (2001) is the basis
for the functions described here. Consult their article or Groemping (2011)
for rigorous mathematical detail of this concept. A brief explanation is also given here,
before explaining the details for the functions: Assume a design with qualitative
factors, for which all factors are coded with specially normalized Helmert `contrasts`

(which orthogonalizes the model matrix columns to the intercept column).
Functions `contr.XuWu`

and `contr.XuWuPoly`

provide such contrasts
based on Helmert contrasts or orthogonal polynomial contrasts,
normalized according to the prescription by Xu and Wu (2001)
which implies that all model matrix columns
have Euclidean norm `sqrt(n)`

, provided that each
individual factor is balanced.

Then, the number of generalized words of length 3 is determined by taking the sum
of squares of the column averages of all three-factor interaction columns
(from a model matrix with all three-factor interactions included).

Likewise, the number of generalized words of length 4 is determined by taking the sum
of squares of the column averages of all four-factor interaction columns
(from a model matrix with all four-factor interactions included), and so on.

A certain plausibility can be found in these numbers by noting that they provide the
more well-known word length pattern for regular fractional factorial 2-level designs,
implying that they are exactly zero for resolution IV or resolution V fractional
factorial 2-level designs, respectively. Furthermore, Groemping and Xu (2014) provided
an interpretation in terms of R^2-values from linear models for the number of
shortest words.

Function `lengths`

calculates the generalized word length
pattern (numbers of generalized words of lengths 2, 3, 4 and 5 respectively),
functions `length2`

, `length3`

, `length4`

and `length5`

calculate
each length separately. For designs with few rows and many columns, the newer
function `GWLP`

is much faster; therefore it will be a better choice
than `lengths`

for most applications. On the other hand, for designs with
many rows, `lengths`

can be much faster. Furthermore, `lengths`

and
the compoment functions `length2`

to `length5`

can calculate additional
detail not available from `GWLP`

.

The most important component length functions are
`length3`

and `length4`

; `length2`

should yield zero for all orthogonal arrays, and `length5`

will in most
cases not be of interest either. The number of shortest possible words, e.g.
length 4 for resolution IV designs, can be calculated in relative terms, if
interest is in the extent of complete aliasing (cf. Groemping 2011).

The length functions are fast for small numbers of factors but can take a
long time if the number of factors is large. Note that an orthogonal array
based design is called resolution III if the result of
function `length3`

is non-zero, resolution IV,
if the result of function `length3`

is zero and the
result of function `length4`

is non-zero,
and resolution V+ (at least V), if the result of both functions `length3`

and `length4`

are zero.

Functions `P3.3`

and `P4.4`

calculate the pattern of generalized words of length 3 for all three-factor
projections of an array and of generalized words of length 3 or 4 for all four-factor
projections of an array. Calculation of such projection frequency tables has been proposed
by Xu, Cheng and Wu (2004). The relative version for `P3.3`

and `P4.4`

has been
introduced by Groemping (2011) for better assessment of the projective properties of a design.
It divides each absolute number of words by the maximum possible number in case one
factor is completely determined by the combinations of the other two factors.
For `P4.4`

, the relative version is valid only for resolution IV designs.
NOTE: For mixed-level designs, it is meanwhile recommended to use
ARFTs (Groemping 2013, 2017) instead of relative `P3.3`

and `P4.4`

;
these can be obtained by functions `GRind`

or `SCFTs`

and have relevant advantages over the projection frequency tables from `P3.3`

and `P4.4`

for mixed level designs. SCFTs (also treated in Groemping 2013, 2017) provide more detail
than ARFTs and are interesting for assessing the suitability of a design for screening purposes.

The functions can be used in selecting among different possibilities to accomodate factors
within a given orthogonal array (cf. examples). For general purposes, it is recommended
to use designs with as small an outcome of `length3`

as possible (either absolute or relative,
either total or worst case), and within the same result
for `length3`

(particularly 0), with as small a result for `length4`

as possible. This
corresponds to (a step towards) generalized minimum aberration. It can also be useful
to consider the patterns, particularly `P3.3`

, or for mixed levels the aforementioned
ARFTs or SCFTs obtainable with functions `GRind`

or `SCFTs`

.
Note that some overall information on a design's behavior is available in the catalogue data frames
`oacat`

and `oacat3`

and can be queried with function `show.oas`

;
this helps for selecting a suitable array from which to start optimization efforts (see below).

Functions `oa.min3`

, `oa.min4`

, `oa.min34`

optimize column allocation for a given array
for which a certain factor combination must be accomodated: They return designs that allocate
columns such that the number of generalized words of length 3 is minimized (`oa.min3`

;
with a choice between minimizing the total number or minimizing the number for the worst-case triple
of factors), or
the number of generalized words of length 4 is minimized within all designs for which the number
of generalized words of length 3 is minimal (`oa.min34`

, total number only);
`oa.min4`

does the same as `oa.min3`

, but for designs of resolution IV, either entirely
(e.g. designs from `oacat3`

) or through the selection of suitable column variants.
Option `rela`

allows to switch
from the default consideration of absolute numbers of words to relative numbers of words
according to Groemping (2011). This relative number corresponds to concentrating on the worst-case
ARFT entry for each set of R factors (R the resolution).

Function `oa.maxGR`

maximizes generalized resolution
according to Deng and Tang (1999) as generalized by Groemping (2011).
**Note that function `oa.maxGR`

can be replaced by the much faster function `oa.min3`

with options
`crit="worst"`

and `rela=TRUE`

, whenever GR<=4. Only for designs with
GR > 4, the extra effort with function `oa.maxGR`

is useful.**

Function `oa.minRelProjAberr`

conducts minimum relative projection aberration
according to Groemping (2011), with the four steps

(a) maximize GR (using function
`oa.min3`

with options `crit="worst"`

and `rela=TRUE`

),

(b) minimize rA3 or
rA4 (depending on resolution),

(c) optimize RPFT (as obtained by `P3.3`

or `P4.4`

) and

(d) minimize absolute words of lengths 4 etc. (only carried through
to length 4 by the function).

Functions `oa.max3`

and `oa.max4`

do the opposite: they search for the worst design in terms of the number of
generalized words of lengths 3 or 4. Such a design can e.g. be used
for demonstrating the benefit of optimizing the number of words,
or for exemplifying theoretical properties.
Occasionally, it may also be useful,
if there are severe restrictions on possible combinations.
(`oa.max4`

should only be used for resolution IV designs.)

Function `tupleSel`

selects worst case tuples of R factors for resolution R designs.
Depending on the type requested, all completely aliased tuples are selected,
or the worst case tuples that exceed the `1-selprop`

quantile of the numbers
of absolute or relative words are selected.

The functions `length3`

and `length4`

(currently) per default
return the number of generalized words.

If option `J=TRUE`

is set, their value
is a named vector of normalized absolute J-characteristics (cf. Ai and Zhang 2004)
for the respective length, based on normalized Helmert contrasts,
with names indicating factor indices.
(For blocked designs with the `with.blocks=TRUE`

option,
the block factor has index 1.)

Functions `P3.3`

and `P4.4`

return a matrix
with the numbers of generalized words of length 3 (4) that do occur
for 3 (4) factor projections (column `length3`

or `length4`

resp.)
and their frequencies. If option `rela=TRUE`

is set, the numbers of generalized
words are normalized by dividing them by the number of words that corresponds
to perfect aliasing among the factors for each projection. For `P4.4`

, the
relative version is only reasonable for resolution IV designs.
The matrix of projection frequencies has the overall number of generalized words
of the respective length as an attribute; in the case `rela=TRUE`

it also
has the generalized resolution and the overall absolute number of generalized words
of the respective length as an attribute.

The functions `oa.min3`

, `oa.min34`

, `oa.max3`

and `oa.max4`

(currently) return a list with elements
`GWP`

(the number(s) of generalized words of length 3 (lengths 3 and 4))
`column.variants`

(the columns to be used for design creation, ordered with
ascending nlevels) and `complete`

(logical indicating whether or not the list is
guaranteed to be complete).
`oa.min3`

, the name of the first element is either `GWP3`

(`crit="total"`

),
`worst.a3`

(`rela=FALSE, crit="worst"`

) or `GR`

(`rela=FALSE, crit="worst"`

).
The function `oa.maxGR`

returns a list with elements `GR`

, `column.variants`

and `complete`

, the function `oa.minRelProjAberr`

returns a list with elements
`GR`

, `GWP`

, `column.variants`

and `complete`

.

The function `nchoosek`

returns a matrix with k rows and `choose(n, k)`

columns,
each of which contains a different subset of k elements.

The function `tupleSel`

returns a sorted list of worst case tuples,
beginning with the worst case. In case of types `"worst"`

or `"worst.rel"`

,
attributes provide the (relative) projection frequency tables and the sorted
vector of the worst case projection values corresponding to the listed tuples.

The functions have been checked on the types of designs for which they are intended (especially orthogonal arrays produced with oa.design) and on 2-level fractional factorial designs produced with package FrF2. They may produce meaningless results for some other types of designs.

Furthermore, all optimizing functions work for relatively small problems only and will break down for larger problems because of storage space requirements (size depends on the number of possible selections among columns; for example, selecting 9 out of 31 columns is not doable on my computer because of storage space issues, while selecting 29 out of 31 columns is doable within the available storage space). Programming of a less storage-intensive algorithm is underway.

Function `nchoosek`

has been taken from Bioconductor package vsn.

Function `GWLP`

is much faster (but also more inaccurate) than function `lengths`

and may be a better choice for designs with many factors.

Ulrike Groemping

Ai, M.-Y. and Zhang, R.-C. (2004). Projection justification of generalized minimum
aberration for asymmetrical fractional factorial designs.
*Metrika* **60**, 279–285.

Groemping, U. (2011). Relative projection frequency tables for orthogonal arrays.
Report 1/2011, *Reports in Mathematics, Physics and Chemistry*
http://www1.beuth-hochschule.de/FB_II/reports/welcome.htm,
Department II, Beuth University of Applied Sciences, Berlin.

Groemping, U. (2013). Frequency tables for the coding invariant ranking of
orthogonal arrays. Report 2/2013, *Reports in Mathematics, Physics and Chemistry*
http://www1.beuth-hochschule.de/FB_II/reports/welcome.htm,
Department II, Beuth University of Applied Sciences, Berlin.

Groemping, U. (2017). Frequency tables for the coding invariant quality assessment
of factorial designs. *IISE Transactions* **49**, 505-517.
https://doi.org/10.1080/0740817X.2016.1241458.

Xu, H.-Q. and Wu, C.F.J. (2001). Generalized minimum aberration for asymmetrical
fractional factorial designs. *The Annals of Statistics* **29**, 1066–1077.

Xu, H., Cheng, S., and Wu, C.F.J. (2004). Optimal projective three-level
designs for factor screening and interaction detection. *Technometrics* **46**,
280–292.

See also `GWLP`

for a version of lengths that is much
faster for designs with not so many runs, and `GRind`

for another set of quality criteria for orthogonal arrays.

Package DoE.MIParray can create
arrays for smallish situations for which the catalogued arrays do not provide
satisfactory results; this package requires at least one of the commercial
softwares Mosek or Gurobi to be installed (both provide free academic licenses).

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 | ```
## check a small design
oa12 <- oa.design(nlevels=c(2,2,6))
length3(oa12)
## length4 is of course 0, because there are only 3 factors
P3.3(oa12)
## the results need not be an integer
oa12 <- oa.design(L12.2.11,columns=1:6)
length3(oa12)
length4(oa12)
P3.3(oa12) ## all projections have the same pattern
## which is known to be true for the complete L12.2.11 as well
P3.3(L18) ## this is the pattern of the Taguchi L18
## also published by Schoen 2009
P3.3(L18[,-2]) ## without the 2nd column (= the 1st 3-level column)
P3.3(L18[,-2], rela=TRUE) ## relative pattern, divided by theoretical upper
## bound for each 3-factor projection
## choosing among different assignment possibilities
## for two 2-level factors and one 3- and 4-level factor each
show.oas(nlevels=c(2,2,3,4))
## default allocation: first two columns for the 2-level factors
oa24.bad <- oa.design(L24.2.13.3.1.4.1, columns=c(1,2,14,15))
length3(oa24.bad)
## much better: columns 3 and 10
oa24.good <- oa.design(L24.2.13.3.1.4.1, columns=c(3,10,14,15))
length3(oa24.good)
length4(oa24.good) ## there are several variants,
## which produce the same pattern for lengths 3 and 4
## the difference matters
plot(oa24.bad, select=c(2,3,4))
plot(oa24.good, select=c(2,3,4))
## generalized resolution differs as well (resolution is III in both cases)
GR(oa24.bad)
GR(oa24.good)
## and analogously also GRind and ARFT and SCFT
GRind(oa24.bad)
GRind(oa24.good)
## GR and GRind can be different
GRind(L18[, c(1:4,6:8)], arft=FALSE, scft=FALSE)
## choices for columns can be explored with functions oa.min3, oa.min34 or oa.max3
oa.min3(L24.2.13.3.1.4.1, nlevels=c(2,2,3,4))
oa.min34(L24.2.13.3.1.4.1, nlevels=c(2,2,3,4))
## columns for designs with maximum generalized resolution
## (can take very long, if all designs have worst-case aliasing)
## then optimize these for overall relative number of words of length 3
## and in addition absolute number of words of length 4
mGR <- oa.maxGR(L18, c(2,3,3,3,3,3,3))
oa.minRelProjAberr(L18, c(2,3,3,3,3,3,3), maxGR=mGR)
oa.max3(L24.2.13.3.1.4.1, nlevels=c(2,2,3,4)) ## this is not for finding
## a good design!!!
## Not run:
## play with selection of optimum design
## somewhat experimental at present
oa.min3(L32.2.10.4.7, nlevels=c(2,2,2,4,4,4,4,4))
best3 <- oa.min3(L32.2.10.4.7, nlevels=c(2,2,2,4,4,4,4,4), rela=TRUE)
oa.min34(L32.2.10.4.7, nlevels=c(2,2,2,4,4,4,4,4))
oa.min34(L32.2.10.4.7, nlevels=c(2,2,2,4,4,4,4,4), min3=best3)
## generalized resolution according to Groemping 2011, manually
best3GR <- oa.min3(L36.2.11.3.12, c(rep(2,3),rep(3,3)), rela=TRUE, crit="worst")
## optimum GR is 3.59
## subsequent optimization w.r.t. rA3
best3reltot.GR <- oa.min3(L36.2.11.3.12, c(rep(2,3),rep(3,3)), rela=TRUE,
variants=best3GR$column.variants)
## optimum rA3 is 0.5069
## (note: different from first optimizing rA3 (0.3611) and then GR (3.5))
## remaining nine designs: optimize RPFTs
L36 <- oa.design(L36.2.11.3.12, randomize=FALSE)
lapply(1:9, function(obj) P3.3(L36[,best3reltot.GR$column.variants[obj,]]))
## all identical
oa.min34(L36, nlevels=c(rep(2,3),rep(3,3)), min3=best3reltot.GR)
## still all identical
## End(Not run)
## select among column variants with projection frequencies
## here, all variants have identical projection frequencies
## for larger problems, this may sometimes be relevant
variants <- oa.min34(L24.2.13.3.1.4.1, nlevels=c(2,2,3,4))
for (i in 1:nrow(variants$column.variants)){
cat("variant ", i, "\n")
print(P3.3(oa.design(L24.2.13.3.1.4.1, columns=variants$column.variants[i,])))
}
## automatic optimization is possible, but can be time-consuming
## (cf. help for oa.design)
plan <- oa.design(L24.2.13.3.1.4.1, nlevels=c(2,2,3,4), columns="min3")
length3(plan)
length4(plan)
plan <- oa.design(L24.2.13.3.1.4.1, nlevels=c(2,2,3,4), columns="min34")
length3(plan)
length4(plan)
## Not run:
## blocked design from FrF2
## the design is of resolution IV
## there is one (generalized) 4-letter word that does not involve the block factor
## there are four more 4-letter words involving the block factor
## all this and more can also be learnt from design.info(plan)
require(FrF2)
plan <- FrF2(32,6,blocks=4)
length3(plan)
length3(plan, with.blocks=TRUE)
length4(plan)
length4(plan, with.blocks=TRUE)
design.info(plan)
## End(Not run)
``` |

DoE.base documentation built on Aug. 23, 2018, 1:03 a.m.

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