R: lm and aov methods for class design objects

lm and aov method for class design objects {DoE.base}

R Documentation

lm and aov methods for class design objects

Description

Methods for automatic linear models for data frames of class design

Usage

lm(formula, ...)
## Default S3 method:
lm(formula, data, subset, weights, na.action, method = "qr", 
    model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE, 
    contrasts = NULL, offset, ...)
## S3 method for class 'design'
lm(formula, ..., response=NULL, degree=NULL, FUN=mean, 
    use.center=NULL, use.star=NULL, use.dummies=FALSE)
aov(formula, ...)
## Default S3 method:
aov(formula, data = NULL, projections = FALSE, qr = TRUE,
    contrasts = NULL, ...)
## S3 method for class 'design'
aov(formula, ..., response=NULL, degree=NULL, FUN=mean, 
    use.center=FALSE)
## S3 method for class 'lm.design'
print(x, ...)
## S3 method for class 'lm.design'
summary(object, ...)
## S3 method for class 'lm.design'
coef(object, ...)
## S3 method for class 'summary.lm.design'
print(x, ...)
## S3 method for class 'aov.design'
print(x, ...)
## S3 method for class 'aov.design'
summary(object, ...)
## S3 method for class 'summary.aov.design'
print(x, ...)
lm.design
summary.lm.design
aov.design
summary.aov.design

Arguments

`formula`	for the default method, cf. documentation for `lm` in package stats;cr for the class `design` method, a data frame of S3 class `design`
`...`	further arguments to functions `lm`, `print.lm` or `print.summary.lm`
`response`	character string giving the name of the response variable (must be among the responses of `x`; for wide format repeated measurement or parameter designs, `response` can also be among the column names of the `responselist` element of the `design.info` attribute) OR integer number giving the position of the response in element `response.names` of attribute `design.info` For the default `NULL`, the first available response variable is used; for wide format designs, this is an aggregation of the variables given in first column from the `responselist` element of the `design.info` attribute of `x`.
`degree`	degree for the formula; if `NULL`, the default for the `formula` method is used
`FUN`	function for the `aggregate.design` method; this must be an unquoted function name; This option is relevant for repeated measurement designs and parameter designs in long format only
`use.center`	`NULL` or logical indicating whether center points are to be used + in the analysis; if `NULL`, the default is FALSE for `pb` and `FrF2` designs with center points and TRUE for `ccd` designs; the option is irrelevant for all other design types. `FALSE` allows usage of simple analysis functions from package `FrF2-package` (e.g. function `IAPlot`)
`use.star`	`NULL` or logical indicating whether the star portion of a CCD design is to be used in the analysis (ignored for all other types of designs). The default TRUE analyses the complete design. Specifying FALSE permits interim analyses of the cube portion of a central composite design.
`use.dummies`	logical indicating whether the error dummies of a Plackett Burman design are to be used in the formula (ignored for all other types of designs).
`projections`	logical indicating whether the projections should be returned; for orthogonal arrays, these are helpful, as they provide the estimated deviation from the overall average attributed to each particular factor; it is not recommended to use them with unbalanced designs
`x`	object of class `lm` or `summary.lm`, for `lm.default` like in `lm`
`object`	object of class `lm.design` created by function `lm.design`
`lm.design`	a class that is identical in content to class `lm`; its purpose is to call a specific print method that provides slightly more detail than the standard printout for linear models
`summary.lm.design`	a class that is identical in content to class `summary.lm`; its purpose is to call a specific print method that provides slightly more detail than the standard summary for linear models
`data`	like in `lm`
`subset`	like in `lm`
`weights`	like in `lm`
`na.action`	like in `lm`
`method`	like in `lm`
`model`	like in `lm`
`y`	like in `lm`
`qr`	like in `lm`
`singular.ok`	like in `lm`
`contrasts`	like in `lm`
`offset`	like in `lm`

Details

The aov and lm methods for class design conduct a default linear model analysis for data frames of class design that do contain at least one response.

The intention for providing default analyses is to support convenient quick inspections. In many cases, there will be good reasons to customize the analysis, for example by including some but not all effects of a certain degree. Also, it may be statistically more wise to work with mixed models for some types of design. The default analyses must not be taken as a statistical recommendation!

The choice of default analyses has been governed by simplicity: It uses fixed effects only and does either main effects models (degree=1, default for pb and oa designs), models with main effects and 2-factor interactions (degree=2, default for most designs) or second order models (that contain quadratic effects in addition to the 2-factor interactions, unchangeable default for designs with quantitative variables). The degree parameter can be used to modify the degree of interactions. If blocks are present, the block main effect is always entered as a fixed effect without interactions.

Designs with center points are per default analysed without the center points; the main reason for this is convenient usage of functions DanielPlot, MEPlot and IAPlot from package FrF2. With the use.center option, this default can be changed; in this case, significance of the center point indicator implies that there are one or more quadratic effect(s) in the model.

Designs with repeated measurements (repeat.only=TRUE) and parameter designs of long format are treated by aggregate.design with aggregation function FUN (default: means are calculated) before applying a linear model.

For designs with repeated measurements (repeat.only=TRUE) and parameter designs of wide format, the default is to use the first aggregated response, if the design has been aggregated already. For a so far unaggregated design, the default is to treat the design by aggregate.design, using the function FUN (default: mean) and then use the first response. The defaults can be overridden by specifying response: Here, response can not only be one of the current responses but also a column name of the responselist element of the design.info attribute of the design (i.e. a response name from the long version of the design).

The implementation of the formulae is not done in functions lm.design or aov.design themselves but based on the method for function formula (formula.design).

The print methods prepend the formula and the number of experimental runs underlying the analysis to the default printout. The purpose of this is meaningful output in case a call from inside function lm.design or aov.design (methods for functions lm and aov ) does not reveal enough information, and another pointer that center points have been omitted or repeated measurements aggregated over. The coef method for objects of class lm.design suppresses NA coefficients, i.e. returns valid coefficients only. For aov objects, this is the default anyway.

Value

The value for the lm functions is a linear model object, exactly like for function lm, except for the added class lm.design in case of the method for class design, and an added list element WholePlotEffects for split plot designs.

The value for the aov functions is an aov object, exactly like for function aov, and an added list element WholePlotEffects for split plot designs.

The value of the summary functions for class lm.design and aov.design respectively is a linear model or aov summary, exactly like documented in summary.lm or summary.aov, except for the added classes summary.lm.design or summary.aov.design, and an added list element WholePlotEffects (for summary.lm.design) or attribute (for summary.aov.design) for split plot designs.

The print functions return NULL; they are used for their side effects only.

Warning

The generics for lm and aov replace the functions from package stats. For normal use, this is not an issue, because their default methods are exactly the functions from package stats.
However, when programming on the language (or when using a package that relies on such constructs), you may see unexpected results. For example, match.call(lm) returns a different result, depending on whether or not package DoE.base is loaded. This can be avoided by explicitly requesting e.g. match.call(stats::lm), which always works in the same way.
Please report any additional issues that you may experience.

Note

The package is currently subject to intensive development; most key functionality is now included. Some changes to input and output structures may still occur.

Author(s)

Ulrike Groemping

Examples

  oa12 <- oa.design(nlevels=c(2,2,6))
  ## add a few variables to oa12
  responses <- cbind(y=rexp(12),z=runif(12))
  oa12 <- add.response(oa12, responses)
  ## want treatment contrasts rather than the default
  ## polynomial contrasts for the factors 
  oa12 <- change.contr(oa12, "contr.treatment")
  linmod.y <- lm(oa12)
  linmod.z <- lm(oa12, response="z")
  linmod.y
  linmod.z
  summary(linmod.y)
  summary(linmod.z)
  
## examples with aggregation
  plan <- oa.design(nlevels=c(2,6,2), replications=2, repeat.only=TRUE)
  y <- rnorm(24)
  z <- rexp(24)
  plan <- add.response(plan, cbind(y=y,z=z))
  lm(plan)
  lm(plan, response="z")
  lm(plan, FUN=sd)
  ## wide format
  plan <- reptowide(plan)
  plan
  design.info(plan)$responselist
  ## default: aggregate variables for first column of responselist
  lm(plan)
  ## request z variables instead (z is the column name of response list)
  lm(plan, response="z") 
  ## force analysis of first z measurement only
  lm(plan, response="z.1")
  ## use almost all options 
  ## (option use.center can only be used with center point designs 
  ##          from package FrF2)
  summary(lm(plan, response="z", degree=2, FUN=sd))

[Package DoE.base version 1.2-4 Index]