lmdme-getters: Getters for lmdme object

In lmdme: Linear Model decomposition for Designed Multivariate Experiments

Description

To obtain lmdme slot information, according to the given function call (see Values). If a term parameter is not specified, it will return all the available terms. Otherwise, just the one specified.

Usage

  ## S4 method for signature 'lmdme'
fitted.values(object, term=NULL,
  drop=TRUE)

  ## S4 method for signature 'lmdme'
fitted(object, term=NULL, drop=TRUE)

  ## S4 method for signature 'lmdme'
coef(object, term=NULL, drop=TRUE)

  ## S4 method for signature 'lmdme'
coefficients(object, term=NULL,
  drop=TRUE)

  ## S4 method for signature 'lmdme'
resid(object, term=NULL, drop=TRUE)

  ## S4 method for signature 'lmdme'
residuals(object, term=NULL, drop=TRUE)

  F.p.values(object, term=NULL, drop=TRUE)

  ## S4 method for signature 'lmdme'
F.p.values(object, term=NULL,
  drop=TRUE)

  p.values(object, term=NULL, drop=TRUE)

  ## S4 method for signature 'lmdme'
p.values(object, term=NULL, drop=TRUE)

  modelDecomposition(object, term=NULL, drop=TRUE)

  ## S4 method for signature 'lmdme'
modelDecomposition(object, term=NULL,
  drop=TRUE)

  components(object, term=NULL, drop=TRUE)

  ## S4 method for signature 'lmdme'
components(object, term=NULL,
  drop=TRUE)

  componentsType(object)

  ## S4 method for signature 'lmdme'
componentsType(object)

  model(object)

  ## S4 method for signature 'lmdme'
model(object)

  design(object)

  ## S4 method for signature 'lmdme'
design(object)

Arguments

object	lmdme class object.
term	character with the corresponding term/s to return. Default value is NULL in order to return every available term/s.
drop	should try to drop list structure if length==1? Default value is TRUE

Value

according to the call one of the following objects can be returned

design	experiment design data.frame used.
model	decomposed formula used.
modelDecomposition	list of decomposed model formulas.
residuals, resid, coef, coefficients, fitted, fitted.values, p.values or F.p.values	list of appropriate slot where each item is a matrix that will have G rows (individuals) x k columns (levels of the corresponding model term).
components	list with corresponding PCA or PLSR terms according to the decomposition function call.
componentsType	character name vector with the information of the component calculations.

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

lmdme, decomposition, print, show

Examples

{
data(stemHypoxia)

##Just to make a balanced dataset in the Fisher sense (2 samples per
## time*oxygen levels)
design<-design[design$time %in% c(0.5, 1, 5) & design$oxygen %in% c(1,5,21),]
design$time<-as.factor(design$time)
design$oxygen<-as.factor(design$oxygen)
rownames(M)<-M[, 1]

##Keeping appropriate samples only
M<-M[, colnames(M) %in% design$samplename]

##ANOVA decomposition
fit<-lmdme(model=~time+oxygen+time:oxygen, data=M, design=design)

##Let's inspect how the decomposition process was carried out:
##a) The model formula used
##b) The design data.frame used
##c) The decomposition itself
fit.model<-model(fit)
fit.design<-design(fit)
fit.modelDecomposition<-modelDecomposition(fit)

##Getting the specific "time" term coefficients, p-values or F-values.
## Omit "term" parameter for all available terms.
timeCoef<-coef(fit,term="time")
fit.p.values<-p.values(fit,term="time")
fit.f.values<-F.p.values(fit,term="time")

##Getting the residuals or fitted values, for the interaction "time:oxygen"
## term. Omit "term" parameter for all available terms.
interactionResid<-resid(fit, term="time:oxygen")
interactionFit<-fitted(fit, term="time:oxygen")
}

Example output

Loading required package: pls

Attaching package: 'pls'

The following object is masked from 'package:stats':

    loadings

Loading required package: stemHypoxia

Attaching package: 'lmdme'

The following object is masked from 'package:stats':

    p.adjust

lmdme documentation built on Nov. 8, 2020, 7:46 p.m.