infoDecompuTE (version 0.5.1)

makeTreatProjectors: Make the Treatment Projectors

Description

Construct a list of treatment contrast matrices.

Usage

makeTreatProjectors(design.df, trtCols, effectsMatrix, trt.contr, contr.matrix)

Arguments

design.df

a data frame containing the design of the experiment. Every column must be factors.

trtCols

a list of treatment terms generated from the terms function.

effectsMatrix

a matrix contains the

trt.contr

a list of treatment contrast vectors, this allows the user to specify the contrasts for each treatment factor. Note that if this arguement is used, it is necessary to specify the contrasts for every treatment factor with the same order as fixed.terms. Default is NA, which uses the C matrix described by John and Williams (1987).

contr.matrix

a logical allows the users to use the contrast matrices or contrast vectors. If contr.matrix = FALSE, the outputs will use the contrast vectors each contributes one DF. If the contr.matrix arguement is TRUE the output will conbine the contrast vector for each treatment factors. The default depends on whether trt.contr has defined, if trt.contr has defined, then contr.matrix becomes FALSE.

Value

This function returns a list of treatment contrast matrices.

Examples

 design1 <- local({ 
    Ani = as.factor(LETTERS[c(1,2,3,4,
                              5,6,7,8)])
    Trt = as.factor(letters[c(1,1,1,1,
                              2,2,2,2)])
    data.frame(Ani, Trt)
  })

  trt.str = "Trt"
  
  	fT = terms(as.formula(paste("~", trt.str, sep = "")), keep.order = TRUE)  #fixed terms

	trtTerm = attr(fT,"term.labels")
		effectsMatrix = attr(fT,"factor")        

		T =  makeTreatProjectors(design1, trtTerm, effectsMatrix, trt.contr = NA , contr.matrix = TRUE)
		
		#Fit with the pre-defined treatment contrasts
    Trt1 = rep(c(1,-1), each = 4)
    
    Trt2 =  rep(c(1,-1), time = 4)
    
    Trt3 = Trt1*Trt2
  
		T =  makeTreatProjectors(design1, trtTerm, effectsMatrix, 
      trt.contr =list(Trt = list(Trt1 = Trt1, Trt2 = Trt2, Trt3 = Trt3)) , contr.matrix = FALSE)