R/housekeeping.R

Defines functions std.nonbinary parse.formula is.binary

#################
#Housekeeping functions
#################



###
#Determine if a vector consists entirely of zeroes and ones
###

is.binary <- function(x) {
  return(identical(as.numeric(unique(x)), c(1,0)) + identical(as.numeric(unique(x)), c(0,1)) ==1)
}

#old code issues following warnings, so updated.
#2: In unique(x) == c(1, 0) :
#longer object length is not a multiple of shorter object length
#
#is.binary <- function(x) {
#  return(sum(unique(x) == c(1,0)) + sum(unique(x) == c(0,1)) ==2)
#}


###
#Parses out response, treatment and covariates from formula
#arguments:
#form: formula object.  1st variable on RHS assumed to be treatment
#data: data object containing variables (may be NULL)
###

parse.formula <- function(formula, resp.cov = NULL, data) {
  
  allVarsRec <- function(object){
    if (is.list(object)) {
      unlist(lapply(object, allVarsRec))
    }
    else {
      all.vars(object)
    }
  }
  
  if (missing(data) || is.null(data))
    data = environment(formula)

  names = c(allVarsRec(resp.cov), allVarsRec(formula[[3]]))
  nrc = switch(is.null(resp.cov)+1, dim(model.matrix(resp.cov))[2]-1,0) 
  form = eval(parse(text = paste(formula[[2]], "~", paste(names, collapse = "+")))[[1]])
  
  mf <- model.frame(form, data)
  mt <- attr(mf, "terms")
  resp <- model.response(mf, "numeric")    	#response from LHS
  if (is.empty.model(mt)) {
    stop("Formula RHS empty")
  }
  else {
    x <- model.matrix(mt, mf, contrasts)
  }
  
  #extract variables from formula & data
  
    trt <- x[,nrc+2]				#assume treatment is 1st var on RHS
    if(dim(x)[2] > 2) {
      if(!is.null(resp.cov)){
        covars <- x[,-c(1:(nrc+2))]			#variables on RHS, less the intercept, treatment, response covariates
        RespX <- x[,(2:(nrc+1))]  		#response-only variables on RHS
      }else{
        covars <- x[,-c(1,2)]			#variables on RHS, less the intercept, treatment, response covariates
        RespX <- NULL
      } 
    }else{
      covars <- NULL
      RespX <-NULL
    }
  
  return(list(resp = resp, trt = trt, covars = covars, RespX = RespX))
}



###
#Standardize non-binary variables
#arguments:
#X: variable to be standardized in vector form
###

std.nonbinary <- function(X) {
  #returns standardized values of vector not consisting of only 0s and 1s
  if(class(X) == "factor" | class(X) == "character")
    return(X)
  if(length(unique(X))!=2)
    X = (X - mean(X, na.rm = T))/sd(X, na.rm = T)
  else if(!is.binary(X))
    X = (X - mean(X, na.rm = T))/sd(X, na.rm = T)
  return(X)
}

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treatSens documentation built on March 18, 2018, 1:54 p.m.