R/nhanes.accel.reweight.R

In nhanesaccel: Process Accelerometer Data from NHANES 2003-2006

nhanes.accel.reweight <-
function(acceldata, wave, seqn.column, include.column) {
  
  # If accel.data is not a matrix or data frame, output error
  if (!is.matrix(acceldata) & !is.data.frame(acceldata)) {
    stop("For acceldata option, please enter matrix or data frame")
  }
  
  # If wave is not 1 or 2, output error
  if (wave != 1 & wave != 2) {
    stop("For wave option, please enter 1 for NHANES 2003-2004 or 2 for NHANES 2005-2006")
  }
  
  # If seqn.column or include.column are out of range, output error
  if (seqn.column < 1 | seqn.column > ncol(acceldata) | include.column < 1 | include.column > ncol(acceldata)) {
    stop("For seqn.column and include.column options, please specify which columns in
         acceldata contain the variables seqn and include, respectively")
  }
  
  # Set variables to NULL to avoid notes from CRAN check
  wave1_demo <- wave2_demo <- NULL
  
  # Load in demographics binary file
  if (wave == 1) {
    data("wave1_demo", envir = environment())
    demo <- wave1_demo
    rm(wave1_demo)
  }
  else {
    data("wave2_demo", envir = environment())
    demo <- wave2_demo
    rm(wave2_demo)
  }
  
  # Calculate adjusted weights
  wtmec2yr_adj <- rep(0, nrow(acceldata))
  for (a in 1:2) {
    for (b in 1:3) {
      for (c in 1:9) {
        indices1 <- which(demo[,2] == a & demo[,4] == b & demo[,3] == c)
        ids_demo <- demo[indices1,1]
        ids_valid <- ids_demo[which(ids_demo %in% acceldata[acceldata[,include.column] == 1,1])]
        indices2 <- which(demo[,2]==a&demo[,4]==b&demo[,3]==c&demo[,1] %in% acceldata[acceldata[,include.column]==1,1])
        indices3 <- which(acceldata[,seqn.column] %in% ids_valid)
        wtmec2yr_adj[indices3] <- demo[indices2,5]*sum(demo[indices1,5])/sum(demo[indices2,5])
      }
    }
  }
  
  # Add weights column to acceldata
  acceldata <- cbind(acceldata, wtmec2yr_adj)
  
  # Return acceldata
  return(acceldata)
}