Initial commit

Package: NMRpackage

Maintainer: John Verzani <jverzani@gmail.com>

License: GPL-3

Title: Functions for Naked Mole Rat analysis

Depends: zoo, ggplot2

Type: Package

LazyLoad: yes

Author: John Verzani

Description: Package containing function for naked mole rat data

Version: 1.0.1

Date: 2011-06-25

Collate: 'process.R' 'visualize.R'

Packaged: 2012-02-22 22:47:59 UTC; verzani

export(readNMRData)

export(createZooObjects)

export(createStateMatrix)

export(nmrTsPlot)

NEWS for NMR package

Changes for 1.0.1

-----------------

* added rtf data file 

Changes for 1.0

-------------------

* Added functions

* Added roxygen documentation

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Version: 1.0

RestoreWorkspace: Default

SaveWorkspace: Default

AlwaysSaveHistory: Default

EnableCodeIndexing: Yes

UseSpacesForTab: Yes

NumSpacesForTab: 2

Encoding: UTF-8

##' Function to read in nmr data from txt csv-like file

##' 

##' @param x file containing data

##' @return data frame with time component being of POSIXct class

##' @seealso \code{\link{createZooObjects}}, \code{\link{createStateMatrix}}

##' @export

##' @examples

##' ## f <- "~/NMRpackage/inst/sampledata/degas.txt"

##' f <- system.file("sampledata","degas.txt", package="NMRpackage")

##' a <- readNMRData(f)

##' b <- createZooObjects(a)

##' m <-  createStateMatrix(b)

##' nmrTsPlot(m[, 1:4])

readNMRData <- function (f) {

  x <- read.table(f, sep=";", comment.char="\\")

  x[5] <- NULL

  names(x) <- c("ID","date", "time","gate")

  x$datetime <- paste(x$date, x$time)

  x$time <- as.POSIXct(x$datetime, format="%m/%d/%Y %H:%M:%S")

  x

}

##' Create zoo objects per mole rat from data frame

##'

##' @param matrix produced by readNMRData

##' @param list of zoo objects, one for reach ID in data set

##' @export  

createZooObjects <- function (x) {

  l <- split(x, x$ID)

  lapply(l, function(i) {

      trimmed <- i[duplicated(i),]

      ## adjust times now 

      trimmed$time <- trimmed$time + (1:nrow(trimmed))/(1000*nrow(trimmed))

      ## now map gate to bubble. The gate are a crossing

      trimmed$bubble <- numeric(nrow(trimmed))

      trimmed$bubble[1] <- trimmed$gate[1]

      ## assume bubbles 1,2,3,4 gates 1,2,3 in gate, bubble, gate, bubble, gate

      for(row in 2:nrow(trimmed)) {

        trimmed$bubble[row] <- trimmed$gate[row] + 

          as.numeric(trimmed$gate[row] >= trimmed$bubble[row-1])

      }

      ## convert to zoo

      z <- zoo(trimmed$bubble, trimmed$time)

      z

  })

}

##' Create state matrix (one row per time holding bubble for each mole rat

##' 

##' @param x list of zoo objects from createZooObjects

##' @return a multivariate zoo object

##' @export

createStateMatrix <- function (x) {

  m <- do.call(merge, x)

  m <- na.locf(m, na.rm=FALSE)

  m

}

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