load nutritech data from dbnp

gistfile1.r

## Fill out your own dbNP user / pass here
authenticate("****", "****", "****")

studies = getStudies()

studyName = "NutriTechHIS"

study = studies[[grep(studyName, sapply(studies, function(x) x$code))]]
studyToken = study['token']

studyAssays = getAssaysForStudy(studyToken)
names(studyAssays) = sapply(studyAssays, getElement, "name")

assayData = list()
for(assayName in names(studyAssays)) {
  message(assayName)
  assayToken = studyAssays[[assayName]][2]
  ad = assayDataAsMatrix(assayToken)
  if(ad != "No data!") assayData[[assayName]] = ad$data
}

studyEvents = getSamplingEventsForStudy(studyToken)
events = namedListToDataFrame(studyEvents)

## Reformat data
data = assayData[[1]] ## Only clinical chemistry for now
subjects = t(namedListToDataFrame(getSubjectsForStudy(studyToken)))

data = cbind(subjects[data$subject,], data)

relativeTimes = unlist(lapply(data$samplingEvent, function(x) studyEvents[[x]]$relativeTimeInRelatedEvent))
eventDay = unlist(lapply(data$samplingEvent, function(x) studyEvents[[x]]$startTime))
data$relatedEvent = unlist(lapply(data$samplingEvent, function(x) studyEvents[[x]]$'samplingNameShort'))
data$eventDay = floor(as.numeric(as.character(eventDay)) / 60 / 60 / 24)
data$relativeTime = as.numeric(as.character(relativeTimes)) / 60

data$relatedEvent = gsub(" $", "", data$relatedEvent)

save(events, subjects, data, file = "data/nutritech.clinchem.RData")