tests/testthat/test_701_unit_norm_find_cases_with_activity.R

In brucehoff/mPowerProcessing: Processes mPower data

# Test normalization - find Cases With Pre/post Activity 
# 
# Author: J. Christopher Bare
###############################################################################

require(testthat)

context("test_unit_normalization")

## fake demographics table
demo <- data.frame(
  healthCode=c(
    'test-10001',
    'test-10002',
    'test-10003',
    'test-10004',
    'test-10005',
    'test-10006',
    'test-10007',
    'test-10008'),
  `professional-diagnosis`=c(
    FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE),
  age=c(
    47, NA, 55, 66, 77, 81, 88, 89),
  check.names=FALSE,
  stringsAsFactors=FALSE)

## fake feature data
featureTables <- list(
  tap=data.frame(
    date=c(
      as.Date('2015-04-24'),
      as.Date('2015-04-24'),
      as.Date('2015-04-28'),
      as.Date('2015-05-15'),
      as.Date('2015-05-28'),
      as.Date('2015-04-28')),
    healthCode=c(
      'test-10001',
      'test-10002',
      'test-10003',
      'test-10004',
      'test-10005',
      'test-10006'),
    medTimepoint=c(
      'Immediately before Parkinson medication',
      'Just after Parkinson medication (at your best)',
      'Another time',
      'Just after Parkinson medication (at your best)',
      'Just after Parkinson medication (at your best)',
      'Just after Parkinson medication (at your best)'),
    featureX=rnorm(6),
    stringsAsFactors=FALSE),
  voice=data.frame(
    date=c(
      as.Date('2015-04-14'),
      as.Date('2015-04-24'),
      as.Date('2015-04-28'),
      as.Date('2015-04-29'),
      as.Date('2015-05-13'),
      as.Date('2015-04-24'),
      as.Date('2015-04-28'),
      as.Date('2015-04-28'),
      as.Date('2015-04-28')),
    healthCode=c(
      'test-10001',
      'test-10002',
      'test-10003',
      'test-10004',
      'test-10005',
      'test-10006',
      'test-10007',
      'test-10007',
      'test-10007'),
    medTimepoint=c(
      'Another time',
      'Immediately before Parkinson medication',
      'Another time',
      NA,
      NA,
      'Another time',
      NA,
      'Another time',
      'Immediately before Parkinson medication'),
    featureY=rnorm(9),
    stringsAsFactors=FALSE),
  balance=data.frame(
    date=c(
      as.Date('2015-04-01'),
      as.Date('2015-04-02'),
      as.Date('2015-04-03'),
      as.Date('2015-04-04'),
      as.Date('2015-04-17'),
      as.Date('2015-04-28'),
      as.Date('2015-04-28')),
    healthCode=c(
      'test-10001',
      'test-10002',
      'test-10003',
      'test-10004',
      'test-10005',
      'test-10006',
      'test-10007'),
    medTimepoint=c(
      'Just after Parkinson medication (at your best)',
      'Immediately before Parkinson medication',
      NA,
      'Another time',
      'Another time',
      'Immediately before Parkinson medication',
      'Another time'),
    featureZ=rnorm(7),
    stringsAsFactors=FALSE))

## define date window
window <- list(start=as.Date("2015-04-01"), end=as.Date("2015-04-30"))

cases <- findCasesWithPrepostActivity(demo, featureTables, window)

cat("\nfound:", cases,"\n")

## Due to MPOW-39, we now want to generate dashboard data for
## participants with pre and post-med activity regardless of
## whether they have a professional diagnosis of Parkinson's
expected_cases = c('test-10001', 'test-10006', 'test-10007')
names(expected_cases) <- expected_cases

expect_equal(cases, expected_cases)

## test-10001 Not a PD patient, but has pre and post activity,
## so, OK under the new rules.

## The other health codes shouldn't be returned for these reasons
## test-10002 age is NA
## test-10003 no pre or post medication
## test-10004 no pre or post inside window
## test-10005 no pre or post inside window
## test-10008 no activity