Data structure with PDR data and descriptors for breath test records

Generates structure of class breathtest_data with required fields and optional fields. Optional fields by default are NA. This structure is used internally as an intermediate when reading in external file formats. All read_xxx functions return this structure, or a list of this structure (e.g. read_breathid_xml), and any converter to a new format should do the same to be used with cleanup_data. To support a new format with, also update breathtest_read_function which returns the most likely function to read the file by reading a few lines in it.

Usage

breathtest_data(
  patient_id,
  name = NA,
  first_name = NA,
  initials = NA,
  dob = NA,
  birth_year = NA,
  gender = NA,
  study = NA,
  pat_study_id = NA,
  file_name,
  device = "generic",
  substrate,
  record_date,
  start_time = record_date,
  end_time = record_date,
  test_no,
  dose = 100,
  height = 180,
  weight = 75,
  t50 = NA,
  gec = NA,
  tlag = NA,
  data = data
)

Arguments

patient_id: required, string or number for unique identification
name: optional
first_name: optional
initials: optional, 2 characters, 1 number
dob: optional date of birth (not to be confused with "delta over baseline")
birth_year: optional
gender: optional m or f
study: optional name of study; can be used in population fit
pat_study_id: optional; patient number within study_ does not need to be globally unique
file_name: required; file where data were read from, or other unique string_ when data are read again, this string is tested and record is skipped when same filename is already in database, therefore uniqueness is important_ when some record does not turn up in database after repeated reading, check if a record with the same file name is already there, and rename the file to avoid collisions_
device: breath_id or iris; default "generic"
substrate: should contain string "ace" or "oct" or "okt", case insensitive_ will be replaced by "acetate" or "octanoate". If empty, "ocatanoate" is assumed.
record_date: required record date_
start_time: optional
end_time: optional
test_no: required integer; unique test number converted to integer if factor
dose: optional, default 100 mg
height: optional, in cm; when pdr must be calculated, default values are used; see dob_to_pdr
weight: optional, in kg
t50: optional, only present if device computes this value
gec: optional, only present if device computes this value
tlag: optional, only present if device computes this value
data: data frame with at least 5 rows and columns minute or time and one or both of dob or pdr. If pdr is missing, and height, weight and substrate are given, computes pdr via function dob_to_pdr. When height and weight are missing, defaults 180 cm and 75 kg are used instead.

Examples

# Read a file with known format
iris_csv_file = btcore_file("IrisCSV.TXT")
iris_csv_data = read_iris_csv(iris_csv_file)
# Note that many filds are NA
str(iris_csv_data)
#> List of 23
#>  $ patient_id  : chr "123456"
#>  $ name        : chr "Einstein"
#>  $ first_name  : chr "Albert"
#>  $ initials    : chr "EA"
#>  $ dob         : logi NA
#>  $ birth_year  : logi NA
#>  $ gender      : logi NA
#>  $ study       : chr "GE FEST"
#>  $ pat_study_id: logi NA
#>  $ file_name   : chr "IrisCSV.TXT"
#>  $ device      : chr "Iris"
#>  $ substrate   : chr "acetate"
#>  $ record_date : chr "2013-09-13"
#>  $ start_time  : chr "2013-09-13"
#>  $ end_time    : chr "2013-09-13"
#>  $ test_no     : int 9999
#>  $ dose        : num 100
#>  $ height      : num 180
#>  $ weight      : num 75
#>  $ t50         : logi NA
#>  $ gec         : logi NA
#>  $ tlag        : logi NA
#>  $ data        :'data.frame':	14 obs. of  3 variables:
#>   ..$ minute: num [1:14] 0 10 20 45 60 75 90 105 120 140 ...
#>   ..$ dob   : num [1:14] 0 2.02 5.22 8.9 9.48 ...
#>   ..$ pdr   : num [1:14] 0 1.11 2.86 4.87 5.19 ...
#>  - attr(*, "class")= chr "breathtest_data"
# Convert to a format that can be fed to one of the fit functions
iris_df = cleanup_data(iris_csv_data)
# Individual curve fit
coef(nls_fit(iris_df)) 
#> # A tibble: 9 × 5
#>   patient_id group parameter method                      value
#>   <chr>      <chr> <chr>     <chr>                       <dbl>
#> 1 123456     A     m         exp_beta                 31.9    
#> 2 123456     A     k         exp_beta                  0.00451
#> 3 123456     A     beta      exp_beta                  1.93   
#> 4 123456     A     deviance  exp_beta                  0.696  
#> 5 123456     A     t50       bluck_coward             70.7    
#> 6 123456     A     t50       maes_ghoos              266.     
#> 7 123456     A     t50       maes_ghoos_scintigraphy 178.     
#> 8 123456     A     tlag      bluck_coward             -7.53   
#> 9 123456     A     tlag      maes_ghoos              146.