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.

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"

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 x 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.