breathtest_data: Data structure with PDR data and descriptors for breath test...

In breathtestcore: Core Functions to Read and Fit 13c Time Series from Breath Tests

Data structure with PDR data and descriptors for breath test records

Description

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)
# 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)) 

breathtestcore documentation built on April 3, 2025, 8:16 p.m.