View source: R/breathtest_data.R
breathtest_data | R Documentation |
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 )
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 |
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 |
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 |
# 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))
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