Read and write utilities

Support for reading from and writing to pipe separated values (.psv) files as used for the PhysioNet Sepsis Challenge.

write_psv(x, dir, na_rows = NULL)

read_psv(dir, col_spec = NULL, id_var = "stay_id", index_var = NULL)

Arguments

x

Object to write to files

dir

Directory to write the (many) files to or read from

na_rows

If TRUE missing time steps are filled with NaN values, if FALSE, rows where all data columns entries are missing are removed and if NULL, data is written as-is

col_spec

A column specification as created by readr::cols()

id_var

Name of the id column (IDs are generated from file names)

index_var

Optional name of index column (will be coerced to difftime)

Value

While write_psv() is called for side effects and returns NULL

invisibly, read_psv() returns an object inheriting from id_tbl.

Details

Data for the PhysioNet Sepsis Challenge is distributed as pipe separated values (.psv) files, split into separate files per patient ID, containing time stamped rows with measured variables as columns. Files are named with patient IDs and do not contain any patient identifiers as data. Functions read_psv() and write_psv() can be used to read from and write to such a data format.

References

Reyna, M., Josef, C., Jeter, R., Shashikumar, S., Moody, B., Westover, M. B., Sharma, A., Nemati, S., & Clifford, G. (2019). Early Prediction of Sepsis from Clinical Data -- the PhysioNet Computing in Cardiology Challenge 2019 (version 1.0.0). PhysioNet. https://doi.org/10.13026/v64v-d857.