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pharmaverse / sdtm.oak

An EDC and Data Standard agnostic SDTM data transformation engine that automates the transformation of raw clinical data in ODM format to SDTM based on standard mapping algorithms
https://pharmaverse.github.io/sdtm.oak/
Apache License 2.0
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Develop a function to calculate study day #16

Closed ShiyuC closed 4 months ago

ShiyuC commented 8 months ago

Feature Idea

Purpose The function performs study day calculation

Functionality The feature uses an algorism that is compliant with CDISC SDTM rules. It uses two date values that are formatted according to ISO8601 rules. One of the dates refdt is called the 'reference' date and is the baseline against which the 'target' date tgdt is used to determine the study day value. The input dates are expected in a data frame The study day (SD) value is computed as follows: If Reference Date <= Target Date then SD = (Target Date) - (Reference Date) + 1 else if Reference Date > Target Date then SD = (Target Date) - (Reference Date)

Relevant Input

The input data frame ds_in should contain refdt and tgdt variables.

Relevant Output

A character vector with the study days that were calculated of the same length as input data frame.

Reproducible Example/Pseudo Code

ds_in <- data.frame( RFSTDTC = c( "2012-01-01", "2012-04-14", "2012-04-14", "2010-05-02", "2010---10", "2012", NA, "2012-01-01", NA, "2010-04-15", "2010-04-15" ), XXDTC = c( "2012-02-01", "2012-04-14", "2012-04-13", "2011-05-02", "2012-02-03", "2012-06-06", "2012-01-01", NA, NA, "2009---12", "2009-12-12" ) ) refdt <- "RFSTDTC" tgdt <- "XXDTC" calculate_study_day(ds_in, refdt, tgdt)

yli110-stat697 commented 8 months ago

I can start on this one. Just wondering if ds_in argument should be a data.frame in R? Do we allow data.table etc?

ShiyuC commented 8 months ago

@yli110-stat697, Yes, ds_in is a data frame in R. I think it would be nice to keep it as a data frame in the domain automation process.

MaguluriVenkata commented 8 months ago

Is it possible to join DM data in air and calculate -DY? (just suggestion) otherwise logic looks perfect. Thanks

ShiyuC commented 8 months ago

@yli110-stat697 I'll modify the description based upon what is discussed today

yli110-stat697 commented 7 months ago

@yli110-stat697 I'll modify the description based upon what is discussed today

Hi @ShiyuC so I will be joining DM to get the reference date right?

ShiyuC commented 7 months ago

@yli110-stat697 I'll modify the description based upon what is discussed today

Hi @ShiyuC so I will be joining DM to get the reference date right?

Hi @yli110-stat697 , no need to join DM. DM is supposed to be in the package environment, so the reference dates just need to be referenced as a vector. You can refer to oak_derive_studyday() in roak package as an example

edgar-manukyan commented 7 months ago

Hi team, I believe for the sdtm.oak we better start explicitly passing the required domains into a functions via a parameter instead of obtaining it from the package environment. Please bring this up during the Wednesday stand-up.