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Adding Period_prior_to_index function #35

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Adding Period_prior_to_index function #35

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Intiaial dispatch for period_prior_to_index function
Jay-sanjay Jun 5, 2024
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trying to debug
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Added the second dispatch
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Tests added for the second dispatch
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debugging
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Update preprocessing.jl
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Create cohort on Eunomia for testing
TheCedarPrince Jun 14, 2024
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Merge branch 'dev' into period_prior_to_index
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Update preprocessing.jl
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Merge branch 'dev' into period_prior_to_index
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Update api.md
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Update preprocessing.jl
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Update preprocessing.jl
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@Jay-sanjay
Jay-sanjay committed Jun 12, 2024
commit 6ce8bd3ff4a238b743d97ab4cb9da10d34363892
36 changes: 18 additions & 18 deletions src/preprocessing.jl
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Expand Up @@ -63,21 +63,21 @@ end
"""
function Period_prior_to_index(cohort_id::Vector, conn; date_prior=Day(100), tab=cohort)
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Given a vector of cohort IDs, this function returna a DataFrame with the cohort_start_date adjusted by the date_prior.
Given a vector of cohort IDs, this function returna a DataFrame with the cohort_start_date adjusted by the date_prior.
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# Arguments:
# Arguments:

- `cohort_id` - vector of cohort IDs
- `conn` - database connection
- `cohort_id` - vector of cohort IDs
- `conn` - database connection

# Keyword Arguments:
# Keyword Arguments:

- `date_prior` - period prior to the index date; default is 100 days
- `tab` - the `SQLTable` representing the cohort table; default `cohort`
- `date_prior` - period prior to the index date; default is 100 days
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- `tab` - the `SQLTable` representing the cohort table; default `cohort`
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# Returns
# Returns

- DataFrame with the cohort_start_date adjusted by the date_prior.
- DataFrame with the cohort_start_date adjusted by the date_prior.
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"""
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function Period_prior_to_index(cohort_id::Vector, conn; date_prior=Day(100), tab=cohort)

Expand All @@ -104,21 +104,21 @@ end
"""
function Period_prior_to_index(person_ids::Vector, start_date_on_person::Function, conn; date_prior=Day(100))

Given a vector of person IDs, this function returns a DataFrame with the cohort_start_date adjusted by the date_prior.
Given a vector of person IDs, this function returns a DataFrame with the cohort_start_date adjusted by the date_prior.

# Arguments:
# Arguments:

- `person_ids` - vector of person IDs
- `start_date_on_person` - function that returns the SQL query to get the start date of the person
- `conn` - database connection
- `person_ids` - vector of person IDs
- `start_date_on_person` - function that returns the SQL query to get the start date of the person
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I would suggest changing this name to index_date_func and in the docstring specifies that the function should accept three arguments being df (the dataframe computed for the cohorts), tables, and conn with a note that it should return a DataFrame and not SQL. I think the function a user passes in should allow for execution of SQL and additional post-processing if they need it.

P.S. This will be cool as that means it could accept TidierDB queries someday down the road too.

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@Jay-sanjay Jay-sanjay Jun 24, 2024 •
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@TheCedarPrince but, then where do we adjust the dates based on date-prior ?

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Oh so I imagine the user manually defines and applies the transformation to the start_date column within the function they pass in. Here's a simplified sketch with pseudo code:

my_func(df, tables, conn)

for patient in eachrow(df)
# Some criteria to meet
    if Criteria 1
        update patient.start_date by some change
# Some criteria to meet
    elseif Criteria 2

# ... Other additional create and transformations

return df

end

So the date_prior variable goes away and instead, the user passes in exactly how they want to transform each patient based on some criteria they are looking for in the function they provide. Does that make more sense?

- `conn` - database connection

# Keyword Arguments:
# Keyword Arguments:

- `date_prior` - period prior to the index date; default is 100 days
- `date_prior` - period prior to the index date; default is 100 days
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Since this method only accepts a function that modifies the cohort_start_date per person, this argument and its usage should be deleted.


# Returns
# Returns

- DataFrame with the cohort_start_date adjusted by the date_prior.
- DataFrame with the cohort_start_date adjusted by the date_prior.
"""
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Could you add an example section here about how to call this function and how to pass in a function into the argument which accepts a user defined function? So show how to make a function? Thanks!

function Period_prior_to_index(
person_ids::Vector,
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