Capr Issue #99: Potential improvements to Capr #105

guuswilmink · 2024-09-20T11:19:33Z

This PR is linked to #99.

Suggested functions:
isStandard.R: Given a path to CSV files with at least fields "sourceCode" and "conceptId", along with a database connection with a CDM and vocabulary schema, return a tibble of non-standard concepts. Allows for export of results for all concepts included (including standard). This function can help in quickly identifying non-standard concepts from tables of concept ids.

isStandardDB.R: Checks whether concepts that exist in a database are standard/non-standard and returns the non-standard concepts. The full table of standard and non-standard concepts can be saved as well. This is probably the most useful out of the 3 isStandard functions.

isStandardCS.R: Similar return as isStandard.R and isStandardDB, but performs the check given a Capr ConceptSet class object rather than CSV files. Does not capture source value (as these are not relevant for concept sets).

countOccurrences.R: Given a vector of concept IDs and a connection to a CDM instance, count the number of occurrences of: 1) persons with concept 'x'; 2) records with concept 'x'; 3) persons with concept 'x' or descendants of 'x'; 4) records with concept 'x' or descendants of 'x'
To demonstrate and further clarify this function I have attached a PDF with example usage. Is this already possible within Capr?

@mdlavallee92 I have incorporated your feedback provided in issue #99; please let me know if this is to your expectations.

Capr v2.0.6 release candidate.

update to v2.0.7 CirceR as remotes

Develop v2.0.8

… to countOccurences

copy files from PHEMS repo && updates to code

sync forks

Feature

gitignore .Rprofile

Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 2 to 4.1.7. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v2...v4.1.7) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

mdlavallee92

Hi @guuswilmink! Many many many apologies for being entirely too late on this review. This is a really nice add, thank you! Would you be interested in other maintenance?

My main two hold ups are the on the signatures of the functions and consolidating export files.

Change them to camelCase as that is part of the HADES style gudie...ie cdmDatabaseSchema, vocabDatabaseSchema. Make v conceptIds. v is way to generic.
consolidate the isStandard functions to 1 file and dont export the links function. That is a stable internal. See example of the same idea here.

I need a bit more examples of how to use the isStandard functions. I believe their utility but not totally seeing its use in the day to day of the package. Do you mind doing a vignette or pointing me to some examples of how you are using this? I love the countOccurrences function. Think that is a handy tool!

mdlavallee92 · 2025-02-18T14:48:16Z

R/countOccurrences.R

+#' )
+#'
+#' @export
+countOccurrences <- function(v, tables, links, db_connection, cdm_schema, vocab_schema, save_path = NULL) {


Some notes on the signature...

v is to generic of a signature...just use conceptIds as the input name if that is what you want the user to input.

signatures should be in camelCase ie conceptIds, dbConnection, cdmDatabaseSchema. this is part of the HADES style guide

Does the links table ever change? If not just make this a non-exported function called within the function.

mdlavallee92 · 2025-02-18T14:49:08Z

R/countOccurrences.R

+  for (table in tables) {
+    concept_id_field <- links[[table]][1]
+
+    # Combined SQL query for direct and descendant counts


prefer to have the sql sourced as an inst file instead of within the code. it ends up being a bit neater. No change required

mdlavallee92 · 2025-02-18T14:49:36Z

R/countOccurrences.R

+#'   db_connection = db_connection, cdm_schema = "public", vocab_schema = "vocabulary"
+#' )
+#'
+#' @export


Nice I like this function a lot!

mdlavallee92 · 2025-02-18T14:50:18Z

R/isStandard.R

+#' @importFrom readr read_csv write_csv
+#' @importFrom dplyr mutate across filter select inner_join
+#' @importFrom DatabaseConnector connect disconnect querySql
+#' @export


Same thing here change to camelCase.

mdlavallee92 · 2025-02-18T14:52:29Z

R/isStandard.R

+  }
+
+  for (table_path in tables) {
+    table_name <- basename(table_path)


No change required. Suggestion is to leverage internal function. it makes the code easier to read and reference. For example, the for loop in L56 seems to be a constant pattern. Functionalize this as like prepAndReadTable function that you leverage here.

mdlavallee92 · 2025-02-18T14:58:52Z

R/isStandardDB.R

+#' @importFrom readr read_csv write_csv
+#' @importFrom dplyr mutate filter rename bind_rows
+#' @importFrom DatabaseConnector querySql
+#' @importFrom SqlRender render translate


For all of these isStandard examples, show me a couple of use cases. I believe you that they are needed but I havent encountered them often

mdlavallee92 · 2025-02-18T14:59:41Z

R/isStandardDB.R

+
+  for (table in tables) {
+    # Read concept table from SQL database
+    concept_table_query <- SqlRender::render(sprintf(


just curious...why sprintf? I usually use glue. Despite adding a dependency i think its a real good package for interpreting string literals

mdlavallee92 · 2025-02-18T15:01:29Z

R/table_linked_to_concept_field.R

+#' print(concept_field)
+#'
+#' @export
+links <- list(


I think this should be a non-exported function. It seems stable since its pegged to the CDM schematic.

mdlavallee92 · 2025-02-18T15:03:18Z

tests/testthat/test-isStandard.R

@@ -0,0 +1,127 @@
+source("R/isStandard.R")


consolidate into 1 isStandard file all of these functions and test. ow looks good

mdlavallee92 · 2025-02-18T15:04:06Z

DESCRIPTION

@@ -3,7 +3,8 @@ Title: Cohort Definition Application Programming
 Version: 2.0.8
 Authors@R: c(
    person("Martin", "Lavallee", , "martin.lavallee@boehringer-ingelheim.com", role = c("aut", "cre")),
-    person("Adam", "Black", , "black@ohdsi.org", role = c("aut"))
+    person("Adam", "Black", , "black@ohdsi.org", role = c("aut")),
+    person("Guus", "Wilmink", , "guus@thehyve.nl", role = c("aut"))


would you like to do more maintenance on Capr? As you can see the package is escaping me given how slow I was to respond to this PR

…ub/workflows/actions/download-artifact-4.1.7 Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows

mdlavallee92 and others added 30 commits September 7, 2023 17:07

Merge pull request OHDSI#78 from OHDSI/develop

e6ad3c1

Capr v2.0.6 release candidate.

Merge pull request OHDSI#84 from OHDSI/develop

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update to v2.0.7 CirceR as remotes

Renaming weekly R check yaml for consistency with rest of HADES

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Merge pull request OHDSI#94 from OHDSI/develop

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Develop v2.0.8

copy files from PHEMS repo

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Function for checking standard concepts; add descendant record counts…

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… to countOccurences

knitted script

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Update main code

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update concept sets

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update cohort json

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update renv

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update concept sets

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update json save

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add PHEMS OMOP mappings (Hyve suggestions)

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Add check for standard concepts

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index=False update for standard concept check save file

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replace python isStandard function with R

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update standard concept tables

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update isStandard.R

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update main code

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knitted html update

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Merge pull request #1 from thehyve/copy-PHEMS-repo-to-Capr-fork

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copy files from PHEMS repo && updates to code

update gitignore

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rename R project

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update renv

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guuswilmink and others added 26 commits August 12, 2024 10:45

Merge pull request #5 from thehyve/fork_sync-remove_temp_files

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sync forks

merge main branch

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update functions

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add test conceptsets

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add tests

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update gitignore

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small updates

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add standardness check for checking in DB

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small fixes

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add test for DB standardness check

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update gitignore

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update functions

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update unit tests

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Merge pull request #6 from thehyve/feature

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Feature

gitignore .Rprofile

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Merge pull request #7 from thehyve/feature

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gitignore .Rprofile

restore .Rproj

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change line endings

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Merge branch 'main' of https://github.com/thehyve/Capr-Enhancements

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clean-up fork

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mdlavallee92 requested changes Feb 18, 2025

View reviewed changes

guuswilmink added 3 commits March 3, 2025 10:38

Merge pull request #8 from thehyve/dependabot/github_actions/dot-gith…

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Capr Issue #99: Potential improvements to Capr #105

Capr Issue #99: Potential improvements to Capr #105

guuswilmink commented Sep 20, 2024

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Capr Issue #99: Potential improvements to Capr #105

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Capr Issue #99: Potential improvements to Capr #105

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