Merge pull request #211 from OHDSI/mah_collectTables

Conduct analyses in the db side
OHDSI · Oct 21, 2024 · 5749f1a · 5749f1a
2 parents d237b73 + 588ed54
commit 5749f1a
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Showing 13 changed files with 13 additions and 564 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -45,20 +45,19 @@ Suggests:
     rmarkdown,
     RPostgres,
     testthat (>= 3.0.0),
-    withr
+    withr,
+    omock (>= 0.3.0)
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Imports: 
     CDMConnector (>= 1.3.0),
     cli,
     clock,
-    CohortCharacteristics (>= 0.3.0),
     CohortConstructor (>= 0.3.1),
     dplyr,
     ggplot2,
-    omock (>= 0.3.0),
     omopgenerics (>= 0.3.1),
-    PatientProfiles (>= 1.2.0),
+    PatientProfiles (>= 1.2.0.900),
     purrr,
     rlang,
     stringr,
@@ -71,4 +70,5 @@ URL: https://OHDSI.github.io/OmopSketch/
 BugReports: https://github.com/OHDSI/OmopSketch/issues
 VignetteBuilder: knitr
 Remotes:  
-    darwin-eu-dev/omopgenerics@mah_vl
+    darwin-eu-dev/omopgenerics@mah_vl,
+    darwin-eu-dev/PatientProfiles@issue_705
diff --git a/NAMESPACE b/NAMESPACE
@@ -14,13 +14,11 @@ export(summariseConceptCounts)
 export(summariseInObservation)
 export(summariseObservationPeriod)
 export(summariseOmopSnapshot)
-export(summarisePopulationCharacteristics)
 export(summariseRecordCount)
 export(suppress)
 export(tableClinicalRecords)
 export(tableObservationPeriod)
 export(tableOmopSnapshot)
-export(tablePopulationCharacteristics)
 importFrom(dplyr,"%>%")
 importFrom(omopgenerics,bind)
 importFrom(omopgenerics,exportSummarisedResult)

diff --git a/R/summariseClinicalRecords.R b/R/summariseClinicalRecords.R
@@ -223,7 +223,7 @@ getNumberPeopleInCdm <- function(cdm, strata, peopleStrata){
   peopleStrata |>
     dplyr::select(-c("observation_period_start_date","observation_period_end_date")) |>
     dplyr::inner_join(cdm[["person"]] |> dplyr::select("person_id"), by = "person_id") |>
-    dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+    # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
     PatientProfiles::summariseResult(strata = strata,
                                      includeOverallStrata = TRUE,
                                      counts = TRUE,
@@ -240,7 +240,7 @@ addCounts <- function(result, strata, omopTable){
     rbind(
       omopTable |>
         dplyr::select("person_id", dplyr::any_of(c("age_group","sex"))) |>
-        dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+        # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
         PatientProfiles::summariseResult(strata = strata,
                                          includeOverallStrata = TRUE,
                                          counts = TRUE,
@@ -291,7 +291,7 @@ addRecordsPerPerson <- function(result, omopTable, recordsPerPerson, cdm, people
           .data$records_per_person
         )) |>
         dplyr::distinct() |>
-        dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+        # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
         PatientProfiles::summariseResult(
           strata = strata,
           includeOverallStrata = TRUE,

diff --git a/R/summariseConceptCounts.R b/R/summariseConceptCounts.R
@@ -178,7 +178,7 @@ getCodeUse <- function(x,
   if(!"number subjects" %in% c(countBy)){records <- records |> dplyr::select(-"person_id")}
 
   cc <- records |>
-    dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+    # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
     PatientProfiles::summariseResult(strata = strata,
                                      variable = "standard_concept_name",
                                      group = "standard_concept_id",

diff --git a/R/summariseObservationPeriod.R b/R/summariseObservationPeriod.R
@@ -50,7 +50,7 @@ summariseObservationPeriod <- function(observationPeriod,
 
   if (omopgenerics::isTableEmpty(observationPeriod)) {
     obsSr <- observationPeriod |>
-      dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+      # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
       PatientProfiles::summariseResult(
         variables = NULL, estimates = NULL, counts = TRUE)
   } else {
@@ -74,7 +74,7 @@ summariseObservationPeriod <- function(observationPeriod,
       dplyr::collect()
 
     obsSr <- obs |>
-      dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+      # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
       PatientProfiles::summariseResult(
         strata = strataId,
         variables = c("duration", "next_obs"),
@@ -86,7 +86,7 @@ summariseObservationPeriod <- function(observationPeriod,
             dplyr::group_by(.data$person_id, dplyr::across(dplyr::any_of(c("sex","age_group")))) |>
             dplyr::tally(name = "n") |>
             dplyr::ungroup() |>
-            dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+            # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
             PatientProfiles::summariseResult(
               variables = c("n"),
               estimates = estimates,

diff --git a/R/summarisePopulationCharacteristics.R b/R/summarisePopulationCharacteristics.R
diff --git a/R/summariseRecordCount.R b/R/summariseRecordCount.R
@@ -236,7 +236,7 @@ createSummarisedResultRecordCount <- function(result, strata, omopTable, omopTab
   result <- result |>
     dplyr::mutate(n = 1) |>
     dplyr::select(-"person_id") |>
-    dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
+    # dplyr::collect() |> # https://github.com/darwin-eu-dev/PatientProfiles/issues/706
     PatientProfiles::summariseResult(
       variables = "n",
       strata = strata,

diff --git a/R/tablePopulationCharacteristics.R b/R/tablePopulationCharacteristics.R
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -28,11 +28,6 @@ reference:
 - contents:
   - summariseConceptCounts
   - plotConceptCounts
-- subtitle: Individual Characteristics
-  desc: Summarise characteristics of the individuals in the OMOP Common Data Model
-- contents:
-  - summarisePopulationCharacteristics
-  - tablePopulationCharacteristics
 - subtitle: Mock Database
   desc: Create a mock database to test the OmopSketch package
 - contents:

diff --git a/man/summarisePopulationCharacteristics.Rd b/man/summarisePopulationCharacteristics.Rd
diff --git a/man/tablePopulationCharacteristics.Rd b/man/tablePopulationCharacteristics.Rd