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union tmp table #321

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Sep 21, 2024
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union tmp table #321

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7 changes: 5 additions & 2 deletions R/unionCohorts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -68,15 +68,17 @@ unionCohorts <- function(cohort,
tmpTable <- omopgenerics::uniqueTableName()
unionedCohort <- cohort |>
dplyr::filter(.data$cohort_definition_id %in% .env$cohortId) |>
joinOverlap(name = name, by = "subject_id", gap = gap) |>
joinOverlap(name = tmpTable,
by = "subject_id",
gap = gap) |>
dplyr::mutate(cohort_definition_id = 1L) |>
dplyr::relocate(dplyr::all_of(omopgenerics::cohortColumns("cohort"))) |>
dplyr::compute(name = tmpTable, temporary = FALSE)
cohCodelist <- attr(cohort, "cohort_codelist")
if (!is.null(cohCodelist)) {
cohCodelist <- cohCodelist |> dplyr::mutate("cohort_definition_id" = 1L)
}
unionedCohort <- unionedCohort |>
dplyr::relocate(dplyr::all_of(omopgenerics::cohortColumns("cohort"))) |>
omopgenerics::newCohortTable(
cohortSetRef = cohSet,
cohortAttritionRef = NULL,
Expand All @@ -91,6 +93,7 @@ unionCohorts <- function(cohort,
cdm <- bind(cohort, unionedCohort, name = name)
}

CDMConnector::dropTable(cdm, name = tmpTable)

return(cdm[[name]])
}
1 change: 1 addition & 0 deletions README.Rmd
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Expand Up @@ -18,6 +18,7 @@ knitr::opts_chunk$set(
<!-- badges: start -->
[![CRAN status](https://www.r-pkg.org/badges/version/CohortConstructor)](https://CRAN.R-project.org/package=CohortConstructor)
[![R-CMD-check](https://github.com/OHDSI/CohortConstructor/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortConstructor/actions)
[![Codecov test coverage](https://codecov.io/gh/OHDSI/CohortConstructor/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OHDSI/CohortConstructor?branch=main)
[![Lifecycle:Experimental](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

<!-- badges: end -->
Expand Down
87 changes: 48 additions & 39 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,8 @@
[![CRAN
status](https://www.r-pkg.org/badges/version/CohortConstructor)](https://CRAN.R-project.org/package=CohortConstructor)
[![R-CMD-check](https://github.com/OHDSI/CohortConstructor/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortConstructor/actions)
[![Codecov test
coverage](https://codecov.io/gh/OHDSI/CohortConstructor/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OHDSI/CohortConstructor?branch=main)
[![Lifecycle:Experimental](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

<!-- badges: end -->
Expand Down Expand Up @@ -112,14 +114,14 @@ cohort_count(cdm$fractures) %>% glimpse()
#> Rows: 3
#> Columns: 3
#> $ cohort_definition_id <int> 1, 2, 3
#> $ number_records <int> 462, 565, 137
#> $ number_subjects <int> 426, 508, 132
#> $ number_records <int> 464, 569, 138
#> $ number_subjects <int> 427, 510, 132
attrition(cdm$fractures) %>% glimpse()
#> Rows: 9
#> Columns: 7
#> $ cohort_definition_id <int> 1, 1, 1, 2, 2, 2, 3, 3, 3
#> $ number_records <int> 462, 462, 462, 565, 565, 565, 137, 137, 137
#> $ number_subjects <int> 426, 426, 426, 508, 508, 508, 132, 132, 132
#> $ number_records <int> 464, 464, 464, 569, 569, 569, 138, 138, 138
#> $ number_subjects <int> 427, 427, 427, 510, 510, 510, 132, 132, 132
#> $ reason_id <int> 1, 2, 3, 1, 2, 3, 1, 2, 3
#> $ reason <chr> "Initial qualifying events", "cohort requirements…
#> $ excluded_records <int> 0, 0, 0, 0, 0, 0, 0, 0, 0
Expand All @@ -134,21 +136,28 @@ our three cohorts to create this overall cohort like so:

``` r
cdm$fractures <- unionCohorts(cdm$fractures,
cohortName = "any_fracture",
name ="fractures")
cohortName = "any_fracture",
keepOriginalCohorts = TRUE,
name ="fractures")
```

``` r
settings(cdm$fractures)
#> # A tibble: 1 × 3
#> cohort_definition_id cohort_name gap
#> <int> <chr> <dbl>
#> 1 1 any_fracture 0
#> # A tibble: 4 × 5
#> cohort_definition_id cohort_name cdm_version vocabulary_version gap
#> <int> <chr> <chr> <chr> <dbl>
#> 1 1 ankle_fracture 5.3 v5.0 18-JAN-19 NA
#> 2 2 forearm_fracture 5.3 v5.0 18-JAN-19 NA
#> 3 3 hip_fracture 5.3 v5.0 18-JAN-19 NA
#> 4 4 any_fracture <NA> <NA> 0
cohortCount(cdm$fractures)
#> # A tibble: 1 × 3
#> # A tibble: 4 × 3
#> cohort_definition_id number_records number_subjects
#> <int> <int> <int>
#> 1 1 1164 922
#> 1 1 464 427
#> 2 2 569 510
#> 3 3 138 132
#> 4 4 1171 924
```

### Require in date range
Expand All @@ -168,11 +177,11 @@ attributes have been updated

``` r
cohort_count(cdm$fractures) %>% glimpse()
#> Rows: 1
#> Rows: 4
#> Columns: 3
#> $ cohort_definition_id <int> 1
#> $ number_records <int> 315
#> $ number_subjects <int> 282
#> $ cohort_definition_id <int> 1, 2, 3, 4
#> $ number_records <int> 108, 152, 62, 322
#> $ number_subjects <int> 104, 143, 60, 287
attrition(cdm$fractures) %>%
filter(reason == "cohort_start_date between 2000-01-01 & 2020-01-01") %>%
glimpse()
Expand Down Expand Up @@ -205,28 +214,28 @@ criteria.
attrition(cdm$fractures) %>%
filter(reason == "Age requirement: 40 to 65") %>%
glimpse()
#> Rows: 1
#> Rows: 4
#> Columns: 7
#> $ cohort_definition_id <int> 1
#> $ number_records <int> 124
#> $ number_subjects <int> 118
#> $ reason_id <int> 4
#> $ reason <chr> "Age requirement: 40 to 65"
#> $ excluded_records <int> 191
#> $ excluded_subjects <int> 164
#> $ cohort_definition_id <int> 1, 2, 3, 4
#> $ number_records <int> 43, 64, 22, 129
#> $ number_subjects <int> 43, 62, 22, 122
#> $ reason_id <int> 6, 6, 6, 4
#> $ reason <chr> "Age requirement: 40 to 65", "Age requirement: 40…
#> $ excluded_records <int> 65, 88, 40, 193
#> $ excluded_subjects <int> 61, 81, 38, 165

attrition(cdm$fractures) %>%
filter(reason == "Sex requirement: Female") %>%
glimpse()
#> Rows: 1
#> Rows: 4
#> Columns: 7
#> $ cohort_definition_id <int> 1
#> $ number_records <int> 64
#> $ number_subjects <int> 62
#> $ reason_id <int> 5
#> $ reason <chr> "Sex requirement: Female"
#> $ excluded_records <int> 60
#> $ excluded_subjects <int> 56
#> $ cohort_definition_id <int> 1, 2, 3, 4
#> $ number_records <int> 19, 37, 12, 68
#> $ number_subjects <int> 19, 36, 12, 65
#> $ reason_id <int> 7, 7, 7, 5
#> $ reason <chr> "Sex requirement: Female", "Sex requirement: Fema…
#> $ excluded_records <int> 24, 27, 10, 61
#> $ excluded_subjects <int> 24, 26, 10, 57
```

### Require presence in another cohort
Expand All @@ -251,15 +260,15 @@ cdm$fractures <- cdm$fractures %>%
attrition(cdm$fractures) %>%
filter(reason == "Not in cohort gibleed between -Inf & 0 days relative to cohort_start_date") %>%
glimpse()
#> Rows: 1
#> Rows: 4
#> Columns: 7
#> $ cohort_definition_id <int> 1
#> $ number_records <int> 64
#> $ number_subjects <int> 62
#> $ reason_id <int> 8
#> $ cohort_definition_id <int> 1, 2, 3, 4
#> $ number_records <int> 14, 30, 10, 54
#> $ number_subjects <int> 14, 30, 10, 52
#> $ reason_id <int> 10, 10, 10, 8
#> $ reason <chr> "Not in cohort gibleed between -Inf & 0 days rela…
#> $ excluded_records <int> 0
#> $ excluded_subjects <int> 0
#> $ excluded_records <int> 5, 7, 2, 14
#> $ excluded_subjects <int> 5, 6, 2, 13
```

``` r
Expand Down
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