Interpreting Results with lc500
a11_interpreting_results_lc500.RmdGoal
This vignette explains what each patient-mode output dataframe stores
in the bundled lc500 study.
For each dataframe:
- You get markdown column descriptions.
- You see
head(...)output.
Object Overview
CohortContrast::loadCohortContrastStudy() returns a
CohortContrastObject with these key components:
data_initialdata_persondata_featuresdata_patientscomplementaryMappingTableselectedFeatureDataconceptsDataconfig
#> [1] "data_patients" "data_initial"
#> [3] "data_person" "data_features"
#> [5] "conceptsData" "complementaryMappingTable"
#> [7] "selectedFeatureData" "trajectoryDataList"
#> [9] "config"
data_initial
One row per cohort episode per subject.
Column descriptions:
-
COHORT_DEFINITION_ID: Cohort label (targetorcontrol). -
SUBJECT_ID: Subject identifier. -
COHORT_START_DATE: Start date of follow-up for that cohort episode. -
COHORT_END_DATE: End date of follow-up for that cohort episode.
#> COHORT_DEFINITION_ID SUBJECT_ID COHORT_START_DATE COHORT_END_DATE
#> 1 target 100001 2019-06-14 2020-06-13
#> 2 target 100002 2020-10-05 2021-10-05
#> 3 target 100003 2020-04-09 2021-04-09
#> 4 target 100004 2019-03-24 2020-03-23
#> 5 target 100005 2020-03-28 2021-03-28
#> 6 target 100006 2020-11-15 2021-11-15
#> 7 target 100007 2019-07-30 2020-07-29
#> 8 target 100008 2019-07-22 2020-07-21
#> 9 target 100009 2019-07-19 2020-07-18
#> 10 target 100010 2020-07-11 2021-07-11
data_person
One row per person with demographics.
Column descriptions:
-
PERSON_ID: Person identifier. -
GENDER_CONCEPT_ID: OMOP concept id for gender. -
YEAR_OF_BIRTH: Year of birth.
#> PERSON_ID GENDER_CONCEPT_ID YEAR_OF_BIRTH
#> 1 100001 8507 1958
#> 2 100002 8507 1967
#> 3 100003 8507 1967
#> 4 100004 8507 1962
#> 5 100005 8532 1955
#> 6 100006 8507 1963
#> 7 100007 8507 1957
#> 8 100008 8507 1968
#> 9 100009 8532 1955
#> 10 100010 8507 1971
data_features
One row per concept (per abstraction level) with enrichment statistics.
Column descriptions:
-
CONCEPT_ID: Concept identifier. -
CONCEPT_NAME: Concept name. -
ABSTRACTION_LEVEL: Concept abstraction level (-1is base/import level). -
TARGET_SUBJECT_COUNT: Number of target subjects with concept present. -
CONTROL_SUBJECT_COUNT: Number of control subjects with concept present. -
TIME_TO_EVENT: List of pooled event times (days from cohort start) for the concept. -
TARGET_SUBJECT_PREVALENCE: Target prevalence proportion. -
CONTROL_SUBJECT_PREVALENCE: Control prevalence proportion. -
PREVALENCE_DIFFERENCE_RATIO: Target/control prevalence ratio. -
CHI2Y: Significant in chi-squared (Yates-corrected) test. -
CHI2Y_P_VALUE: P-value from chi-squared test. -
LOGITTEST: Significant in logistic regression test. -
LOGITTEST_P_VALUE: P-value from logistic regression test. -
HERITAGE: Domain/heritage (for examplecondition_occurrence,death,visit_detail).
#> CONCEPT_ID CONCEPT_NAME ABSTRACTION_LEVEL TARGET_SUBJECT_COUNT
#> 1 443388 Malignant tumor of lung -1 483
#> 2 32280 Death -1 156
#> 3 32815 Death Certificate -1 147
#> 4 4182985 Diffusion capacity of lung -1 371
#> 5 4306655 Death -1 150
#> 6 4014023 Palliative care -1 147
#> 7 4032404 Bronchoscopy -1 462
#> 8 4008226 Chemotherapy -1 164
#> 9 2107967 Lobectomy -1 165
#> 10 2107968 Lobectomy of lung -1 168
#> CONTROL_SUBJECT_COUNT
#> 1 6
#> 2 0
#> 3 0
#> 4 50
#> 5 2
#> 6 1
#> 7 10
#> 8 2
#> 9 1
#> 10 3
#> TIME_TO_EVENT
#> 1 4, 1, 4, 2, 6, 0, 6, 5, 5, 3, 5, 5, 8, 7, 6, 8, 4, 0, 10, 2, 7, 0, 7, 5, 2, 1, 9, 3, 4, 3, 3, 14, 2, 6, 2, 3, 6, 0, 8, 10, 5, 14, 0, 6, 5, 11, 6, 7, 6, 8, 4, 7, 0, 5, 7, 9, 8, 9, 0, 6, 8, 6, 4, 3, 16, 11, 4, 4, 5, 11, 3, 6, 6, 5, 8, 0, 2, 1, 4, 4, 5, 3, 5, 9, 10, 4, 6, 6, 10, 3, 4, 0, 5, 4, 0, 8, 5, 9, 5, 14, 0, 0, 4, 10, 5, 4, 13, 3, 1, 5, 2, 3, 0, 4, 11, 7, 0, 0, 13, 6, 4, 8, 6, 8, 9, 5, 0, 2, 4, 3, 13, 1, 5, 7, 3, 9, 5, 0, 3, 10, 3, 7, 8, 8, 6, 1, 3, 10, 8, 8, 4, 0, 15, 9, 0, 5, 4, 11, 7, 8, 6, 4, 1, 12, 0, 1, 3, 1, 12, 0, 6, 5, 11, 2, 0, 6, 2, 0, 6, 5, 6, 2, 11, 9, 1, 8, 3, 3, 5, 12, 3, 1, 6, 10, 8, 10, 4, 8, 3, 9, 11, 5, 3, 7, 7, 8, 2, 5, 10, 7, 4, 1, 5, 9, 6, 4, 2, 2, 13, 9, 16, 1, 2, 7, 3, 4, 3, 10, 2, 6, 7, 7, 6, 6, 3, 6, 4, 0, 6, 5, 10, 2, 9, 7, 3, 0, 6, 4, 10, 2, 5, 8, 1, 0, 2, 6, 5, 6, 3, 9, 5, 10, 11, 6, 6, 8, 0, 1, 8, 0, 0, 1, 1, 0, 2, 3, 5, 1, 4, 5, 6, 6, 9, 5, 1, 0, 0, 5, 11, 0, 7, 4, 2, 0, 5, 5, 11, 0, 3, 3, 2, 5, 7, 5, 7, 1, 6, 5, 3, 4, 6, 1, 10, 1, 4, 7, 3, 16, 4, 5, 0, 5, 5, 6, 3, 2, 8, 7, 3, 3, 0, 7, 10, 8, 3, 0, 7, 5, 8, 3, 3, 6, 5, 4, 6, 12, 6, 5, 3, 11, 7, 9, 14, 4, 0, 10, 1, 6, 11, 10, 2, 6, 2, 0, 7, 2, 0, 2, 1, 1, 5, 2, 3, 2, 7, 4, 6, 0, 7, 4, 10, 8, 5, 6, 1, 0, 18, 2, 2, 0, 2, 1, 10, 2, 9, 2, 4, 5, 5, 0, 0, 4, 4, 2, 13, 4, 13, 5, 6, 8, 3, 4, 7, 7, 1, 11, 13, 10, 3, 6, 1, 8, 2, 7, 8, 1, 3, 5, 4, 10, 2, 6, 0, 4, 2, 8, 1, 7, 0, 3, 6, 0, 10, 1, 8, 3, 7, 4, 1, 4, 4, 9, 1, 5, 3, 7, 9, 7, 6, 2, 7, 11, 3, 0, 7, 10, 1, 4, 13, 0, 9, 4, 2, 5, 4, 7, 13, 0, 0, 11, 2, 0, 2
#> 2 11, 244, 150, 165, 204, 148, 224, 191, 199, 214, 170, 212, 213, 200, 206, 190, 259, 192, 193, 232, 187, 191, 219, 180, 193, 157, 178, 158, 175, 175, 214, 183, 189, 201, 202, 194, 185, 166, 180, 212, 171, 171, 198, 193, 214, 224, 170, 168, 145, 187, 171, 213, 224, 203, 171, 209, 212, 195, 205, 270, 216, 213, 215, 183, 167, 178, 192, 152, 219, 177, 175, 190, 192, 193, 193, 173, 185, 250, 177, 160, 183, 173, 204, 174, 194, 189, 192, 186, 264, 181, 123, 176, 193, 260, 208, 226, 224, 211, 202, 243, 214, 187, 201, 217, 206, 164, 272, 189, 224, 167, 208, 216, 156, 151, 156, 199, 205, 175, 192, 170, 169, 224, 126, 176, 190, 187, 196, 173, 175, 209, 174, 150, 198, 232, 196, 178, 172, 219, 199, 243, 235, 190, 187, 217, 230, 173, 185, 212, 216, 203, 223, 211, 192, 168, 206, 200
#> 3 19, 90, 27, 220, 225, 267, 272, 244, 262, 299, 258, 245, 250, 247, 235, 237, 257, 207, 235, 224, 253, 254, 225, 248, 251, 235, 261, 253, 245, 230, 276, 230, 240, 237, 255, 256, 245, 260, 200, 224, 241, 240, 280, 113, 240, 192, 220, 227, 279, 255, 253, 242, 258, 234, 249, 198, 235, 263, 234, 259, 247, 260, 265, 226, 258, 214, 247, 273, 276, 248, 229, 227, 258, 235, 262, 253, 249, 279, 220, 248, 213, 292, 267, 247, 229, 249, 257, 255, 230, 231, 262, 226, 233, 268, 252, 244, 264, 211, 263, 249, 231, 243, 254, 267, 232, 250, 242, 271, 257, 217, 266, 251, 213, 256, 243, 286, 256, 281, 249, 264, 262, 226, 248, 262, 243, 254, 281, 235, 223, 276, 230, 293, 261, 245, 222, 220, 255, 237, 233, 268, 244, 265, 269, 235, 251, 255, 253
#> 4 11, 18, 23, 23, 2, 13, 19, 48, 23, 21, 0, 28, 14, 17, 0, 42, 9, 18, 0, 28, 13, 0, 6, 27, 12, 16, 24, 21, 34, 29, 16, 28, 25, 18, 18, 20, 20, 21, 27, 30, 23, 17, 1, 30, 13, 9, 13, 16, 15, 23, 6, 40, 21, 24, 22, 10, 12, 37, 2, 18, 27, 15, 24, 26, 7, 10, 19, 19, 16, 26, 0, 7, 10, 12, 24, 9, 11, 13, 20, 24, 0, 33, 7, 2, 0, 32, 2, 8, 24, 14, 34, 14, 33, 4, 3, 22, 25, 9, 30, 40, 35, 20, 6, 11, 36, 18, 33, 22, 2, 14, 15, 24, 16, 24, 0, 16, 11, 7, 7, 27, 9, 11, 28, 20, 15, 22, 17, 8, 33, 18, 15, 3, 11, 9, 28, 13, 25, 29, 9, 20, 28, 18, 2, 7, 15, 19, 29, 22, 25, 8, 34, 15, 7, 23, 23, 23, 9, 20, 21, 23, 7, 14, 28, 14, 26, 16, 32, 19, 0, 18, 30, 1, 7, 26, 28, 2, 33, 24, 23, 0, 6, 34, 8, 29, 18, 26, 6, 21, 17, 12, 11, 39, 12, 9, 17, 10, 37, 28, 24, 28, 32, 9, 26, 13, 18, 15, 28, 18, 29, 15, 40, 22, 3, 12, 37, 32, 7, 0, 20, 10, 38, 0, 29, 25, 9, 29, 27, 25, 34, 31, 31, 26, 22, 1, 14, 15, 16, 13, 18, 21, 0, 13, 9, 23, 15, 27, 19, 28, 5, 14, 5, 37, 8, 36, 16, 0, 26, 31, 43, 33, 20, 0, 52, 30, 32, 25, 0, 13, 10, 23, 1, 40, 5, 20, 18, 12, 14, 18, 17, 18, 28, 16, 32, 24, 3, 15, 22, 23, 20, 16, 0, 23, 24, 2, 31, 56, 23, 24, 7, 18, 18, 0, 38, 0, 11, 21, 9, 25, 28, 42, 18, 3, 23, 25, 32, 4, 23, 22, 30, 20, 11, 21, 0, 9, 27, 16, 5, 39, 26, 21, 38, 16, 11, 48, 16, 16, 22, 45, 19, 11, 29, 0, 22, 23, 19, 31, 12, 18, 25, 19, 31, 24, 34, 21, 27, 19, 29, 35, 33, 19, 30, 12, 13, 11, 24, 33, 33, 29, 13, 29, 29
#> 5 69, 53, 100, 89, 225, 216, 206, 192, 182, 171, 172, 208, 116, 177, 165, 217, 168, 221, 192, 199, 213, 189, 262, 178, 175, 208, 191, 189, 163, 132, 212, 226, 201, 232, 161, 187, 174, 139, 195, 181, 157, 152, 240, 177, 156, 210, 187, 213, 144, 212, 198, 177, 191, 212, 187, 189, 199, 218, 144, 226, 140, 139, 206, 167, 214, 224, 194, 221, 196, 223, 209, 224, 192, 195, 228, 170, 228, 205, 178, 217, 172, 199, 191, 212, 227, 209, 195, 209, 201, 214, 171, 232, 177, 181, 193, 163, 203, 177, 209, 177, 237, 164, 198, 167, 255, 213, 171, 244, 197, 236, 171, 206, 220, 217, 181, 201, 176, 193, 228, 170, 148, 197, 217, 180, 188, 200, 167, 234, 181, 234, 230, 189, 255, 151, 193, 154, 209, 244, 209, 203, 194, 230, 159, 281, 170, 300, 206, 200, 158, 182
#> 6 121, 39, 63, 209, 224, 283, 221, 201, 165, 180, 192, 226, 232, 217, 183, 152, 229, 166, 233, 226, 216, 234, 215, 250, 202, 266, 223, 261, 175, 268, 183, 184, 244, 186, 242, 235, 199, 227, 159, 226, 265, 234, 217, 214, 276, 241, 203, 209, 197, 202, 257, 164, 267, 300, 136, 186, 168, 173, 250, 237, 201, 166, 269, 217, 228, 202, 198, 212, 228, 224, 166, 180, 187, 199, 220, 185, 229, 236, 206, 220, 168, 204, 222, 187, 209, 165, 204, 242, 190, 162, 250, 227, 190, 210, 248, 176, 209, 262, 193, 170, 243, 162, 75, 227, 219, 190, 207, 195, 193, 189, 220, 217, 222, 219, 219, 194, 226, 224, 190, 213, 193, 169, 195, 216, 189, 206, 226, 194, 176, 192, 199, 234, 252, 217, 173, 214, 255, 171, 263, 251, 203, 172, 208, 196, 161, 214, 226
#> 7 0, 3, 5, 7, 7, 16, 7, 29, 0, 7, 10, 5, 4, 2, 8, 12, 4, 16, 12, 17, 10, 16, 0, 7, 14, 8, 12, 11, 18, 10, 3, 2, 13, 15, 6, 21, 10, 23, 15, 13, 5, 14, 20, 10, 10, 10, 5, 0, 11, 2, 9, 0, 8, 11, 11, 25, 8, 3, 0, 0, 4, 0, 16, 16, 0, 21, 21, 12, 0, 16, 1, 11, 12, 17, 8, 16, 7, 13, 9, 12, 4, 19, 3, 16, 17, 7, 15, 8, 10, 13, 12, 12, 16, 12, 9, 6, 9, 17, 7, 19, 11, 17, 7, 11, 10, 18, 10, 9, 0, 19, 8, 6, 18, 0, 11, 9, 3, 8, 31, 0, 0, 17, 16, 0, 9, 4, 12, 20, 0, 1, 6, 9, 13, 12, 0, 11, 17, 2, 14, 0, 7, 16, 19, 6, 7, 4, 1, 16, 10, 2, 25, 0, 3, 1, 11, 14, 0, 13, 11, 9, 14, 9, 10, 5, 0, 18, 18, 8, 31, 7, 11, 10, 8, 13, 10, 1, 0, 0, 14, 17, 16, 8, 8, 10, 0, 4, 17, 5, 19, 9, 11, 5, 2, 11, 22, 16, 15, 11, 5, 10, 7, 0, 13, 4, 15, 0, 8, 24, 12, 7, 15, 0, 7, 13, 17, 0, 18, 20, 2, 13, 14, 14, 5, 8, 0, 4, 12, 13, 12, 0, 10, 4, 15, 17, 19, 14, 10, 2, 0, 9, 1, 10, 9, 15, 11, 24, 5, 0, 16, 10, 13, 3, 0, 9, 22, 12, 10, 2, 22, 6, 5, 9, 16, 13, 3, 6, 12, 20, 9, 16, 11, 0, 8, 30, 11, 30, 15, 6, 7, 13, 12, 19, 27, 7, 0, 11, 10, 11, 7, 5, 7, 28, 0, 9, 13, 18, 11, 16, 6, 28, 24, 14, 4, 16, 9, 9, 18, 11, 0, 11, 7, 13, 23, 13, 8, 4, 0, 0, 10, 4, 5, 13, 5, 6, 21, 0, 12, 9, 17, 12, 11, 13, 15, 7, 3, 14, 25, 2, 23, 9, 14, 18, 15, 17, 9, 6, 7, 0, 18, 17, 6, 9, 24, 10, 3, 14, 10, 6, 0, 10, 14, 8, 12, 16, 16, 0, 16, 6, 22, 5, 7, 7, 3, 18, 4, 18, 11, 7, 4, 12, 10, 15, 5, 11, 22, 1, 25, 3, 8, 17, 8, 23, 9, 11, 15, 9, 22, 14, 16, 11, 27, 19, 13, 4, 9, 13, 6, 8, 9, 21, 3, 16, 11, 23, 7, 12, 21, 7, 23, 6, 13, 14, 18, 11, 1, 9, 11, 7, 11, 7, 10, 20, 5, 8, 5, 7, 14, 14, 7, 11, 13, 7, 5, 2, 0, 15, 5, 9, 9, 9, 8, 11, 8, 5, 4, 23, 10, 0, 6, 1, 3, 8
#> 8 24, 27, 6, 32, 20, 17, 18, 11, 0, 21, 25, 19, 26, 10, 9, 22, 13, 10, 13, 0, 20, 0, 29, 29, 0, 16, 24, 26, 16, 18, 18, 18, 21, 16, 20, 25, 18, 23, 17, 21, 22, 14, 21, 16, 33, 25, 12, 12, 15, 29, 28, 23, 13, 24, 27, 16, 22, 23, 29, 28, 25, 23, 21, 8, 16, 30, 13, 11, 20, 22, 24, 9, 0, 18, 18, 28, 7, 5, 16, 16, 5, 12, 25, 27, 15, 17, 0, 16, 26, 36, 13, 26, 23, 22, 16, 25, 6, 25, 13, 8, 23, 23, 14, 26, 0, 2, 30, 25, 0, 15, 48, 6, 16, 41, 0, 11, 18, 29, 16, 20, 28, 20, 11, 31, 3, 18, 22, 7, 12, 21, 32, 10, 6, 22, 27, 16, 18, 21, 29, 13, 42, 3, 25, 9, 22, 15, 27, 28, 0, 12, 11, 21, 17, 20, 36, 13, 29, 23, 11, 21, 21, 15, 151, 28
#> 9 113, 80, 120, 22, 22, 31, 19, 20, 22, 19, 20, 14, 17, 27, 6, 33, 6, 30, 28, 34, 11, 25, 0, 14, 11, 27, 18, 29, 17, 8, 24, 26, 14, 33, 21, 18, 27, 17, 14, 14, 15, 9, 13, 17, 26, 28, 26, 24, 18, 12, 14, 23, 12, 17, 18, 14, 17, 18, 19, 25, 22, 21, 17, 23, 20, 17, 16, 36, 30, 27, 17, 38, 16, 15, 25, 27, 22, 7, 23, 24, 17, 10, 30, 11, 25, 8, 23, 16, 19, 29, 22, 19, 20, 18, 32, 12, 26, 21, 6, 16, 18, 15, 23, 20, 18, 28, 20, 25, 35, 30, 13, 23, 30, 15, 26, 12, 12, 14, 25, 20, 16, 25, 12, 1, 16, 11, 26, 36, 22, 26, 21, 19, 18, 19, 21, 21, 18, 23, 12, 18, 1, 6, 17, 29, 17, 27, 21, 10, 26, 16, 24, 15, 26, 18, 32, 15, 29, 13, 16, 23, 92, 28, 30, 35, 75
#> 10 104, 65, 47, 121, 8, 25, 11, 19, 12, 28, 11, 24, 21, 14, 15, 16, 6, 44, 31, 28, 10, 20, 13, 16, 7, 16, 15, 12, 14, 20, 8, 18, 22, 23, 25, 13, 24, 15, 16, 11, 19, 5, 25, 33, 12, 11, 82, 20, 15, 20, 20, 29, 9, 14, 26, 18, 13, 11, 25, 24, 13, 16, 25, 14, 24, 16, 26, 17, 30, 8, 18, 2, 4, 19, 23, 15, 8, 26, 18, 31, 24, 11, 18, 0, 22, 17, 19, 21, 17, 20, 16, 23, 29, 30, 17, 21, 15, 19, 17, 32, 19, 17, 13, 13, 16, 38, 12, 9, 15, 10, 17, 22, 32, 28, 26, 24, 27, 13, 22, 16, 8, 10, 19, 18, 17, 22, 20, 15, 29, 13, 21, 16, 16, 7, 26, 24, 27, 7, 11, 24, 16, 14, 23, 16, 21, 13, 15, 11, 25, 9, 29, 22, 13, 23, 12, 18, 22, 24, 22, 28, 6, 13, 3, 25, 46, 59, 116, 19
#> TARGET_SUBJECT_PREVALENCE CONTROL_SUBJECT_PREVALENCE
#> 1 0.966 0.012
#> 2 0.312 0.000
#> 3 0.294 0.000
#> 4 0.742 0.100
#> 5 0.300 0.004
#> 6 0.294 0.002
#> 7 0.924 0.020
#> 8 0.328 0.004
#> 9 0.330 0.002
#> 10 0.336 0.006
#> PREVALENCE_DIFFERENCE_RATIO CHI2Y CHI2Y_P_VALUE LOGITTEST LOGITTEST_P_VALUE
#> 1 80.50 TRUE 0.001 TRUE 0.002
#> 2 100.00 TRUE 0.001 TRUE 0.002
#> 3 100.00 TRUE 0.001 TRUE 0.002
#> 4 7.42 TRUE 0.001 TRUE 0.002
#> 5 75.00 TRUE 0.001 TRUE 0.002
#> 6 147.00 TRUE 0.001 TRUE 0.002
#> 7 46.20 TRUE 0.001 TRUE 0.002
#> 8 82.00 TRUE 0.001 TRUE 0.002
#> 9 165.00 TRUE 0.001 TRUE 0.002
#> 10 56.00 TRUE 0.001 TRUE 0.002
#> HERITAGE
#> 1 condition_occurrence
#> 2 death
#> 3 death
#> 4 measurement
#> 5 observation
#> 6 observation
#> 7 procedure_occurrence
#> 8 procedure_occurrence
#> 9 procedure_occurrence
#> 10 procedure_occurrence
data_patients
One row per patient-concept record.
Column descriptions:
-
COHORT_DEFINITION_ID: Cohort label for the patient (target/control). -
PERSON_ID: Patient identifier. -
CONCEPT_ID: Concept identifier. -
CONCEPT_NAME: Concept name. -
HERITAGE: Concept domain. -
ABSTRACTION_LEVEL: Abstraction level. -
PREVALENCE: Number of occurrences for this patient-concept. -
TIME_TO_EVENT: List of event times (days from cohort start) for this patient-concept.
#> COHORT_DEFINITION_ID PERSON_ID CONCEPT_ID
#> 1 target 100001 443388
#> 2 target 100001 9201
#> 3 target 100001 9202
#> 4 target 100001 4008211
#> 5 target 100001 4008226
#> 6 target 100001 4176729
#> 7 target 100001 4032404
#> 8 target 100001 4167262
#> 9 target 100002 443388
#> 10 target 100002 4182985
#> CONCEPT_NAME HERITAGE
#> 1 Malignant tumor of lung condition_occurrence
#> 2 Inpatient Visit visit_detail
#> 3 Outpatient Visit visit_detail
#> 4 Radiotherapy procedure_occurrence
#> 5 Chemotherapy procedure_occurrence
#> 6 Treatment planning for external beam radiation therapy procedure_occurrence
#> 7 Bronchoscopy procedure_occurrence
#> 8 Needle biopsy of lung procedure_occurrence
#> 9 Malignant tumor of lung condition_occurrence
#> 10 Diffusion capacity of lung measurement
#> ABSTRACTION_LEVEL PREVALENCE TIME_TO_EVENT
#> 1 -1 1 4
#> 2 -1 2 32, 52
#> 3 -1 3 34, 36, 64
#> 4 -1 3 22, 25, 42
#> 5 -1 4 24, 31, 33, 39
#> 6 -1 1 34
#> 7 -1 2 0, 15
#> 8 -1 2 2, 18
#> 9 -1 2 1, 6
#> 10 -1 2 11, 23
complementaryMappingTable
Mapping history table for concept merges.
Column descriptions:
-
CONCEPT_ID: Original concept id. -
CONCEPT_NAME: Original concept name. -
NEW_CONCEPT_ID: Mapped concept id. -
NEW_CONCEPT_NAME: Mapped concept name. -
TYPE: Mapping type (custom,hierarchy,correlation, etc.). -
HERITAGE: Mapping heritage/domain.
#> [1] CONCEPT_ID CONCEPT_NAME NEW_CONCEPT_ID NEW_CONCEPT_NAME
#> [5] TYPE HERITAGE
#> <0 rows> (or 0-length row.names)
selectedFeatureData
selectedFeatureData stores the selected concept subset
used by downstream analyses.
List elements:
-
selectedFeatureNames: Character vector of selected concept names. -
selectedFeatureIds: Numeric vector of selected concept ids. -
selectedFeatures: Dataframe with one row per selected concept.
selectedFeatureData$selectedFeatureNames preview
#> CONCEPT_NAME
#> 1 Malignant tumor of lung
#> 2 Death
#> 3 Death Certificate
#> 4 Diffusion capacity of lung
#> 5 Palliative care
#> 6 Bronchoscopy
#> 7 Chemotherapy
#> 8 Lobectomy
#> 9 Lobectomy of lung
#> 10 Needle biopsy of lung
selectedFeatureData$selectedFeatureIds preview
#> CONCEPT_ID
#> 1 443388
#> 2 32280
#> 3 32815
#> 4 4182985
#> 5 4306655
#> 6 4014023
#> 7 4032404
#> 8 4008226
#> 9 2107967
#> 10 2107968
selectedFeatureData$selectedFeatures
selectedFeatures has the same schema as
data_features, but only for selected concepts.
Column descriptions:
-
CONCEPT_ID: Concept identifier. -
CONCEPT_NAME: Concept name. -
ABSTRACTION_LEVEL: Abstraction level. -
TARGET_SUBJECT_COUNT: Number of target subjects with concept present. -
CONTROL_SUBJECT_COUNT: Number of control subjects with concept present. -
TIME_TO_EVENT: List of pooled concept time-to-event values. -
TARGET_SUBJECT_PREVALENCE: Target prevalence proportion. -
CONTROL_SUBJECT_PREVALENCE: Control prevalence proportion. -
PREVALENCE_DIFFERENCE_RATIO: Target/control prevalence ratio. -
CHI2Y: Chi-squared significance flag. -
CHI2Y_P_VALUE: Chi-squared p-value. -
LOGITTEST: Logistic regression significance flag. -
LOGITTEST_P_VALUE: Logistic regression p-value. -
HERITAGE: Concept heritage/domain.
#> CONCEPT_ID CONCEPT_NAME ABSTRACTION_LEVEL TARGET_SUBJECT_COUNT
#> 1 443388 Malignant tumor of lung -1 483
#> 2 32280 Death -1 156
#> 3 32815 Death Certificate -1 147
#> 4 4182985 Diffusion capacity of lung -1 371
#> 5 4306655 Death -1 150
#> 6 4014023 Palliative care -1 147
#> 7 4032404 Bronchoscopy -1 462
#> 8 4008226 Chemotherapy -1 164
#> 9 2107967 Lobectomy -1 165
#> 10 2107968 Lobectomy of lung -1 168
#> CONTROL_SUBJECT_COUNT
#> 1 6
#> 2 0
#> 3 0
#> 4 50
#> 5 2
#> 6 1
#> 7 10
#> 8 2
#> 9 1
#> 10 3
#> TIME_TO_EVENT
#> 1 4, 1, 4, 2, 6, 0, 6, 5, 5, 3, 5, 5, 8, 7, 6, 8, 4, 0, 10, 2, 7, 0, 7, 5, 2, 1, 9, 3, 4, 3, 3, 14, 2, 6, 2, 3, 6, 0, 8, 10, 5, 14, 0, 6, 5, 11, 6, 7, 6, 8, 4, 7, 0, 5, 7, 9, 8, 9, 0, 6, 8, 6, 4, 3, 16, 11, 4, 4, 5, 11, 3, 6, 6, 5, 8, 0, 2, 1, 4, 4, 5, 3, 5, 9, 10, 4, 6, 6, 10, 3, 4, 0, 5, 4, 0, 8, 5, 9, 5, 14, 0, 0, 4, 10, 5, 4, 13, 3, 1, 5, 2, 3, 0, 4, 11, 7, 0, 0, 13, 6, 4, 8, 6, 8, 9, 5, 0, 2, 4, 3, 13, 1, 5, 7, 3, 9, 5, 0, 3, 10, 3, 7, 8, 8, 6, 1, 3, 10, 8, 8, 4, 0, 15, 9, 0, 5, 4, 11, 7, 8, 6, 4, 1, 12, 0, 1, 3, 1, 12, 0, 6, 5, 11, 2, 0, 6, 2, 0, 6, 5, 6, 2, 11, 9, 1, 8, 3, 3, 5, 12, 3, 1, 6, 10, 8, 10, 4, 8, 3, 9, 11, 5, 3, 7, 7, 8, 2, 5, 10, 7, 4, 1, 5, 9, 6, 4, 2, 2, 13, 9, 16, 1, 2, 7, 3, 4, 3, 10, 2, 6, 7, 7, 6, 6, 3, 6, 4, 0, 6, 5, 10, 2, 9, 7, 3, 0, 6, 4, 10, 2, 5, 8, 1, 0, 2, 6, 5, 6, 3, 9, 5, 10, 11, 6, 6, 8, 0, 1, 8, 0, 0, 1, 1, 0, 2, 3, 5, 1, 4, 5, 6, 6, 9, 5, 1, 0, 0, 5, 11, 0, 7, 4, 2, 0, 5, 5, 11, 0, 3, 3, 2, 5, 7, 5, 7, 1, 6, 5, 3, 4, 6, 1, 10, 1, 4, 7, 3, 16, 4, 5, 0, 5, 5, 6, 3, 2, 8, 7, 3, 3, 0, 7, 10, 8, 3, 0, 7, 5, 8, 3, 3, 6, 5, 4, 6, 12, 6, 5, 3, 11, 7, 9, 14, 4, 0, 10, 1, 6, 11, 10, 2, 6, 2, 0, 7, 2, 0, 2, 1, 1, 5, 2, 3, 2, 7, 4, 6, 0, 7, 4, 10, 8, 5, 6, 1, 0, 18, 2, 2, 0, 2, 1, 10, 2, 9, 2, 4, 5, 5, 0, 0, 4, 4, 2, 13, 4, 13, 5, 6, 8, 3, 4, 7, 7, 1, 11, 13, 10, 3, 6, 1, 8, 2, 7, 8, 1, 3, 5, 4, 10, 2, 6, 0, 4, 2, 8, 1, 7, 0, 3, 6, 0, 10, 1, 8, 3, 7, 4, 1, 4, 4, 9, 1, 5, 3, 7, 9, 7, 6, 2, 7, 11, 3, 0, 7, 10, 1, 4, 13, 0, 9, 4, 2, 5, 4, 7, 13, 0, 0, 11, 2, 0, 2
#> 2 11, 244, 150, 165, 204, 148, 224, 191, 199, 214, 170, 212, 213, 200, 206, 190, 259, 192, 193, 232, 187, 191, 219, 180, 193, 157, 178, 158, 175, 175, 214, 183, 189, 201, 202, 194, 185, 166, 180, 212, 171, 171, 198, 193, 214, 224, 170, 168, 145, 187, 171, 213, 224, 203, 171, 209, 212, 195, 205, 270, 216, 213, 215, 183, 167, 178, 192, 152, 219, 177, 175, 190, 192, 193, 193, 173, 185, 250, 177, 160, 183, 173, 204, 174, 194, 189, 192, 186, 264, 181, 123, 176, 193, 260, 208, 226, 224, 211, 202, 243, 214, 187, 201, 217, 206, 164, 272, 189, 224, 167, 208, 216, 156, 151, 156, 199, 205, 175, 192, 170, 169, 224, 126, 176, 190, 187, 196, 173, 175, 209, 174, 150, 198, 232, 196, 178, 172, 219, 199, 243, 235, 190, 187, 217, 230, 173, 185, 212, 216, 203, 223, 211, 192, 168, 206, 200
#> 3 19, 90, 27, 220, 225, 267, 272, 244, 262, 299, 258, 245, 250, 247, 235, 237, 257, 207, 235, 224, 253, 254, 225, 248, 251, 235, 261, 253, 245, 230, 276, 230, 240, 237, 255, 256, 245, 260, 200, 224, 241, 240, 280, 113, 240, 192, 220, 227, 279, 255, 253, 242, 258, 234, 249, 198, 235, 263, 234, 259, 247, 260, 265, 226, 258, 214, 247, 273, 276, 248, 229, 227, 258, 235, 262, 253, 249, 279, 220, 248, 213, 292, 267, 247, 229, 249, 257, 255, 230, 231, 262, 226, 233, 268, 252, 244, 264, 211, 263, 249, 231, 243, 254, 267, 232, 250, 242, 271, 257, 217, 266, 251, 213, 256, 243, 286, 256, 281, 249, 264, 262, 226, 248, 262, 243, 254, 281, 235, 223, 276, 230, 293, 261, 245, 222, 220, 255, 237, 233, 268, 244, 265, 269, 235, 251, 255, 253
#> 4 11, 18, 23, 23, 2, 13, 19, 48, 23, 21, 0, 28, 14, 17, 0, 42, 9, 18, 0, 28, 13, 0, 6, 27, 12, 16, 24, 21, 34, 29, 16, 28, 25, 18, 18, 20, 20, 21, 27, 30, 23, 17, 1, 30, 13, 9, 13, 16, 15, 23, 6, 40, 21, 24, 22, 10, 12, 37, 2, 18, 27, 15, 24, 26, 7, 10, 19, 19, 16, 26, 0, 7, 10, 12, 24, 9, 11, 13, 20, 24, 0, 33, 7, 2, 0, 32, 2, 8, 24, 14, 34, 14, 33, 4, 3, 22, 25, 9, 30, 40, 35, 20, 6, 11, 36, 18, 33, 22, 2, 14, 15, 24, 16, 24, 0, 16, 11, 7, 7, 27, 9, 11, 28, 20, 15, 22, 17, 8, 33, 18, 15, 3, 11, 9, 28, 13, 25, 29, 9, 20, 28, 18, 2, 7, 15, 19, 29, 22, 25, 8, 34, 15, 7, 23, 23, 23, 9, 20, 21, 23, 7, 14, 28, 14, 26, 16, 32, 19, 0, 18, 30, 1, 7, 26, 28, 2, 33, 24, 23, 0, 6, 34, 8, 29, 18, 26, 6, 21, 17, 12, 11, 39, 12, 9, 17, 10, 37, 28, 24, 28, 32, 9, 26, 13, 18, 15, 28, 18, 29, 15, 40, 22, 3, 12, 37, 32, 7, 0, 20, 10, 38, 0, 29, 25, 9, 29, 27, 25, 34, 31, 31, 26, 22, 1, 14, 15, 16, 13, 18, 21, 0, 13, 9, 23, 15, 27, 19, 28, 5, 14, 5, 37, 8, 36, 16, 0, 26, 31, 43, 33, 20, 0, 52, 30, 32, 25, 0, 13, 10, 23, 1, 40, 5, 20, 18, 12, 14, 18, 17, 18, 28, 16, 32, 24, 3, 15, 22, 23, 20, 16, 0, 23, 24, 2, 31, 56, 23, 24, 7, 18, 18, 0, 38, 0, 11, 21, 9, 25, 28, 42, 18, 3, 23, 25, 32, 4, 23, 22, 30, 20, 11, 21, 0, 9, 27, 16, 5, 39, 26, 21, 38, 16, 11, 48, 16, 16, 22, 45, 19, 11, 29, 0, 22, 23, 19, 31, 12, 18, 25, 19, 31, 24, 34, 21, 27, 19, 29, 35, 33, 19, 30, 12, 13, 11, 24, 33, 33, 29, 13, 29, 29
#> 5 69, 53, 100, 89, 225, 216, 206, 192, 182, 171, 172, 208, 116, 177, 165, 217, 168, 221, 192, 199, 213, 189, 262, 178, 175, 208, 191, 189, 163, 132, 212, 226, 201, 232, 161, 187, 174, 139, 195, 181, 157, 152, 240, 177, 156, 210, 187, 213, 144, 212, 198, 177, 191, 212, 187, 189, 199, 218, 144, 226, 140, 139, 206, 167, 214, 224, 194, 221, 196, 223, 209, 224, 192, 195, 228, 170, 228, 205, 178, 217, 172, 199, 191, 212, 227, 209, 195, 209, 201, 214, 171, 232, 177, 181, 193, 163, 203, 177, 209, 177, 237, 164, 198, 167, 255, 213, 171, 244, 197, 236, 171, 206, 220, 217, 181, 201, 176, 193, 228, 170, 148, 197, 217, 180, 188, 200, 167, 234, 181, 234, 230, 189, 255, 151, 193, 154, 209, 244, 209, 203, 194, 230, 159, 281, 170, 300, 206, 200, 158, 182
#> 6 121, 39, 63, 209, 224, 283, 221, 201, 165, 180, 192, 226, 232, 217, 183, 152, 229, 166, 233, 226, 216, 234, 215, 250, 202, 266, 223, 261, 175, 268, 183, 184, 244, 186, 242, 235, 199, 227, 159, 226, 265, 234, 217, 214, 276, 241, 203, 209, 197, 202, 257, 164, 267, 300, 136, 186, 168, 173, 250, 237, 201, 166, 269, 217, 228, 202, 198, 212, 228, 224, 166, 180, 187, 199, 220, 185, 229, 236, 206, 220, 168, 204, 222, 187, 209, 165, 204, 242, 190, 162, 250, 227, 190, 210, 248, 176, 209, 262, 193, 170, 243, 162, 75, 227, 219, 190, 207, 195, 193, 189, 220, 217, 222, 219, 219, 194, 226, 224, 190, 213, 193, 169, 195, 216, 189, 206, 226, 194, 176, 192, 199, 234, 252, 217, 173, 214, 255, 171, 263, 251, 203, 172, 208, 196, 161, 214, 226
#> 7 0, 3, 5, 7, 7, 16, 7, 29, 0, 7, 10, 5, 4, 2, 8, 12, 4, 16, 12, 17, 10, 16, 0, 7, 14, 8, 12, 11, 18, 10, 3, 2, 13, 15, 6, 21, 10, 23, 15, 13, 5, 14, 20, 10, 10, 10, 5, 0, 11, 2, 9, 0, 8, 11, 11, 25, 8, 3, 0, 0, 4, 0, 16, 16, 0, 21, 21, 12, 0, 16, 1, 11, 12, 17, 8, 16, 7, 13, 9, 12, 4, 19, 3, 16, 17, 7, 15, 8, 10, 13, 12, 12, 16, 12, 9, 6, 9, 17, 7, 19, 11, 17, 7, 11, 10, 18, 10, 9, 0, 19, 8, 6, 18, 0, 11, 9, 3, 8, 31, 0, 0, 17, 16, 0, 9, 4, 12, 20, 0, 1, 6, 9, 13, 12, 0, 11, 17, 2, 14, 0, 7, 16, 19, 6, 7, 4, 1, 16, 10, 2, 25, 0, 3, 1, 11, 14, 0, 13, 11, 9, 14, 9, 10, 5, 0, 18, 18, 8, 31, 7, 11, 10, 8, 13, 10, 1, 0, 0, 14, 17, 16, 8, 8, 10, 0, 4, 17, 5, 19, 9, 11, 5, 2, 11, 22, 16, 15, 11, 5, 10, 7, 0, 13, 4, 15, 0, 8, 24, 12, 7, 15, 0, 7, 13, 17, 0, 18, 20, 2, 13, 14, 14, 5, 8, 0, 4, 12, 13, 12, 0, 10, 4, 15, 17, 19, 14, 10, 2, 0, 9, 1, 10, 9, 15, 11, 24, 5, 0, 16, 10, 13, 3, 0, 9, 22, 12, 10, 2, 22, 6, 5, 9, 16, 13, 3, 6, 12, 20, 9, 16, 11, 0, 8, 30, 11, 30, 15, 6, 7, 13, 12, 19, 27, 7, 0, 11, 10, 11, 7, 5, 7, 28, 0, 9, 13, 18, 11, 16, 6, 28, 24, 14, 4, 16, 9, 9, 18, 11, 0, 11, 7, 13, 23, 13, 8, 4, 0, 0, 10, 4, 5, 13, 5, 6, 21, 0, 12, 9, 17, 12, 11, 13, 15, 7, 3, 14, 25, 2, 23, 9, 14, 18, 15, 17, 9, 6, 7, 0, 18, 17, 6, 9, 24, 10, 3, 14, 10, 6, 0, 10, 14, 8, 12, 16, 16, 0, 16, 6, 22, 5, 7, 7, 3, 18, 4, 18, 11, 7, 4, 12, 10, 15, 5, 11, 22, 1, 25, 3, 8, 17, 8, 23, 9, 11, 15, 9, 22, 14, 16, 11, 27, 19, 13, 4, 9, 13, 6, 8, 9, 21, 3, 16, 11, 23, 7, 12, 21, 7, 23, 6, 13, 14, 18, 11, 1, 9, 11, 7, 11, 7, 10, 20, 5, 8, 5, 7, 14, 14, 7, 11, 13, 7, 5, 2, 0, 15, 5, 9, 9, 9, 8, 11, 8, 5, 4, 23, 10, 0, 6, 1, 3, 8
#> 8 24, 27, 6, 32, 20, 17, 18, 11, 0, 21, 25, 19, 26, 10, 9, 22, 13, 10, 13, 0, 20, 0, 29, 29, 0, 16, 24, 26, 16, 18, 18, 18, 21, 16, 20, 25, 18, 23, 17, 21, 22, 14, 21, 16, 33, 25, 12, 12, 15, 29, 28, 23, 13, 24, 27, 16, 22, 23, 29, 28, 25, 23, 21, 8, 16, 30, 13, 11, 20, 22, 24, 9, 0, 18, 18, 28, 7, 5, 16, 16, 5, 12, 25, 27, 15, 17, 0, 16, 26, 36, 13, 26, 23, 22, 16, 25, 6, 25, 13, 8, 23, 23, 14, 26, 0, 2, 30, 25, 0, 15, 48, 6, 16, 41, 0, 11, 18, 29, 16, 20, 28, 20, 11, 31, 3, 18, 22, 7, 12, 21, 32, 10, 6, 22, 27, 16, 18, 21, 29, 13, 42, 3, 25, 9, 22, 15, 27, 28, 0, 12, 11, 21, 17, 20, 36, 13, 29, 23, 11, 21, 21, 15, 151, 28
#> 9 113, 80, 120, 22, 22, 31, 19, 20, 22, 19, 20, 14, 17, 27, 6, 33, 6, 30, 28, 34, 11, 25, 0, 14, 11, 27, 18, 29, 17, 8, 24, 26, 14, 33, 21, 18, 27, 17, 14, 14, 15, 9, 13, 17, 26, 28, 26, 24, 18, 12, 14, 23, 12, 17, 18, 14, 17, 18, 19, 25, 22, 21, 17, 23, 20, 17, 16, 36, 30, 27, 17, 38, 16, 15, 25, 27, 22, 7, 23, 24, 17, 10, 30, 11, 25, 8, 23, 16, 19, 29, 22, 19, 20, 18, 32, 12, 26, 21, 6, 16, 18, 15, 23, 20, 18, 28, 20, 25, 35, 30, 13, 23, 30, 15, 26, 12, 12, 14, 25, 20, 16, 25, 12, 1, 16, 11, 26, 36, 22, 26, 21, 19, 18, 19, 21, 21, 18, 23, 12, 18, 1, 6, 17, 29, 17, 27, 21, 10, 26, 16, 24, 15, 26, 18, 32, 15, 29, 13, 16, 23, 92, 28, 30, 35, 75
#> 10 104, 65, 47, 121, 8, 25, 11, 19, 12, 28, 11, 24, 21, 14, 15, 16, 6, 44, 31, 28, 10, 20, 13, 16, 7, 16, 15, 12, 14, 20, 8, 18, 22, 23, 25, 13, 24, 15, 16, 11, 19, 5, 25, 33, 12, 11, 82, 20, 15, 20, 20, 29, 9, 14, 26, 18, 13, 11, 25, 24, 13, 16, 25, 14, 24, 16, 26, 17, 30, 8, 18, 2, 4, 19, 23, 15, 8, 26, 18, 31, 24, 11, 18, 0, 22, 17, 19, 21, 17, 20, 16, 23, 29, 30, 17, 21, 15, 19, 17, 32, 19, 17, 13, 13, 16, 38, 12, 9, 15, 10, 17, 22, 32, 28, 26, 24, 27, 13, 22, 16, 8, 10, 19, 18, 17, 22, 20, 15, 29, 13, 21, 16, 16, 7, 26, 24, 27, 7, 11, 24, 16, 14, 23, 16, 21, 13, 15, 11, 25, 9, 29, 22, 13, 23, 12, 18, 22, 24, 22, 28, 6, 13, 3, 25, 46, 59, 116, 19
#> TARGET_SUBJECT_PREVALENCE CONTROL_SUBJECT_PREVALENCE
#> 1 0.966 0.012
#> 2 0.312 0.000
#> 3 0.294 0.000
#> 4 0.742 0.100
#> 5 0.300 0.004
#> 6 0.294 0.002
#> 7 0.924 0.020
#> 8 0.328 0.004
#> 9 0.330 0.002
#> 10 0.336 0.006
#> PREVALENCE_DIFFERENCE_RATIO CHI2Y CHI2Y_P_VALUE LOGITTEST LOGITTEST_P_VALUE
#> 1 80.50 TRUE 0.001 TRUE 0.002
#> 2 100.00 TRUE 0.001 TRUE 0.002
#> 3 100.00 TRUE 0.001 TRUE 0.002
#> 4 7.42 TRUE 0.001 TRUE 0.002
#> 5 75.00 TRUE 0.001 TRUE 0.002
#> 6 147.00 TRUE 0.001 TRUE 0.002
#> 7 46.20 TRUE 0.001 TRUE 0.002
#> 8 82.00 TRUE 0.001 TRUE 0.002
#> 9 165.00 TRUE 0.001 TRUE 0.002
#> 10 56.00 TRUE 0.001 TRUE 0.002
#> HERITAGE
#> 1 condition_occurrence
#> 2 death
#> 3 death
#> 4 measurement
#> 5 observation
#> 6 observation
#> 7 procedure_occurrence
#> 8 procedure_occurrence
#> 9 procedure_occurrence
#> 10 procedure_occurrence
conceptsData
conceptsData stores optional OMOP vocabulary context
tables.
conceptsData$concept_ancestor
Column descriptions:
-
ancestor_concept_id: Ancestor concept id in hierarchy. -
descendant_concept_id: Descendant concept id in hierarchy. -
min_levels_of_separation: Minimum hierarchy distance. -
max_levels_of_separation: Maximum hierarchy distance.
#> ancestor_concept_id descendant_concept_id min_levels_of_separation
#> 1 4008211 4176729 1
#> 2 2107967 2107968 1
#> 3 2107967 2108158 1
#> 4 32280 32815 1
#> max_levels_of_separation
#> 1 1
#> 2 1
#> 3 1
#> 4 1
conceptsData$concept
Typical OMOP concept columns:
-
concept_id: Concept identifier. -
concept_name: Human-readable concept name. -
domain_id: Domain label. -
vocabulary_id: Vocabulary source. -
concept_class_id: Concept class. -
standard_concept: Standard concept flag. -
concept_code: Source code inside vocabulary. -
valid_start_date: Validity start date. -
valid_end_date: Validity end date. -
invalid_reason: Invalidation code (if concept is retired).
#> No `concept` table available in this study.