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Interpreting Results with lc500

Goal

This vignette explains what each patient-mode output dataframe stores in the bundled lc500 study.

For each dataframe:

Object Overview

CohortContrast::loadCohortContrastStudy() returns a CohortContrastObject with these key components:

#> [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 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 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_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 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:

#> [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:

selectedFeatureData$selectedFeatureNames preview

#>                  CONCEPT_NAME
#> 1                Bronchoscopy
#> 2                Chemotherapy
#> 3                       Death
#> 4           Death Certificate
#> 5  Diffusion capacity of lung
#> 6             Inpatient Visit
#> 7                   Lobectomy
#> 8           Lobectomy of lung
#> 9     Malignant tumor 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_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 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_name invalid_reason
#> 1        9201         Inpatient Visit           <NA>
#> 2        9202        Outpatient Visit           <NA>
#> 3       32280                   Death           <NA>
#> 4       32815       Death Certificate           <NA>
#> 5      443388 Malignant tumor of lung           <NA>
#> 6     2107967               Lobectomy           <NA>
#> 7     2107968       Lobectomy of lung           <NA>
#> 8     2108158   Partial pneumonectomy           <NA>
#> 9     4008211            Radiotherapy           <NA>
#> 10    4008226            Chemotherapy           <NA>

config

config stores study-level metadata loaded with the saved study.

Top-level fields:

#>          field value
#> 1    complName lc500
#> 2 has_metadata  TRUE

config$metadata scalar fields preview

#>              field value
#> 1            study lc500
#> 2  target_patients   500
#> 3 control_patients   500
#> 4      chi2y_count    16

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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