EAVE Helpers
Install
To install the helper package, install remotes and then install directly from GitHub like so:
Data Dictionary
Look up labels and descriptions of variables in the EAVE-II datasets:
'Study marked as at risk of COVID-19 due to Chronic obstructive pulmonary disease (COPD) indicator'
Get the full data dictionary if you want to explore more / lookup more data
A data.frame: 233 × 7
| name <chr> | label <chr> | description <chr> | type <chr> | min <chr> | max <chr> | values <list> | |---|---|---|---|---|---|---| | EAVE_LINKNO | EAVE Study Identifier | EAVE-II Identifier, pseudoynmised CHI numbers are used to create randomly assigned study index numbers. | chr | <!----> | <!----> | NULL | | SampleID | Sample ID | Original Sample ID from the serology team | chr | <!----> | <!----> | NULL | | age | Age | Age of the study given in years, extracted from the serology files - and shouldn't be well trusted | dbl | 17 | 84 | 57, 55, 56, 54, 52 | | sex | Sex (number) | Sex at birth - extracted from the serology files/team - it should not be trusted as being reliable | chr | <!----> | <!----> | F, M | | isoweek | Week Number | Week number since the start of the pandemic | dbl | 1 | 53 | 28, 36, 32, 41, 51 | | year | Year | Year of the lookup file used to determine the Health Boards | dbl | 2020 | 2022 | 2021, 2020, 2022 | | Sampledate_iso | Sample Date | The date the serology measurement was taken from the individual (in ISO format) | dttm | <!----> | <!----> | 2021-12-20, 2020-07-02, 2021-12-30, 2020-07-06, 2022-01-14 | | hb | Health Board | The Scottish Health Board in which the individual was registered with | chr | <!----> | <!----> | NHS Lothian , NHS Greater Glasgow and Clyde, NHS Tayside , NHS Grampian , NHS Lanarkshire | | assay | Assay | Antibody Assay machine was was used when measuring the blood serum sample for the presence of IgG antibodies to SARs-CoV-2 | chr | <!----> | <!----> | Euroimmune, Abbott | | test_result_qual | Qualitative Test Result | Qualitative test results from the assay for the presence (or lack thereof) of IgG to SARs-CoV-2. The assay defines the threshold that determines +ve or -ve tests. | chr | <!----> | <!----> | Positive , Negative , Equivocal | | test_result_quant | Quantative Test Result | IgG measurements in Binding Activation Units [BAUs] that are measured by the assay. There are values that are truncated above/below certain values as the result was out-of-bounds of the assay's sensitivity for these. | chr | <!----> | <!----> | 0.1 , 0.02, 0.2 , 0.01, 0.03 | | EAVE_LINKNO | EAVE Study Identifier | EAVE-II Identifier, pseudoynmised CHI numbers that were used to link this dataset | chr | <!----> | <!----> | NULL | | CIS_MARKER | <!----> | <!----> | dbl | 1 | 1906 | 2, 3, 4, 1, 6 | | ADMISSION_DATE | Admission Date | Date the study was admitted into hospital | dttm | <!----> | <!----> | 2019-06-11, 2019-08-12, 2018-03-07, 2018-06-05, 2019-03-04 | | DISCHARGE_DATE | Discharge Date | Date the study was discharged from hospital | dttm | <!----> | <!----> | 2019-06-18, 2019-03-04, 2019-08-12, 2019-08-30, 2020-01-17 | | MAIN_CONDITION | Main Condition | The reason the study was admitted into hospital (ICD10 code) | chr | <!----> | <!----> | H269, N390, U071, A419, J22X | | OTHER_CONDITION_1 | <!----> | Other reasons identified for hospital admission (ICD10 codes) | chr | <!----> | <!----> | NA , Z511, N390, I10X, N179 | | OTHER_CONDITION_2 | <!----> | Other reasons identified for hospital admission | chr | <!----> | <!----> | NA , I10X, E119, I489, Z511 | | OTHER_CONDITION_3 | <!----> | Other reasons identified for hospital admission | chr | <!----> | <!----> | NA , I10X, E119, I489, N179 | | OTHER_CONDITION_4 | <!----> | Other reasons identified for hospital admission | chr | <!----> | <!----> | NA , I10X, E119, I489, Z867 | | OTHER_CONDITION_5 | <!----> | Other reasons identified for hospital admission | chr | <!----> | <!----> | NA , I10X, E119, Z038, Z867 | | EAVE_LINKNO | EAVE Study Identifier | EAVE-II Identifier, pseudoynmised CHI numbers are used to create randomly assigned study index numbers. | chr | <!----> | <!----> | NULL | | Sex | Sex | Sex at birth | chr | <!----> | <!----> | M, F | | ageYear | Age | Age in years | dbl | -1 | 111 | 51, 26, 50, 55, 27 | | hb2019 | NHS Health Board Code | Codes of 2019 NHS Health Boards | chr | <!----> | <!----> | S08000031, S08000024, S08000032, S08000020, S08000030 | | hb2019name | NHS Health Board Name | Names of 2019 NHS Health Boards | chr | <!----> | <!----> | NHS Greater Glasgow and Clyde, NHS Lothian , NHS Lanarkshire , NHS Grampian , NHS Tayside | | District | Postcode District | Outward code of their postcode (Area + Disrict) | chr | <!----> | <!----> | EH54, EH4 , KY11, EH6 , ML3 | | DataZone | Data Zone | Data Zone | chr | <!----> | <!----> | NA , S01010286, S01008425, S01010048 | | ur6_2016 | Urban/Rural classification | Urban/Rural 6-fold classification (2016 classification) | int | NA | NA | 1, 2, 3, 5, 6 | | ur6_2016_name | Urban/Rural classification name | Urban/Rural 6-fold classification (2016 classification) | chr | <!----> | <!----> | 1 Large Urban Areas , 2 Other Urban Areas , 3 Accessible Small Towns, 5 Accessible Rural , 6 Remote Rural | | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | | SpecimenTypeRaw | Specimen Type Raw | Raw code for the specimen type (always STS as this is blood serum data) | chr | <!----> | <!----> | STS | | SpecimenType | Specimen Type | Always 'Serum' as this is serology dataset | chr | <!----> | <!----> | Serum | | SpecLevel2Group | <!----> | <!----> | chr | <!----> | <!----> | Blood other | | SpecLevel1Group | <!----> | <!----> | chr | <!----> | <!----> | Normally Sterile Site | | OrganismRaw | Organism Raw | Raw data of the test result from the assay | chr | <!----> | <!----> | (stest) covid-19 (sars-cov-2) igg,negative , (stest) covid-19 (sars-cov-2) igg,>positive, (stest) covid-19 (sars-cov-2) igg,equivocal | | Type | Type | Type of measurement (almost always IgG 2019-nCoV) | chr | <!----> | <!----> | 2019-nCoV IgG | | OriginalOrganism | Original organism | Original organism - Coronavirus 2019 positive or negative | chr | <!----> | <!----> | Coronavirus 2019-nCoV IgG negative , Coronavirus 2019-nCoV IgG , Coronavirus 2019-nCoV IgG equivocal | | test_result_qual | Qualitative Test Result | Qualitative test results from the assay for the presence (or lack thereof) of IgG to SARs-CoV-2. The assay defines the threshold that determines +ve or -ve tests. | chr | <!----> | <!----> | Negative , Positive , Equivocal | | test_result_quant | Quantative Test Result | IgG measurements in Binding Activation Units [BAUs] that are measured by the assay. There are values that are truncated above/below certain values as the result was out-of-bounds of the assay's sensitivity for these. | chr | <!----> | <!----> | <3.8 , >2080.00, <4.81 , <3.80 , >400.0 | | QNum | Quantative Measumrent Value (Number) | The raw quantative number value, removing truncated values (note: not so safe to use this as values below AND above the assay threshold have been set as NA | dbl | NA | NA | NA , 4.9, 3.9, 4.3, 4.4 | | Text | Text | Raw text output from the final report | chr | <!----> | <!----> | covid-19 - antibodies covid-19 (sars-cov-2) igg: positive specimen type: serum -------------------------------------------------------------------- dr sally mavin, clinical scientist final report , NA , covid-19 - antibodies covid-19 (sars-cov-2) igg: negative specimen type: serum -------------------------------------------------------------------- released from instrument: liaisonxl 12/06/20 at 1:37 pm final report, covid-19 - antibodies covid-19 (sars-cov-2) igg: negative specimen type: serum -------------------------------------------------------------------- released from instrument: liaisonxl 05/03/21 at 9:19 am final report, covid-19 - antibodies covid-19 (sars-cov-2) igg: negative specimen type: serum -------------------------------------------------------------------- released from instrument: liaisonxl 14/09/20 at 11:13 am final report | | EAVE_LINKNO | EAVE Study Identifier | EAVE-II Identifier, pseudoynmised CHI numbers are used to create randomly assigned study index numbers. | chr | <!----> | <!----> | NULL | | NRS.Date.Death | Date of NRS death record | Date of death | date | <!----> | <!----> | 2020-04-13, 2020-12-26, 2022-03-20, 2020-04-04, 2020-04-18 | | NRS.Reg.Date | Date of death registered | Date of death registered | date | <!----> | <!----> | 2020-03-27, 2022-01-05, 2020-03-31, 2020-12-30, 2021-01-06 | | NRS.Reg.Dist | <!----> | <!----> | dbl | 118 | 875 | 564, 722, 518, 350, 592 | | NRS.Entry | <!----> | <!----> | dbl | 1 | 999 | 11, 8 , 35, 4 , 51 | | NRS.Reg.Year | <!----> | <!----> | dbl | 2020 | 2022 | 2020, 2021, 2022 | | NRS.age_at_death | <!----> | <!----> | dbl | 0 | 106 | 84, 85, 83, 87, 90 | | UNDERLYING_CAUSE_OF_DEATH | <!----> | <!----> | chr | <!----> | <!----> | U071, I219, C349, F03 , G301 | | CAUSE_OF_DEATH_CODE_0 | <!----> | <!----> | chr | <!----> | <!----> | R688, C349, J189, F019, I259 | | CAUSE_OF_DEATH_CODE_1 | <!----> | <!----> | chr | <!----> | <!----> | NA , I259, U071, R688, I489 | | CAUSE_OF_DEATH_CODE_2 | <!----> | <!----> | chr | <!----> | <!----> | NA , E119, I259, J449, I10 | | CAUSE_OF_DEATH_CODE_3 | <!----> | <!----> | chr | <!----> | <!----> | NA , J449, E119, I10 , I259 | | CAUSE_OF_DEATH_CODE_4 | <!----> | <!----> | chr | <!----> | <!----> | NA , J449, E119, N189, I10 | | CAUSE_OF_DEATH_CODE_5 | <!----> | <!----> | chr | <!----> | <!----> | NA , I10 , J449, W19 , E119 | | CAUSE_OF_DEATH_CODE_6 | <!----> | <!----> | chr | <!----> | <!----> | NA , I10 , T424, N189, T403 | | CAUSE_OF_DEATH_CODE_7 | <!----> | <!----> | chr | <!----> | <!----> | NA , T424 | | CAUSE_OF_DEATH_CODE_8 | <!----> | <!----> | chr | <!----> | <!----> | NULL | | CAUSE_OF_DEATH_CODE_9 | <!----> | <!----> | chr | <!----> | <!----> | NULL | | source | <!----> | <!----> | chr | <!----> | <!----> | SMRA , daily |
Created: August 25, 2022