Quality and Outcomes Framework

Primary Care Domain reference sets (refsets)

Exploratory

Explore the QOF Primary Care Domain reference sets (refsets)

Author

Alasdair Warwick

Published

September 30, 2024

Code

library(targets)
library(dplyr)
library(purrr)
library(reactable)
library(flextable)
library(stringr)
library(UpSetR)

withr::with_dir(here::here(), {
  tar_load(pcd_refset)
})

reactable2 <- function(df) {
  reactable::reactable(df,
                       searchable = TRUE,
                       filterable = TRUE,
                       showPagination = TRUE,
                       paginationType = "jump",
                       pageSizeOptions = c(10, 25, 50, 100, 200),
                       showPageSizeOptions = TRUE,
                       resizable = TRUE)
}

Overview

Key resources:

Primary Care Domain Reference Set: contains text files that include code lists for various QOF (and other) outcomes
QOF business rules: details implementation of QOF codes

Terminology:

Code lists are grouped under “Cluster IDs” (e.g. AST_CODE for “Asthma diagnosis codes”)
Various Cluster IDs may contribute to one or more “Output IDs” (e.g. AST_COD & ASTTRT_COD & ASTRES_COD for Output ID AST_REG, “Asthma register”)
Output IDs fall under “Ruleset mappings”, which fall under “Service mappings”

graph TD
    A{{Service Mappings}}
    B{{Ruleset Mappings}}
    C{{Output IDs}}
    D{{Cluster IDs}}

    A --> B
    B --> C
    C --> D

    subgraph Service Mappings
        A1[QOF]
        A2[Network Contract DES]
        A3[CC Core GP Contract]
    end

    subgraph Ruleset Mappings
        B1[Asthma]
        B2[Dementia]
        B3[Diabetes]
    end

    subgraph Output IDs
        C1[AST_REG<br>Asthma register]
        C2[DEM_REG<br>Dementia register]
    end

    subgraph Cluster IDs
        D1[AST_COD<br>Asthma diagnosis codes]
        D2[ASTTRT_COD<br>Asthma treatment codes]
        D3[ASTRES_COD<br>Asthma review codes]
        D4[DEM_COD<br>Dementia diagnosis codes]
    end

    A1 --> B1
    A1 --> B2
    A2 --> B3

    B1 --> C1
    B2 --> C2

    C1 --> D1
    C1 --> D2
    C1 --> D3
    C2 --> D4

Registers:

GPs are required to maintain a register of patients with certain conditions (e.g. dementia, cancer, diabetes)
See Output IDs with suffix _REG for code lists
Output IDs (also termed “Indicator IDs” in the Business Rules word documents) typically apply to patient populations defined by these registers (e.g. AST007, AST008 & AST011 are all applied to population AST_REG)

General

Preview tables

Code

pcd_refset$PCD_SERVICE_FULL_NAME_MAPPINGS |>
  flextable()

Service	Service_Full_Name
CC	Core Contract (CC)
ES	Enhanced Service (ES)
INLIQ	Indicators No Longer In QOF (INLIQ)
NCD	Network Contract DES
Other	Other
PLE	Patient Level Extract (PLE)
QOF	Quality and Outcomes Framework (QOF)
VI	Vaccination and Immunisations (VI)

Code

pcd_refset$PCD_RULSET_FULL_NAME_MAPPINGS |>
  reactable2()

Code

pcd_refset$PCD_SERVICE_OUTPUT_DESCRIPTIONS |>
  reactable2()

Content

Code

pcd_refset$PCD_REFSET_CONTENT |>
  count(Service_and_Ruleset,
        Cluster_description,
        Cluster_ID) |>
  reactable2()

Content by output

Code

pcd_refset$PCD_REFSET_CONTENT_BY_OUTPUT |>
  count(Output_ID,
        Cluster_Description,
        Cluster_ID) |>
  reactable2()

‘Content’ and ‘content by output’ have some non-overlapping code sets

Code

list(
  content = unique(pcd_refset$PCD_REFSET_CONTENT$Cluster_ID),
  content_by_output = unique(pcd_refset$PCD_REFSET_CONTENT_BY_OUTPUT$Cluster_ID)
) |>
  purrr::map(as.character) |>
  ggVennDiagram::ggVennDiagram()

QOF codes for register outcomes

Code

qof_service_reg_output_ids <- pcd_refset$PCD_SERVICE_OUTPUT_DESCRIPTIONS |>
  filter(Service_ID == "QOF") |>
  filter(str_detect(Output_ID, "_REG$"))

Code

pcd_refset$PCD_REFSET_CONTENT_BY_OUTPUT |>
  filter(Output_ID %in% !!qof_service_reg_output_ids$Output_ID) |>
  reactable2()

Code

qof_service_reg_output_ids |>
  flextable() |>
  autofit()

Service_ID	Ruleset_ID	Output_ID	Output_Description	Type
QOF	Asthma	AST_REG	Asthma Register: Patients aged at least 6 years old with an unresolved asthma diagnosis and have received asthma-related drug treatment in the preceding 12 months, up to the end of the reporting period	P
QOF	Atrial fibrillation	AFIB_REG	Atrial fibrillation register: Patients with an unresolved diagnosis of atrial fibrillation	P
QOF	Cancer	CAN_REG	Cancer register; patients diagnosed with cancer since 1st April 2003	P
QOF	Cervical screening	CS_REG	Cervical screening register: Females aged 25 to 64 years on the achievement date	P
QOF	CHD	CHD_REG	CHD register: Register of patients with a coronary heart disease (CHD) diagnosis.	P
QOF	Cholesterol	CHOL_REG	Cholesterol register: Patients with a diagnosis of any of coronary heart disease (CHD), peripheral arterial disease (PAD), stroke or transient ischaemic attack (TIA) or who are aged 18 years or over with chronic kidney disease (CKD) category G3a to G5.	P
QOF	Cholesterol	CHOL2_REG	Cholesterol register: Patients with a diagnosis of any of coronary heart disease (CHD), peripheral arterial disease (PAD), stroke or transient ischaemic attack (TIA).	P
QOF	CKD	CKD_REG	CKD register: Register of patients aged 18 years or over with CKD with classification of categories G3a to G5	P
QOF	COPD	COPD_REG	COPD register: Register of patients with a clinical diagnosis of COPD before1 April 2023; and Patients with a clinical diagnosis of COPD on or after 1 April 2023 whose diagnosis has been confirmed by a quality assured post-bronchodilator spirometry FEV1/FVC ratio below 0.7 between 3 months before or 6 months after diagnosis (or if newly registered at the practice in the preceding 12 months without a record of spirometry having been performed, a record of an FEV1/FVC ratio below 0.7 recorded within 6 months of registration); and Patients with a clinical diagnosis of COPD on or after 1 April 2023 who are unable to undertake spirometry.	P
QOF	Dementia	DEM_REG	Dementia register: Patients with a dementia diagnosis up to the end of the reporting period	P
QOF	Depression	DEP1_REG	Depression register: Patients aged at least 18 years old whose latest unresolved episode of depression is since 1st April 2006.	P
QOF	Diabetes	DM_REG	Diabetes register: Patients aged at least 17 years old with an unresolved diabetes diagnosis	P
QOF	Epilepsy	EPIL_REG	Epilepsy register: Patients aged at least 18 years old with an unresolved diagnosis of epilepsy who have a record of being on drug treatment for epilepsy in the last 6 months	P
QOF	Heart failure	HF1_REG	Heart failure register 1: Patients with an unresolved diagnosis of heart failure	P
QOF	Heart failure	HF2_REG	Heart failure register 2: Patients with an unresolved diagnosis of heart failure due to left ventricular systolic dysfunction (LVSD) or reduced ejection fraction	P
QOF	Hypertension	HYP_REG	Hypertension register: Patients with an unresolved diagnosis of hypertension	P
QOF	Learning disability	LD_REG	Learning disability register: Patients with a learning disability	P
QOF	Mental health	MH1_REG	Mental health register 1: Patients with a diagnosis of psychosis, schizophrenia or bipolar affective disease	P
QOF	Mental health	MH2_REG	Mental health register 2: Patients with a lithium prescription in the last 6 months whose lithium treatment has not been subsequently stopped	P
QOF	Non-diabetic hyperglycaemia	NDH_REG	Non-diabetic hyperglycaemia register: Patients aged 18 years or over with a diagnosis of non-diabetic hyperglycaemia.	P
QOF	Obesity	OBES_REG	Obesity register: Patients aged 18 years or over with a body mass index (BMI) greater than or equal to 30 kg/m2 in the preceding 12 months or a BMI greater than or equal to 27.5 kg/m2 recorded in the preceding 12 months for patients with a South Asian, Chinese, other Asian, Middle Eastern, Black African or African-Caribbean family background.	P
QOF	Osteoporosis	OSTEO1_REG	Osteoporosis register 1: Patients aged 50 or over who have not attained the age of 75 with a record of a fragility fracture on or after 1 April 2012 and a diagnosis of osteoporosis confirmed on a DXA scan	P
QOF	Osteoporosis	OSTEO2_REG	Osteoporosis register 2: Patients aged 75 and over with a record of fragility fracture on or after 1 April 2014 and an osteoporosis diagnosis.	P
QOF	PAD	PAD_REG	PAD register: Register of patients with peripheral arterial disease	P
QOF	Palliative care	PALCARE_REG	Palliative Care register: Patients who have been identified as requiring palliative care	P
QOF	Rheumatoid arthritis	RA_REG	Rheumatoid arthritis register: Patients aged 16 years or over with a diagnosis of rheumatoid arthritis	P
QOF	Smoking	SMOK1_REG	Register of patients with a co-morbidity of CHD, PAD, stroke or TIA, hypertension, diabetes, COPD, asthma, CKD, schizophrenia, bipolar affective disorder or other psychoses	P
QOF	Smoking	SMOK2_REG	Register of patients who are aged 15 years and over	P
QOF	Stroke	STIA_REG	Stroke/TIA register: Register of patients with a Stroke or TIA diagnosis	P

Code

pcd_refset$PCD_REFSET_CONTENT_BY_OUTPUT |>
  filter(Output_ID %in% !!qof_service_reg_output_ids$Output_ID) |>
  count(Output_ID, Cluster_ID) |>
  left_join(qof_service_reg_output_ids |>
              select(Output_ID,
                     Output_Description),
            by = "Output_ID") |>
  tidyr::unite("Output",
               Output_ID,
               Output_Description, 
               sep = "\n", 
               remove = TRUE) |>
  as_grouped_data("Output") |>
  flextable() |>
  autofit()

Output	Cluster_ID	n
AFIB_REG Atrial fibrillation register: Patients with an unresolved diagnosis of atrial fibrillation
	AFIBRES_COD	1
	AFIB_COD	24
AST_REG Asthma Register: Patients aged at least 6 years old with an unresolved asthma diagnosis and have received asthma-related drug treatment in the preceding 12 months, up to the end of the reporting period
	ASTRES_COD	1
	ASTTRT_COD	1
	AST_COD	141
CAN_REG Cancer register; patients diagnosed with cancer since 1st April 2003
	CAN_COD	6,024
CHD_REG CHD register: Register of patients with a coronary heart disease (CHD) diagnosis.
	CHD_COD	336
CHOL2_REG Cholesterol register: Patients with a diagnosis of any of coronary heart disease (CHD), peripheral arterial disease (PAD), stroke or transient ischaemic attack (TIA).
	CHD_COD	336
	PAD_COD	47
	STRK_COD	264
	TIA_COD	17
CHOL_REG Cholesterol register: Patients with a diagnosis of any of coronary heart disease (CHD), peripheral arterial disease (PAD), stroke or transient ischaemic attack (TIA) or who are aged 18 years or over with chronic kidney disease (CKD) category G3a to G5.
	CHD_COD	336
	CKD1AND2_COD	27
	CKDRES_COD	1
	CKD_COD	54
	PAD_COD	47
	STRK_COD	264
	TIA_COD	17
CKD_REG CKD register: Register of patients aged 18 years or over with CKD with classification of categories G3a to G5
	CKD1AND2_COD	27
	CKDRES_COD	1
	CKD_COD	54
COPD_REG COPD register: Register of patients with a clinical diagnosis of COPD before1 April 2023; and Patients with a clinical diagnosis of COPD on or after 1 April 2023 whose diagnosis has been confirmed by a quality assured post-bronchodilator spirometry FEV1/FVC ratio below 0.7 between 3 months before or 6 months after diagnosis (or if newly registered at the practice in the preceding 12 months without a record of spirometry having been performed, a record of an FEV1/FVC ratio below 0.7 recorded within 6 months of registration); and Patients with a clinical diagnosis of COPD on or after 1 April 2023 who are unable to undertake spirometry.
	COPDRES_COD	1
	COPD_COD	55
	FEV1FVCL70_COD	1
	FEV1FVC_COD	1
DEM_REG Dementia register: Patients with a dementia diagnosis up to the end of the reporting period
	DEM_COD	322
DEP1_REG Depression register: Patients aged at least 18 years old whose latest unresolved episode of depression is since 1st April 2006.
	DEPRES_COD	1
	DEPR_COD	106
DM_REG Diabetes register: Patients aged at least 17 years old with an unresolved diabetes diagnosis
	DMRES_COD	1
	DM_COD	86
EPIL_REG Epilepsy register: Patients aged at least 18 years old with an unresolved diagnosis of epilepsy who have a record of being on drug treatment for epilepsy in the last 6 months
	EPILDRUG_COD	1
	EPILRES_COD	1
	EPIL_COD	210
HF1_REG Heart failure register 1: Patients with an unresolved diagnosis of heart failure
	HFRES_COD	1
	HF_COD	41
HF2_REG Heart failure register 2: Patients with an unresolved diagnosis of heart failure due to left ventricular systolic dysfunction (LVSD) or reduced ejection fraction
	HFLVSD_COD	5
	HFRES_COD	1
	HF_COD	41
	REDEJCFRAC_COD	5
HYP_REG Hypertension register: Patients with an unresolved diagnosis of hypertension
	HYPRES_COD	1
	HYP_COD	117
LD_REG Learning disability register: Patients with a learning disability
	LD_COD	696
MH1_REG Mental health register 1: Patients with a diagnosis of psychosis, schizophrenia or bipolar affective disease
	MH_COD	198
MH2_REG Mental health register 2: Patients with a lithium prescription in the last 6 months whose lithium treatment has not been subsequently stopped
	LITSTP_COD	1
	LIT_COD	1
NDH_REG Non-diabetic hyperglycaemia register: Patients aged 18 years or over with a diagnosis of non-diabetic hyperglycaemia.
	DMRES_COD	1
	DM_COD	86
	IGT_COD	10
	NDH_COD	1
	PRD_COD	2
OBES_REG Obesity register: Patients aged 18 years or over with a body mass index (BMI) greater than or equal to 30 kg/m2 in the preceding 12 months or a BMI greater than or equal to 27.5 kg/m2 recorded in the preceding 12 months for patients with a South Asian, Chinese, other Asian, Middle Eastern, Black African or African-Caribbean family background.
	BMI30_COD	12
	BMIVAL_COD	3
	ETH2016AB_COD	2
	ETH2016AC_COD	3
	ETH2016AI_COD	2
	ETH2016AO_COD	1
	ETH2016AP_COD	2
	ETH2016BA_COD	1
	ETH2016BC_COD	1
	ETH2016BO_COD	1
	ETH2016MO_COD	1
	ETH2016MWA_COD	2
	ETH2016MWBA_COD	1
	ETH2016MWBC_COD	2
	ETH2016NSTAT_COD	1
	ETH2016OA_COD	2
	ETH2016OO_COD	3
	ETH2016WB_COD	2
	ETH2016WGT_COD	4
	ETH2016WI_COD	2
	ETH2016WO_COD	1
OSTEO1_REG Osteoporosis register 1: Patients aged 50 or over who have not attained the age of 75 with a record of a fragility fracture on or after 1 April 2012 and a diagnosis of osteoporosis confirmed on a DXA scan
	DXA2_COD	5
	DXA_COD	3
	FF_COD	2
	OSTEO_COD	40
OSTEO2_REG Osteoporosis register 2: Patients aged 75 and over with a record of fragility fracture on or after 1 April 2014 and an osteoporosis diagnosis.
	FF_COD	2
	OSTEO_COD	40
PAD_REG PAD register: Register of patients with peripheral arterial disease
	PAD_COD	47
PALCARE_REG Palliative Care register: Patients who have been identified as requiring palliative care
	PALCARENI_COD	2
	PALCARE_COD	79
RA_REG Rheumatoid arthritis register: Patients aged 16 years or over with a diagnosis of rheumatoid arthritis
	RARTH_COD	131
SMOK1_REG Register of patients with a co-morbidity of CHD, PAD, stroke or TIA, hypertension, diabetes, COPD, asthma, CKD, schizophrenia, bipolar affective disorder or other psychoses
	ASTRES_COD	1
	ASTTRT_COD	1
	AST_COD	141
	CHD_COD	336
	CKD1AND2_COD	27
	CKDRES_COD	1
	CKD_COD	54
	COPDRES_COD	1
	COPD_COD	55
	DMRES_COD	1
	DM_COD	86
	HYPRES_COD	1
	HYP_COD	117
	MH_COD	198
	PAD_COD	47
	STRK_COD	264
	TIA_COD	17
STIA_REG Stroke/TIA register: Register of patients with a Stroke or TIA diagnosis
	STRK_COD	264
	TIA_COD	17

Examples

Dementia

Cluster ID DEM_COD contains all codes for dementia diagnosis
Other Cluster IDs pertaining to dementia diagnosis contain subsets of these codes: DEMALZ_COD, DEMVASC_COD, DEMOTHER_COD, DEMFTEMP_COD DEMLEWY_COD, DEMMIX_COD & DEMOTHER_COD

Code

pcd_refset$PCD_REFSET_CONTENT |>
  filter(str_detect(Cluster_ID, "^DEM")) |>
  count(Cluster_ID, Cluster_description) |>
  arrange(desc(n)) |>
  flextable()

Cluster_ID	Cluster_description	n
DEM_COD	Codes for dementia	322
DEMOTHER_COD	Dementia diagnosis codes excluding Alzheimer's, Vascular, Lewy Body, Frontotemporal, and Mixed	200
DEMALZ_COD	Alzheimer’s disease dementia codes	48
DEMVASC_COD	Vascular dementia codes	39
DEMFTEMP_COD	Frontotemporal dementia codes	20
DEMMEDRVW_COD	Dementia medication review codes	17
DEMASS_COD	Assessment for dementia codes	16
DEMLEWY_COD	Lewy body dementia codes	14
DEMINVITE_COD	Invite for dementia care review codes	9
DEMCPRVWDEC_COD	Codes indicating the patient has chosen not to receive dementia care plan review	3
DEMCPRVW_COD	Dementia care plan review codes	3
DEMCPDEC_COD	Codes indicating the patient has chosen not to receive dementia care plan	2
DEMCP_COD	Dementia care plan codes	2
DEMMIX_COD	Mixed dementia codes	1
DEMPCADEC_COD	Codes indicating the patient has chosen not to receive dementia quality indicator care	1
DEMPCAPU_COD	Codes for dementia quality indicator care unsuitable for patient	1

Code

pcd_refset$PCD_REFSET_CONTENT |>
  filter(str_detect(Cluster_ID, "^DEM")) |>
  pull(Cluster_ID) |>
  unique() |>
  set_names() |>
  map(\(x) pcd_refset$PCD_REFSET_CONTENT |>
        filter(Cluster_ID == !!x) |>
        pull(SNOMED_code)) |>
  fromList() |>
  upset(order.by = "freq", 
        nsets = 50)