Prevalence estimates: summary input values by practice

This a brief analysis of the underlying data used to populate prevalence models to prodcuce practice level estimates.

1 Calculating summary data

1.1 For COPD

library(dplyr)
gp %>%
    filter(disease == "COPD") %>%
    select(disease, GP.Practice.Code, indicator, indicator1, value) %>%
    group_by(indicator, indicator1) %>%
    summarise(n= length(unique(GP.Practice.Code)), 
              mean = round(mean(value, na.rm = TRUE),2),
              sd = round(sd(value, na.rm = TRUE),2),
              min = round(min(value, na.rm = TRUE),2),
              max = round(max(value, na.rm = TRUE),2)) %>%
    knitr::kable()

indicator	indicator1	n	mean	sd	min	max
age	Total <40	7681	3796.51	2589.89	0	38071.00
age	Total 40-50	7681	1039.65	646.42	0	8842.00
age	Total 50-60	7681	983.96	625.71	0	8421.00
age	Total 60-70	7681	792.28	553.33	0	5759.00
age	Total 70-80	7681	544.89	413.01	0	4128.00
age	Total 80+	7681	346.85	279.65	0	2792.00
ethnicity	Non-smokers	7681	0.46	0.09	0	0.80
gender	Total Females	7681	3767.55	2352.15	0	29769.00
gender	Total Males	7681	3736.59	2280.32	0	30606.00
imd	IMD Quintile 1 (%)	7681	0.17	0.22	0	0.99
imd	IMD Quintile 2 (%)	7681	0.18	0.16	0	1.00
imd	IMD Quintile 3 (%)	7681	0.20	0.16	0	1.00
imd	IMD Quintile 4 (%)	7681	0.22	0.17	0	1.00
imd	IMD Quintile 5 (%)	7681	0.24	0.27	0	0.99
population	Total All	7681	7504.14	4621.85	1	60375.00
smoking	Current smokers	7681	0.21	0.07	0	0.51
smoking	Ex-smokers	7681	0.32	0.08	0	0.66

1.2 For hypertension

indicator	indicator1	n	mean	sd	min	max
age	Total 16-24	8107	874.69	939.08	0.00	25616.00
age	Total 25-34	8107	986.54	742.48	0.00	8456.00
age	Total 35-44	8107	956.36	616.15	0.00	7547.00
age	Total 45-54	8107	978.90	630.22	0.00	7319.00
age	Total 55-64	8107	771.28	524.18	0.00	5242.00
age	Total 65-74	8107	624.69	471.79	0.00	4332.00
age	Total 75+	8107	530.80	420.25	0.00	4074.00
bmi	BMI <18.5kg/m2 (%)	8107	0.01	0.01	0.00	0.05
bmi	BMI >18.5 <25kg/m2 (%)	8107	0.34	0.07	0.00	0.53
bmi	BMI>25 <30kg/m2 (%)	8107	0.39	0.07	0.00	0.51
bmi	BMI>30kg/m2 (%)	8107	0.22	0.05	0.00	0.35
education	Foreign/Other (%)	8107	0.23	0.05	0.13	0.49
education	No qualfications (%)	8107	0.35	0.13	0.08	0.89
education	NVQ1/CSE other grade equiv (%)	8107	0.41	0.05	0.21	0.67
education	NVQ2/GCE O Level equiv (%)	8107	0.48	0.08	0.25	0.77
education	NVQ3/GCE A Level equiv (%)	8107	0.35	0.08	0.16	0.69
education	NVQ4/NVQ5/Degree or equiv + Higher ed below degree (%)	8107	0.35	0.13	0.08	0.89
ethnicity	African/Afro-Caribbean (%)	8107	0.04	0.07	0.00	0.44
ethnicity	Mixed (%)	8107	0.02	0.02	0.00	0.10
ethnicity	Other (%)	8107	0.04	0.04	0.00	0.27
ethnicity	South Asian (%)	8107	0.07	0.11	0.00	0.69
ethnicity	White (%)	8107	0.83	0.20	0.11	0.99
gender	Total Female	8107	3502.63	2202.97	0.00	26554.00
gender	Total Male	8107	3464.35	2129.27	48.00	25832.00
imd	IMD Quintile 1 (%)	8107	0.17	0.22	0.00	1.00
imd	IMD Quintile 2 (%)	8107	0.17	0.16	0.00	1.00
imd	IMD Quintile 3 (%)	8107	0.20	0.16	0.00	1.00
imd	IMD Quintile 4 (%)	8107	0.22	0.18	0.00	1.00
imd	IMD Quintile 5 (%)	8107	0.24	0.27	0.00	1.00
limiting long term illness	Limiting long-lasting disease (%)	8107	0.18	0.04	0.06	0.39
limiting long term illness	No limiting long-lasting disease (%)	8107	0.82	0.04	0.61	0.94
occupational classification	Higher Managerial, Administrative and Professional Occupations (%)	8107	0.20	0.09	0.03	0.63
occupational classification	Intermediate Occupations (%)	8107	0.13	0.02	0.03	0.28
occupational classification	Lower Managerial, Administrative and Professional Occupations (%)	8107	0.20	0.05	0.06	0.36
occupational classification	Lower Supervisory and Technical Occupations (%)	8107	0.07	0.02	0.01	0.13
occupational classification	Never Worked and Long-Term Unemployed (%)	8107	0.06	0.04	0.01	0.28
occupational classification	Others (%)	8107	0.09	0.06	0.01	0.70
occupational classification	Routine Occupations (%)	8107	0.11	0.04	0.02	0.27
occupational classification	Semi-Routine Occupations (%)	8107	0.14	0.04	0.03	0.26
occupational classification	Small Employers and Own Account Workers (%)	8107	0.09	0.03	0.02	0.27
population	Total All	8107	6966.98	4322.62	102.00	52386.00
population	Total People	8107	5723.26	3653.70	0.00	43017.00

1.3 For CHD

gp %>%
    filter(disease == "Coronary Heart Disease") %>%
    select(disease, GP.Practice.Code, indicator, indicator1, value) %>%
    group_by(indicator, indicator1) %>%
    summarise(n= length(unique(GP.Practice.Code)), 
              mean = round(mean(value, na.rm = TRUE),2),
              sd = round(sd(value, na.rm = TRUE),2),
              min = round(min(value, na.rm = TRUE),2),
              max = round(max(value, na.rm = TRUE),2)) %>%
    knitr::kable()

indicator	indicator1	n	mean	sd	min	max
age	Total 55-59	7541	460.71	290.79	0.00	3805.00
age	Total 60-64	7541	395.62	260.62	0.00	2983.00
age	Total 65-69	7541	406.44	292.63	0.00	2776.00
age	Total 70-74	7541	311.59	234.25	0.00	2284.00
age	Total 75-79	7541	240.37	178.49	0.00	1844.00
bmi	BMI <18.5kg/m2 (%)	7541	0.01	0.01	0.00	0.05
bmi	BMI >18.5 <25kg/m2 (%)	7541	0.35	0.05	0.23	0.53
bmi	BMI>25 <30kg/m2 (%)	7541	0.41	0.04	0.30	0.51
bmi	BMI>30kg/m2 (%)	7541	0.23	0.04	0.11	0.35
ckd	Chronic Kidney Disease (%)	7541	0.04	0.02	0.00	0.27
ckd	No Chronic Kidney Disease (%)	7541	0.96	0.02	0.73	1.00
diabetes	Diabetes (%)	7541	0.07	0.02	0.00	0.20
diabetes	No Diabetes (%)	7541	0.93	0.02	0.80	1.00
ethnicity	Non white (%)	7541	0.17	0.20	0.00	0.89
ethnicity	White (%)	7541	0.83	0.20	0.11	0.99
gender	Total Female	7541	3801.39	2338.80	1.00	29769.00
gender	Total Male	7541	3769.08	2266.91	0.00	30606.00
imd	IMD Quintile 1 (%)	7541	0.17	0.22	0.00	0.99
imd	IMD Quintile 2 (%)	7541	0.18	0.16	0.00	1.00
imd	IMD Quintile 3 (%)	7541	0.20	0.16	0.00	1.00
imd	IMD Quintile 4 (%)	7541	0.22	0.17	0.00	1.00
imd	IMD Quintile 5 (%)	7541	0.24	0.27	0.00	0.99
physical acticity	Physical Activity 1 (%)	7541	0.29	0.04	0.17	0.40
physical acticity	Physical Activity 2 (%)	7541	0.15	0.02	0.00	0.22
physical acticity	Physical Activity 3 (%)	7541	0.56	0.05	0.44	0.68
population	Total All	7541	7570.47	4595.07	1.00	60375.00
population	Total People	7541	6179.67	3817.83	1.00	49067.00
smoking	Current smoker (%)	7541	0.21	0.07	0.00	0.51
smoking	Not current smoker (%)	7541	0.79	0.07	0.49	1.00

1.4 For depression

gp %>%
    filter(disease == "Depression") %>%
    select(disease, GP.Practice.Code, indicator, indicator1, value) %>%
    group_by(indicator, indicator1) %>%
    summarise(n= length(unique(GP.Practice.Code)), 
              mean = round(mean(value, na.rm = TRUE),2),
              sd = round(sd(value, na.rm = TRUE),2),
              min = round(min(value, na.rm = TRUE),2),
              max = round(max(value, na.rm = TRUE),2)) %>%
    knitr::kable()

indicator	indicator1	n	mean	sd	min	max
age	Total 16-24	7681	830.24	1001.48	0.00	27447.00
age	Total 25-34	7681	1078.92	803.98	0.00	9812.00
age	Total 35-44	7681	1008.73	650.61	0.00	8327.00
age	Total 45-54	7681	1066.89	667.88	0.00	9332.00
age	Total 55-64	7681	846.47	552.44	0.00	6788.00
age	Total 65-74	7681	708.95	527.66	0.00	5060.00
age	Total 75+	7681	584.13	455.83	0.00	4620.00
bmi	BMI <18.5kg/m2 (%)	7681	0.01	0.01	0.00	0.05
bmi	BMI >18.5 <25kg/m2 (%)	7681	0.35	0.05	0.23	0.53
bmi	BMI>25 <30kg/m2 (%)	7681	0.41	0.04	0.30	0.51
bmi	BMI>30kg/m2 (%)	7681	0.23	0.04	0.11	0.35
ethnicity	Asian (%)	7681	0.07	0.11	0.00	0.69
ethnicity	Black (%)	7681	0.04	0.07	0.00	0.44
ethnicity	Mixed (%)	7681	0.02	0.02	0.00	0.10
ethnicity	Other (%)	7681	0.04	0.04	0.00	0.27
ethnicity	White (%)	7681	0.83	0.20	0.11	0.99
gender	Total Female	7681	3767.55	2352.15	0.00	29769.00
gender	Total Male	7681	3736.59	2280.32	0.00	30606.00
imd	IMD Quintile 1 (%)	7681	0.17	0.22	0.00	1.00
imd	IMD Quintile 2 (%)	7681	0.17	0.16	0.00	1.00
imd	IMD Quintile 3 (%)	7681	0.20	0.16	0.00	1.00
imd	IMD Quintile 4 (%)	7681	0.22	0.18	0.00	1.00
imd	IMD Quintile 5 (%)	7681	0.24	0.27	0.00	1.00
limiting long term illness	Limiting long-lasting disease (%)	7681	0.18	0.04	0.06	0.39
limiting long term illness	No limiting long-lasting disease (%)	7681	0.82	0.04	0.61	0.94
occupational classification	Higher Managerial, Administrative and Professional Occupations (%)	7681	0.18	0.07	0.04	0.48
occupational classification	Intermediate Occupations (%)	7681	0.12	0.02	0.02	0.26
occupational classification	Lower Managerial, Administrative and Professional Occupations (%)	7681	0.18	0.04	0.06	0.31
occupational classification	Lower Supervisory and Technical Occupations (%)	7681	0.06	0.02	0.01	0.12
occupational classification	Never Worked and Long-Term Unemployed (%)	7681	0.06	0.04	0.01	0.27
occupational classification	Others (%)	7681	0.08	0.05	0.01	0.66
occupational classification	Routine Occupations (%)	7681	0.10	0.04	0.02	0.27
occupational classification	Semi-Routine Occupations (%)	7681	0.13	0.04	0.02	0.25
occupational classification	Small Employers and Own Account Workers (%)	7681	0.09	0.03	0.02	0.26
population	Total All	7681	7504.14	4621.85	1.00	60375.00
population	Total People	7681	6124.32	3837.88	1.00	49067.00

1.5 For peripheral arterial disease

gp %>%
    filter(disease == "Peripheral arterial disease") %>%
    select(disease, GP.Practice.Code, indicator,  indicator1, value) %>%
    group_by(indicator, indicator1) %>%
    summarise(n= length(unique(GP.Practice.Code)), 
              mean = round(mean(value, na.rm = TRUE),2),
              sd = round(sd(value, na.rm = TRUE),2),
              min = round(min(value, na.rm = TRUE),2),
              max = round(max(value, na.rm = TRUE),2)) %>%
    knitr::kable()

indicator	indicator1	n	mean	sd	min	max
age	Total 55-59	7541	460.71	290.79	0.00	3805.00
age	Total 60-64	7541	395.62	260.62	0.00	2983.00
age	Total 65-69	7541	406.44	292.63	0.00	2776.00
age	Total 70-74	7541	311.59	234.25	0.00	2284.00
age	Total 75-79	7541	240.37	178.49	0.00	1844.00
bmi	BMI <18.5kg/m2 (%)	7541	0.01	0.01	0.00	0.05
bmi	BMI >18.5 <25kg/m2 (%)	7541	0.35	0.05	0.23	0.53
bmi	BMI>25 <30kg/m2 (%)	7541	0.41	0.04	0.30	0.51
bmi	BMI>30kg/m2 (%)	7541	0.23	0.04	0.11	0.35
ckd	Chronic Kidney Disease (%)	7541	0.04	0.02	0.00	0.27
ckd	No Chronic Kidney Disease (%)	7541	0.96	0.02	0.73	1.00
diabetes	Diabetes (%)	7541	0.07	0.02	0.00	0.20
diabetes	No Diabetes (%)	7541	0.93	0.02	0.80	1.00
ethnicity	Non white (%)	7541	0.17	0.20	0.00	0.89
ethnicity	White (%)	7541	0.83	0.20	0.00	0.99
gender	Females	7541	3801.39	2338.80	1.00	29769.00
gender	Males	7541	3769.08	2266.91	0.00	30606.00
imd	IMD Quintile 1 (%)	7541	0.17	0.22	0.00	0.99
imd	IMD Quintile 2 (%)	7541	0.18	0.16	0.00	1.00
imd	IMD Quintile 3 (%)	7541	0.20	0.16	0.00	1.00
imd	IMD Quintile 4 (%)	7541	0.22	0.17	0.00	1.00
imd	IMD Quintile 5 (%)	7541	0.24	0.27	0.00	0.99
physical acticity	Physical Activity 1 (%)	7541	0.29	0.04	0.17	0.40
physical acticity	Physical Activity 2 (%)	7541	0.15	0.02	0.00	0.22
physical acticity	Physical Activity 3 (%)	7541	0.56	0.05	0.44	0.68
population	Total All	7541	7570.47	4595.07	1.00	60375.00
population	Total People	7541	6179.67	3817.83	1.00	49067.00
smoking	Current smoker (%)	7541	0.21	0.07	0.00	0.51
smoking	Not current smoker (%)	7541	0.79	0.07	0.49	1.00

1.6 For stroke

gp %>%
    filter(disease == "Stroke") %>%
    select(disease, GP.Practice.Code, indicator, indicator1, value) %>%
    group_by(indicator, indicator1) %>%
    summarise(n= length(unique(GP.Practice.Code)), 
              mean = round(mean(value, na.rm = TRUE),2),
              sd = round(sd(value, na.rm = TRUE),2),
              min = round(min(value, na.rm = TRUE),2),
              max = round(max(value, na.rm = TRUE),2)) %>%
    knitr::kable()

indicator	indicator1	n	mean	sd	min	max
age	Total 55-59	7541	460.71	290.79	0.00	3805.00
age	Total 60-64	7541	395.62	260.62	0.00	2983.00
age	Total 65-69	7541	406.44	292.63	0.00	2776.00
age	Total 70-74	7541	311.59	234.25	0.00	2284.00
age	Total 75-79	7541	240.37	178.49	0.00	1844.00
bmi	BMI <18.5kg/m2 (%)	7541	0.01	0.01	0.00	0.05
bmi	BMI >18.5 <25kg/m2 (%)	7541	0.35	0.05	0.23	0.53
bmi	BMI>25 <30kg/m2 (%)	7541	0.41	0.04	0.30	0.51
bmi	BMI>30kg/m2 (%)	7541	0.23	0.04	0.11	0.35
ckd	Chronic Kidney Disease (%)	7541	0.04	0.02	0.00	0.27
ckd	No Chronic Kidney Disease (%)	7541	0.96	0.02	0.73	1.00
diabetes	Diabetes (%)	7541	0.07	0.02	0.00	0.20
diabetes	No Diabetes (%)	7541	0.93	0.02	0.80	1.00
ethnicity	Non white (%)	7541	0.17	0.20	0.00	0.89
ethnicity	White (%)	7541	0.83	0.20	0.00	0.99
gender	Total Female	7541	3801.39	2338.80	1.00	29769.00
gender	Total Male	7541	3769.08	2266.91	0.00	30606.00
imd	IMD Quintile 1 (%)	7541	0.17	0.22	0.00	0.99
imd	IMD Quintile 2 (%)	7541	0.18	0.16	0.00	1.00
imd	IMD Quintile 3 (%)	7541	0.20	0.16	0.00	1.00
imd	IMD Quintile 4 (%)	7541	0.22	0.17	0.00	1.00
imd	IMD Quintile 5 (%)	7541	0.24	0.27	0.00	0.99
physical acticity	Physical Activity 1 (%)	7541	0.29	0.04	0.17	0.40
physical acticity	Physical Activity 2 (%)	7541	0.15	0.02	0.00	0.22
physical acticity	Physical Activity 3 (%)	7541	0.56	0.05	0.44	0.68
population	Total All	7541	7570.47	4595.07	1.00	60375.00
population	Total People	7541	6179.67	3817.83	1.00	49067.00
smoking	Current smoker (%)	7541	0.21	0.07	0.00	0.51
smoking	Not current smoker (%)	7541	0.79	0.07	0.49	1.00