Add national primary care inequalities overview #119

camappel · 2024-11-18T11:33:31Z

We present the latest NHS primary care data, using Index of Multiple Deprivation (IMD) to examine inequalities existing in primary care access, experience and outcomes, across the following categories:

-   **Resources (supply)**: Payments, Workforce
-   **Population (demand)**: Disease prevalence, Health-related behaviours
-   **Service quality**: QOF achievement
-   **Access**: Patient experience, Appointments
-   **Impact on secondary care**: Emergency admissions, A&E attendances

camappel · 2024-11-26T14:34:50Z

@Lextuga007 Would it better for me to add the NHSRtheme to the Qmd?

Lextuga007 · 2024-12-03T11:08:48Z

@camappel - applying the brand would be a great idea but I think we should use the new _brand.yml file https://github.com/nhs-r-community/assets/tree/main/brand. There is an important issue on that repository though about accessibility following the code published to put the brand on Posit's Gallery https://posit-dev.github.io/brand-yml/inspiration/

england.qmd

Lextuga007 · 2024-12-05T17:12:50Z

england.qmd

+df[is.na(df$quin_4) & is.na(df$quin_5), ]
+df %<>%
+  mutate(quin_5 = ifelse(is.na(quin_5), quin_4, quin_5))
+


Is line 36 filtering by nothing in quin_4 and quin_5 but then lines 37-38 are mutating quin_5 to populate from two columns that are NA. Is that right? I struggle with reading base R and the magrittr pipe %<>% is new to me! I only have ever used %>%!

Edit: Is line 50 not used in the later code?

If quin_5 is NA (missing), it assigns the value from quin_4 to quin_5. If quin_5 is not NA, it retains its value.

This shouldn't be necessary for this national level analysis, so I can remove it (or comment it out).

I'm not sure what line 50 refers to (I think the line numbers have changed), but the line was only run once as it applied to all indicators across all ICBs. This is so that if there were no practices in the most deprived quintile in the ICB, there would still be a datapoint representing the most deprived practices in that ICB (not the country)

Ah sorry, you are right about the lines being out of synch - that was local to me! I think it's good to keep the ICB level code in but comment it out and leave a note about that because it's highly likely if anyone wishes to replicate this for their area they will need this logic.

I can add this code back in with the comments to explain. Thanks

…lse.

Lextuga007 · 2024-12-05T21:49:58Z

england.qmd

+
+Average payment per weighted patient is **£`r round(df_filter[df_filter$Indicator == "payment_per_patient_all", ]$quin_5, 2)`** in the most deprived 20% of practices, versus **£`r round(df_filter[df_filter$Indicator == "payment_per_patient_all", ]$quin_1, 2)`** in the least deprived 20%.
+
+If there are no dispensing practices in the most deprived quintile, we use the second most deprived. If both are missing, we omit the data point from the figure.


I assume this relates to when the data is used for other areas as these charts are for England and so there is data at these quintiles. Could this be amended to advise this is guidance as the code doesn't include this logic? I'm assuming that readers of this may well be new to R and want to follow the same principles.

Yes, you're right - removed

Lextuga007 · 2024-12-05T21:59:57Z

england.qmd

+  labs(
+    x = NULL, y = NULL,
+    title = paste0("Life expectancy by practice, birth cohort 2016-20 (England)"),
+    subtitle = "Practices in most and least deprived IMD quintiles. Larger circles represent stronger socio-economic gradient.",


Is there code that relates to changing circle sizes? These all render the at the same size.

This was an old feature that I removed as it wasn't very interpretable - thank you for spotting

…qualities-notebook into camappel-add-qmd-file

Lextuga007 · 2024-12-05T22:03:55Z

Note for fixing - there are font issues which are suppressed with warning: false in global:

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database

Font size is still quite small even with code removed in commit 2fe3385

Lextuga007 · 2024-12-06T14:54:45Z

england.qmd

+
+-   The work of the Health Equity Evidence Centre is made possible through seed funding from NHS East of England team.
+
+-   The views expressed in this publication are those of the Health Equity Evidence Centre and not necessarily those of NHS England.


I've been giving this line a bit of thought. NHS-R Community is not part of NHS England and, for this year at least, we aren't funded by NHSE so it might be these sentences are written more as a recognition of the contribution you have made to NHS-R Community:

This work has been provided by the Health Equity Evidence Centre which was made possible through seed funding from NHS East of England team.

Before I accept this PR and with this in mind, are you aware and happy that all the code and text you have submitted is subject to our CC0 and MIT licences for reuse?

Yes that's much better.

Yes, happy with re-use and licenses etc!

camappel · 2024-12-09T12:16:30Z

Note for fixing - NHS logo not in repo

/nhsr-logo.svg (404: Not Found)

camappel · 2024-12-09T12:18:22Z

Note for fixing - there are font issues which are suppressed with warning: false in global:

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database

Font size is still quite small even with code removed in commit 2fe3385

I've added 20 to the font size for all chart elements:

theme_set(
  theme_minimal() +
    theme(
      axis.title = element_text(size = 100),
      axis.text = element_text(size = 100),
      plot.caption = element_text(size = 80),
      plot.title = element_text(size = 120),
      plot.subtitle = element_text(size = 110),
      panel.grid = element_line(size = 5),
      legend.title = element_text(size = 80),
      legend.text = element_text(size = 80),
      legend.key.width = unit(3.5, "cm"),
      plot.title.position = "plot"
    )
)

camappel · 2024-12-09T12:20:33Z

Thanks very much for the code review! I've now submitted the changes

BTW I pushed new changes after submitting the review so it thinks there are more changes that need to be reviewed

Lextuga007 · 2024-12-10T17:24:12Z

@all-contributors please add @camappel for content

allcontributors · 2024-12-10T17:24:22Z

@Lextuga007

I've put up a pull request to add @camappel! 🎉

Lextuga007 · 2024-12-10T17:25:04Z

@all-contributors please add @camappel for code

allcontributors · 2024-12-10T17:25:14Z

@Lextuga007

I've put up a pull request to add @camappel! 🎉

camappel and others added 2 commits November 18, 2024 11:14

add england file

43366de

Update england.qmd

5dc4198

camappel mentioned this pull request Nov 18, 2024

[NEW CHAPTER]: ICB-level inequalities in General Practice #118

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camappel added 2 commits November 18, 2024 11:49

add authors

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small fixes

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camappel added 2 commits December 3, 2024 13:40

add nhs-r brand

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changes

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camappel requested a review from Lextuga007 December 3, 2024 14:08

camappel and others added 7 commits December 3, 2024 14:09

add brand

ed76e93

Updated with the logo and alt text (as corrected by Garrick Aden-Buie

60e9a1c

Moved brand YAML to _quarto.yml to apply to whole book

fec9d11

Removed Google font code as chart text is small on rendered book

2fe3385

Added ref to imd page

587acb0

Removed theme as brand replaces

9ec0831

Removed knitr for Quarto YAML and added code fold

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Lextuga007 added 5 commits December 5, 2024 17:30

Changed label text to same as data for males and females

41d578a

Removed base R checking code and to use code-fold removed include: fa…

4c649e4

…lse.

Added alt text to charts

3e1186d

Removed chunk YAML as set globally

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fixup! Added alt text to charts

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Lextuga007 requested changes Dec 5, 2024

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Moved warning to global YAML

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Merge branch 'add-qmd-file' of https://github.com/camappel/health-ine…

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…qualities-notebook into camappel-add-qmd-file

Lextuga007 requested changes Dec 6, 2024

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code review

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font size

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life expenctancy 2020 not 2019

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camappel requested a review from Lextuga007 December 9, 2024 14:45

Lextuga007 added 2 commits December 10, 2024 17:16

Removed family text from font as not installed

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Added ICB level code but commented out

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Lextuga007 merged commit b831c74 into nhs-r-community:main Dec 10, 2024

allcontributors bot mentioned this pull request Dec 10, 2024

docs: add camappel as a contributor for content #120

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allcontributors bot mentioned this pull request Dec 10, 2024

docs: add camappel as a contributor for code #121

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Add national primary care inequalities overview #119

Add national primary care inequalities overview #119

camappel commented Nov 18, 2024

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allcontributors bot commented Dec 10, 2024


		Average payment per weighted patient is £`r round(df_filter[df_filter$Indicator == "payment_per_patient_all", ]$quin_5, 2)` in the most deprived 20% of practices, versus £`r round(df_filter[df_filter$Indicator == "payment_per_patient_all", ]$quin_1, 2)` in the least deprived 20%.

		If there are no dispensing practices in the most deprived quintile, we use the second most deprived. If both are missing, we omit the data point from the figure.


		- The work of the Health Equity Evidence Centre is made possible through seed funding from NHS East of England team.

		- The views expressed in this publication are those of the Health Equity Evidence Centre and not necessarily those of NHS England.

Add national primary care inequalities overview #119

Add national primary care inequalities overview #119

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