Scope of the possible with R

R
overview
Published

September 26, 2024

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Welcome

  • this session is a non-technical overview designed for service leads

Session outline

  • Why R, and why this session?
  • R demo - take some data, load, tidy, analyse
  • Strengths and weaknesses
    • obvious
    • less obvious
  • Alternatives
  • Skill development

R

  • free and open-source
  • multi-platform
  • large user base
  • prominent in health, industry, biosciences

Why this session?

  • R can be confusing
    • it’s code-based, and most of us don’t have much code experience
    • it’s used for some inherently complicated tasks
    • it’s a big product with lots of add-ons and oddities
  • But R is probably the best general-purpose toolbox we have for data work at present
    • big user base in health and social care
    • focus on health and care-like applications
    • not that hard to learn
    • extensible and flexible
    • capable of enterprise-y, fancy uses

R demo

  • this is about showing what’s possible, and give you a flavour of how R works
  • we won’t explain code in detail during this session
  • using live open data
    https://www.opendata.nhs.scot/dataset/weekly-accident-and-emergency-activity-and-waiting-times

Load that data

library(readr)
ae_activity <- read_csv("data/weekly_ae_activity_20240609.csv")

One small bit of cheating: renaming

names(ae_activity) <- c("date", "country", "hb", "loc", "type", "attend", "n_within", "n_4", "perc_4", "n_8", "perc_8", "n_12", "perc_12")

Preview

Preview of data
date country hb loc type attend n_within n_4 perc_4 n_8 perc_8 n_12 perc_12
20151115 S92000003 S08000028 W107H Emergency Department 107 107 0 100.0 0 0.0 0 0.0
20190707 S92000003 S08000020 N101H Emergency Department 1242 1073 169 86.4 5 0.4 0 0.0
20190602 S92000003 S08000025 R103H Emergency Department 122 116 6 95.1 1 0.8 0 0.0
20200802 S92000003 S08000032 L308H Emergency Department 1275 1132 143 88.8 16 1.3 1 0.1
20240512 S92000003 S08000015 A111H Emergency Department 1292 813 479 62.9 186 14.4 99 7.7

Removing data

ae_activity <- ae_activity |>
    select(!c(country, contains("perc_")))
Preview of data
date hb loc type attend n_within n_4 n_8 n_12
20200927 S08000024 S319H Emergency Department 858 837 21 0 0
20181014 S08000020 N121H Emergency Department 330 325 5 0 0
20160821 S08000017 Y144H Emergency Department 238 233 5 0 0
20220619 S08000031 G405H Emergency Department 1706 723 983 254 41
20151025 S08000030 T101H Emergency Department 850 839 11 0 0

Tidying data

ae_activity <- ae_activity |>
    mutate(date = lubridate::ymd(date))
Preview of data
date hb loc type attend n_within n_4 n_8 n_12
2024-05-26 S08000020 N101H Emergency Department 1050 475 575 248 88
2016-08-14 S08000016 B120H Emergency Department 538 510 28 0 0
2015-05-17 S08000020 N101H Emergency Department 1074 1038 36 3 0
2019-02-24 S08000031 G405H Emergency Department 1947 1487 460 41 2
2016-10-30 S08000017 Y146H Emergency Department 634 616 18 0 0

Subset data

  • we’ll take a random selection of 5 health boards to keep things tidy
ae_activity <- ae_activity |>
    filter(hb %in% boards)
Preview of data
date hb loc type attend n_within n_4 n_8 n_12
2022-06-05 S08000030 T202H Emergency Department 541 492 49 3 0
2021-02-28 S08000022 C121H Emergency Department 81 81 0 0 0
2018-11-04 S08000022 H103H Emergency Department 155 152 3 0 0
2017-07-02 S08000032 L106H Emergency Department 1235 1208 27 2 0
2018-09-23 S08000017 Y146H Emergency Department 671 605 66 2 0

Basic plots

library(ggplot2)
ae_activity |>
    ggplot() +
    geom_line(aes(x = date, y = attend, colour = hb, group = loc))

Joining data

ae_activity |>
    left_join(read_csv("data/boards_data.csv"), by = c("hb" = "HB")) |>
    select(!any_of(c("_id", "HB", "HBDateEnacted", "HBDateArchived", "Country"))) |>
    ggplot() +
    geom_line(aes(x = date, y = attend, colour = HBName, group = loc))

and again…

Add to a map

ae_activity_loc |>
    leaflet::leaflet() |>
    leaflet::addTiles() |>
    leaflet::addMarkers(~longitude, ~latitude, label = ~HospitalName)

Then make that map more useful

ae_activity_loc |>
    group_by(HospitalName) |>
    summarise(attend = sum(attend), n_within = sum(n_within), longitude = min(longitude), latitude = min(latitude)) |>
    mutate(rate = paste(HospitalName, "averages", scales::percent(round(n_within / attend, 1)))) |>
    leaflet::leaflet() |>
    leaflet::addTiles() |>
    leaflet::addMarkers(~longitude, ~latitude, label = ~rate)

Then add to reports, dashboards…

Strengths

  • enormous scope and flexibility
  • a force-multiplier for fancier data work
    • helps collaboration within teams, between teams, between orgs
    • reproducible analytics
    • modular approaches to large projects
  • decreasing pain curve: the fancier the project, the better

Weaknesses

  • harder to learn than competitors
  • very patchy expertise across H+SC Scotland
  • complex IG landscape
  • messy skills development journey