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Scope of the possible with R
R
overview
Session materials
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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
Load that data
One small bit of cheating: renaming
Preview
date | country | hb | loc | type | attend | n_within | n_4 | perc_4 | n_8 | perc_8 | n_12 | perc_12 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
20211003 | S92000003 | S08000016 | B120H | Emergency Department | 511 | 421 | 90 | 82.4 | 12 | 2.3 | 5 | 1 |
20190414 | S92000003 | S08000019 | V217H | Emergency Department | 1237 | 1091 | 146 | 88.2 | 4 | 0.3 | 0 | 0 |
20190526 | S92000003 | S08000031 | C418H | Emergency Department | 1443 | 1280 | 163 | 88.7 | 17 | 1.2 | 0 | 0 |
20180211 | S92000003 | S08000022 | H103H | Emergency Department | 139 | 134 | 5 | 96.4 | 1 | 0.7 | 0 | 0 |
20200719 | S92000003 | S08000024 | S319H | Emergency Department | 743 | 731 | 12 | 98.4 | 1 | 0.1 | 0 | 0 |
Removing data
ae_activity <- ae_activity |>
select(!c(country, contains("perc_")))
date | hb | loc | type | attend | n_within | n_4 | n_8 | n_12 |
---|---|---|---|---|---|---|---|---|
20220320 | S08000026 | Z102H | Emergency Department | 116 | 116 | 0 | 0 | 0 |
20150329 | S08000017 | Y144H | Emergency Department | 265 | 255 | 10 | 1 | 0 |
20180805 | S08000016 | B120H | Emergency Department | 606 | 562 | 44 | 6 | 1 |
20170305 | S08000032 | L308H | Emergency Department | 1298 | 1042 | 256 | 33 | 5 |
20180812 | S08000024 | S308H | Emergency Department | 1122 | 974 | 148 | 14 | 2 |
Tidying data
ae_activity <- ae_activity |>
mutate(date = lubridate::ymd(date))
date | hb | loc | type | attend | n_within | n_4 | n_8 | n_12 |
---|---|---|---|---|---|---|---|---|
2022-03-06 | S08000025 | R103H | Emergency Department | 119 | 112 | 7 | 0 | 0 |
2021-10-10 | S08000029 | F704H | Emergency Department | 1208 | 855 | 353 | 99 | 9 |
2020-06-28 | S08000031 | C313H | Emergency Department | 417 | 404 | 13 | 0 | 0 |
2017-08-20 | S08000022 | C121H | Emergency Department | 161 | 160 | 1 | 0 | 0 |
2017-04-30 | S08000031 | C313H | Emergency Department | 658 | 632 | 26 | 0 | 0 |
Subset data
- we’ll take a random selection of 5 health boards to keep things tidy
date | hb | loc | type | attend | n_within | n_4 | n_8 | n_12 |
---|---|---|---|---|---|---|---|---|
2022-01-16 | S08000015 | A111H | Emergency Department | 871 | 658 | 213 | 119 | 91 |
2021-04-25 | S08000015 | A111H | Emergency Department | 1174 | 1084 | 90 | 17 | 6 |
2023-01-08 | S08000030 | T202H | Emergency Department | 418 | 381 | 37 | 1 | 0 |
2022-06-19 | S08000026 | Z102H | Emergency Department | 171 | 164 | 7 | 0 | 0 |
2016-02-28 | S08000025 | R103H | Emergency Department | 86 | 85 | 1 | 0 | 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