R Not Only in Production

I will share what our team has learned from successfully integrating R in all areas of our company's operations. InsightRX is a precision medicine company whose goal is to ensure that each patient receives the right drug at the optimal dose. At InsightRX, R is a first-class language that's used for purposes ranging from customer-facing products to internal data infrastructure, new product prototypes, and regulatory reporting. Using R in this way has given us the opportunity to forge fruitful collaborations with other teams in which we can both learn and teach.

Transcript

1. Kara Woo posit::conf(2023) R not only in production
5. How can the strengths of R, and the people who use it, influence the organization as a whole?
6. Meet Angela
8. Vancomycin can treat MRSA
10. There’s no one dose that works for everyone
11. We use pharmacological models + patient’s unique characteristics to recommend the optimal dose
13. Patient data, lab results, past doses
14. Patient data, lab results, past doses Recommended dose
15. R is core to our product
16. R is core to fulfilling our mission
18. ETL
24. • REST API • Data processing pipeline • Analyses and new models • Model validation • Regulatory reporting • New product prototypes • …
27. { "firstName": "First name", "lastName": "Last name", "dob": "Date of birth", "changeMyPassword": "Change my password", "logout": "Logout", ... } { "firstName": "Vorname", "lastName": "Nachname", "dob": "Geburtsdatum", "changeMyPassword": "Ändere mein Passwort", "logout": "Ausloggen", ... }
28. { "firstName": "First name", "lastName": "Last name", "dob": "Date of birth", "changeMyPassword": "Change my password", "logout": "Logout", ... }
29. { "firstName": "First name", "lastName": "Last name", "dob": "Date of birth", "age": "Age", "changeMyPassword": "Change my password", "logout": "Logout", ... } 👀
30. { "firstName": "First name", "lastName": "Last name", "dob": "Date of birth", "age": "Age", "changeMyPassword": "Change my password", "logout": "Logout", ... } { "firstName": "Vorname", "lastName": "Nachname", "dob": "Geburtsdatum", "changeMyPassword": "Ändere mein Passwort", "logout": "Ausloggen", ... } 👀
31. { "firstName": "First name", "lastName": "Last name", "dob": "Date of birth", "age": "Age", "changeMyPassword": "Change my password", "logout": "Logout", ... } { "firstName": "Vorname", "lastName": "Nachname", "dob": "Geburtsdatum", "age": "Alter", "changeMyPassword": "Ändere mein Passwort", "logout": "Ausloggen", ... } 👀
32. The mindset of R as a first class language empowers us to solve problems.
36. We can do this in R!
37. 💡 Idea
38. 💡 Idea “It works on my machine”
39. 💡 Idea “It works on my machine” ? Final product ? ?
40. 💡 Idea “It works on my machine” ? Final product ? ?
41. Reliability Deployability
42. We need to detect kidney injury accurately, all the time.
44. Elevated creatinine suggests kidney damage Easy, right? • Data gaps • Out of order data • Data in di ff erent units • Missing baseline • Non-numeric data • Data entry errors
45. test_that("AKI stage is calculated correctly", { result <- calc_aki_stage( scr = c(0.7, 1.0), t = c(0, 24), egfr = c(60, 40) ) expect_equal(result$stage, "stage 1") })
46. test_that("AKI stage is calculated correctly", { result <- calc_aki_stage( scr = c(0.7, 1.0), t = c(0, 24), egfr = c(60, 40) ) expect_equal(result$stage, "stage 1") })
47. test_that("AKI stage is calculated correctly", { result <- calc_aki_stage( scr = c(0.7, 1.0), t = c(0, 24), egfr = c(60, 40) ) expect_equal(result$stage, "stage 1") })
48. test_that("AKI stage is calculated correctly", { result <- calc_aki_stage( scr = c(0.7, 1.0), t = c(0, 24), egfr = c(60, 40) ) expect_equal(result$stage, "stage 1") })
49. test_that("stage correct: 0.3 mg/dl rise", { # ... }) test_that("stage correct: 1.5x baseline rise", { # ... }) test_that("sorts times correctly", { # ... }) test_that("handles non-numeric inputs", { # ... }) test_that("handles only 1 observation", { # ... })
50. Jenny Bryan “If you use software that lacks automated tests, you are the tests.”
51. Get latest code Build the R package Run the tests Continuous integration
52. 5d01863 Add function to detect AKI ✅ a28vf11 Rewrite AKI function to improve performance ❌ 682hcKa Fix handling of missing data ✅
53. Continuous integration • Find bugs quickly • Be lazy free up time for more important work • Make sure the code continues to behave as intended
54. 💡 Idea “It works on my machine” ? Final product Testing Continuous Integration
55. 💡 Idea “It works on my machine” Docker Final product Testing Continuous Integration
56. R R packages your code Docker
57. FROM rstudio/plumber:v1.1.0 RUN Rscript -e "install.packages('clinPK')" COPY . /myproject WORKDIR /myproject ENTRYPOINT ["Rscript", "entrypoint.R"] Dockerfile
58. FROM rstudio/plumber:v1.1.0 RUN Rscript -e "install.packages('clinPK')" COPY . /myproject WORKDIR /myproject ENTRYPOINT ["Rscript", "entrypoint.R"] Dockerfile
59. FROM rstudio/plumber:v1.1.0 RUN Rscript -e "install.packages('clinPK')" COPY . /myproject WORKDIR /myproject ENTRYPOINT ["Rscript", "entrypoint.R"] Dockerfile
60. FROM rstudio/plumber:v1.1.0 RUN Rscript -e "install.packages('clinPK')" COPY . /myproject WORKDIR /myproject ENTRYPOINT ["Rscript", "entrypoint.R"] Dockerfile
61. FROM rstudio/plumber:v1.1.0 RUN Rscript -e "install.packages('clinPK')" COPY . /myproject WORKDIR /myproject ENTRYPOINT ["Rscript", "entrypoint.R"] Dockerfile
62. FROM rstudio/plumber:v1.1.0 RUN Rscript -e "install.packages('clinPK')" COPY . /myproject WORKDIR /myproject ENTRYPOINT ["Rscript", "entrypoint.R"] Dockerfile https://github.com/karawoo/dockerdemo
63. Image: Royyan Razka, Noun Project
64. Get latest code Build the 
 R package Run the tests Continuous integration
65. Get latest code Build the docker image Run the tests Continuous integration
66. 💡 Idea “It works on my machine” Docker Final product Testing Continuous Integration
69. We are motivated to answer questions
71. Database query was too slow
72. Database query was too slow Added an index to the database
73. Database query was too slow Added an index to the database Data processing pipeline was too slow
74. Database query was too slow Added an index to the database Data processing pipeline was too slow Removed the index
76. If you can’t make changes because you’re afraid of breaking something, it’s already broken.
78. We can visualize and communicate our findings
80. Tests test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... })
81. Tests test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) test_that("...", { # ... }) become data
83. We are used to dealing with uncertainty
86. Motivated to answer questions Skilled at visualizing and communicating results Able to handle uncertainty
88. Using R throughout the stack = doing science throughout the stack
90. pos.it/slido-keynote