Why Clinical Laboratorians Should Embrace the R Programming Language | Hacker News Reader

Why Clinical Laboratorians Should Embrace the R Programming Language

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49 pointsteleforce60 comments

I basically worked as an R troubleshooter in a Pharmaceutical company, and honestly I wish python or Julia would take its place. There's so many instances when R would return a nonsense answer rather than fail, but you wouldn't realise until you did a deep dive of someone's code.

It would be so easy to write a very similar article on why clinical laboratories show NOT use 'R' in their analyses. I use 'R' extensively for data presentation, but I am constantly bitten by plots that look great, but do not in fact represent the data, because of some weird "factor" issue. I have never used a language where it is so easy to get beautiful results that are wrong. 'R' has very limited error checking, if it can figure out a way to do something (incorrectly), it's happy to do it. With its hidden 'statefulness' and tricky 'factor' effects, it would be a disaster in the clinical setting. Clinical labs need languages and procedures that will fail, rather than present an incorrect result. Unfortunately, 'R' does the opposite.

So the question is, who was writing the code and why were they so evidently incompetent? Easy for anyone to pick up a bit of R and start working with it. Thus it's hardly surprising to find the situation you describe. Why weren't these folk put through a rigorous course before being let loose in a pharmaceutical company of all places? Hardly their fault unless they exaggerated their skills.

My goto resource on this would be aRrgh which goes through some of the many rough edges of the language. Silent failures and data type castings can bite even those experienced in the language.

R is a data analysis DSL that also happens to be a full programming language.

[0] http://arrgh.tim-smith.us/

While your standards could be different from mine, I don’t think that all programmers who fail to write perfect code the first time are incompetent. Many competent programmers are not perfect, and rely on error messages and debuggers to produce correct code. Unfortunately, R does often fails to give the information required to find bugs.

So many dynamic languages take this strange ethos of never wanting to throw an error and instead just guessing what the programmer meant and just doing something wacky instead of throwing an error. It's a real problem.

Reasons I prefer R to python:

- Rmarkdown. I prefer a text document over a web notebook for exploratory research

- The standard library is for statistics and data: dataframe, lm, anova, etc. are builtin

- A huge range of probability distributions are built-in. I don't need to import extra libs to do simulations.

- Between functional programming techniques and vectorization, I can write very clean and concise code

- Tidyverse and data.table are lovely and coherent approaches to data management. Data.table is fast and memory efficient.

- Advanced models are trustworthy: For example, glmnet, mgcv, nlme, rms are authored by statistical heavyweights, and have accompanying books that are excellent. I don't have the same confidence in python's statsmodels.

- CRAN is easy to use, I can access it from my R session, and there are rarely problems (big thanks to Uwe Ligges)

- Libraries for design of experiments and surveys are available. R supports the entire design -> data management -> model cycle.

- base graphics/lattice/ggplot2 are excellent for plotting. If I need something advanced, I can use grid. If I need vector graphics, I can use tikzDevice for latex.

- Rstudio is a an excellent IDE, and Emacs Speaks Statistics is an excellent Emacs plugin

- It is very easy to get help without going to google. (?foo, ??bar, etc) Documentation is well organized, and the documents often contain citations and relevant links.

- Lots of advanced models can't be found outside of R. Today I fit a splines-on-a-sphere model using mgcv (https://stat.ethz.ch/R-manual/R-patched/library/mgcv/html/sm...)

- Rapid iteration in modeling using Wilkinson notation formulas. Built-in formulas are the actual killer app of R, IMO.

- Things are generally fast, but if you need extra horsepower, plugging into c++ is easy using Rcpp.

- R feels like lisp. Experimentation is easy, and I don't feel forced into any particular paradigm while using R. I have a lot of ways to evaluate code (https://ess.r-project.org/Manual/ess.html#Evaluating-code)

Agreed, also R with vim is really a joy to work with (Nvim-R plugin) I can't replicate the experience with any other IDE. For example, I can define my own key bindings to show a certain summary statistic or a custom plot for the variable I'm at.

Thanks for this. I might give it Nvim-R a shot. I've been using Evil+ESS for a long time, but Emacs runs like a dog on Windows 10.

Does RStudio already work on Linux wayland? Last time it failed because of a QT-component but AFAIK the whole thing is transitioning to electron.

It works as long as you set the right flag before launching it.

To me, R seems more like a cobbled together ecosystem of automation within statistics, rather than an actual language.

Compared with Python the language ergonomics of R are confusing and inconsistent.

I guess momentum and establishment is also a feature in itself though I’ve personally never felt that, one of the selling points, the esoteric statistics packages at the edge would be of any use to me.

The use I’ve seen is reminiscent of Spyder and Notebooks: tangled, unreadable mess of line-by-line execution where people are prone to re-running stuff out of order.

Actually, it most probably reverse. Python, numpy, pandas, etc are cobbled together with duct tape to do what R does elegantly. There is no consistency with Python ecosystem.

Agree. One thing is very clear in the R vs. Python debate is that a lot of programmers seem to know either or, not both.

They are different tools for different purposes.

I know both pretty well at this point, and would say that python is a much better language overall, but the stats/ML parts (especially pandas) are pretty inconsistent with both Python and themselves.

That being said, R is amazing for exploratory work, while Python is better for integrating with the rest of the world.

I see a lot of R is very hard to reproduce use Python, or R is hardly a programming language, and I honestly have to wonder if this is really written in good faith, and on a forum that's supposedly a bastion of Scheme love, no less.

R is far more of a Lisp than Python, and in a field that heavily relies on DSL abstractions (which definitely includes clinical laboratories), R is going to fight you a lot less than most choices.

In regards to packaging, you have MRAN snapshots, you have conda (which will give you binaries on Linux), you have renv, roughly in order of preference. The situation is not ideal, but it's certainly not worse than Python, this is not a hill I'd die on!

Julia might be an exciting and welcome alternative to both; from where I'm sitting, it hardly even enters the conversation currently (in data science where I'm at, it's all Python and R, with Python unfortunately taking by far the larger slice of the pie), but I wish it a bright future, it's a great language.

I would say you could replace R with Python or Julia and do just fine. Anything must be better than SPSS.

That said, R had come a long way in recent years and is enjoyable to use. It is very complete as far as statistics go.

I think that R libraries have edge over Python and Julia in quality and quantity.

If you like to write lots of code, Python might be better. But if you use it in clinical research, R has probably better packages for whatever you need.

R packages are the wild west as far as code quality goes. In one corner you have Hadley Wickam producing phenomenal efforts like tidyverse and ggplot. In the other corner you have a herd of feral cats.

Python gets scrutiny but most packages are on github and feedback can be received. Although, you should read the source code regardless.

EDIT: And I re-emphasize -- never trust the source code, even if the company you work with indemnifies. One commercial product we used in particular had an insidious bug in one of the new time series packages that got corrected with in later versions, but we never would have found it if model testing requirements didn't also require implementing in R or Python. Since the package didn't exist for Python, and we wrote it ourselves, we found the performance issues.

There are different qualities. Code quality and quality of the functionality.

In R you more packages that do what you expect (mathematically) but the implementation is inelegant and slow. Written by someone who knows exactly what they need and what the package should do, but has difficulty of writing it down.

In python you many well implemented neat packages where the code is well implemented and performs well, but is not exactly doing what user need or skips important features because they are conceptually difficult.

> In R you more packages that do what you expect (mathematically)

I disagree with this point explicitly. Many packages are not only poorly written programmatically and systemically, they also produce bad results in common cases and fail silently. This has been discussed well before on our very own YCombinator.

https://news.ycombinator.com/item?id=17308554

> is not exactly doing what user need or skips important features because they are conceptually difficult.

This is why classes are cool. You can extend them, modify them, and so on. Perhaps we should teach this more to fellow data scientists.

https://docs.python.org/3/tutorial/classes.html

> This is why classes are cool

You may be unaware, but there are vast similarities between the object system of R and Python, mostly due to their common inheritance from the Art of the Metaobject protocol. They look very different (generic functions vs classes), but they are equally extensible.

The trouble with R's systems is that there's three of them, and people use whichever works without really understanding any of them, but all the tools are there.

Aware, yes. The point I made before was pointing out that you can implement what you want in Python relatively easy. That R has a wild west set of systems is exactly my point.

I don't really get what you mean.

You said, in the context of ensuring conceptually difficult parts of a model/method were implemented:

> This is why classes are cool. You can extend them, modify them, and so on. Perhaps we should teach this more to fellow data scientists.

I pointed out that both R and Python have similar object systems.

> ou can implement what you want in Python relatively easy.

I don't get why this is necessarily true, but I might be missing something. Can you clarify?

The only thing worse than an object system is...three object systems. I never quite know what is the cool kid implementation, and I don't even like oo.

One’s who come from programming background prefer Python. The one’s who come from scientific or statistics background prefer R.

IME, for production Python rules and for data exploration, graphics, stats and adhoc analysis R rules.

R has much better syntax with tidyverse for data wrangling and even up to models with tidymodels and all. Python in comparison is hard to read.

What... Have you seen the piping syntax in tidyverse? It's incomprehensible unless you put in a lot of effort to understand all that's going on.

What is incomprehensible about it?

Grandparent commenter mentioned the piping syntax, specifically.

I dunno, I got pretty sick of writing head(filter(df, value>10)) and it's (a little) easier to indent as df %>% filter(value>10) %>% head().

It's problematic because people abuse it for everything (300 line pipes are common, sadly) but it's a really useful tool in moderation.

This is such an odd take. I program almost exclusively Python these days and I miss the elegance of piped functions daily.

It depends on what you're doing, there's a lot of genomics related packages for R that do not exist in python.

Exactly. Bioconductor is essential to genomics.

There are some specific advantages that R has over other languages in this context. One is that you can use (almost)* a single source document to produce docx, pdf, and interactive html output.

* I can't quite get htmlwidgets and docx formats to work together in bookdown without using separate commands for the interactive tables (DT and flextable).

Rmarkdown is certainly a big win in terms of reporting and its integration with Rstudio makes it a breeze to work with it

R might be a perfectly fine language, but the culture and ecosystem around R seem to produce a lot of untested, difficult to read code. Globals everywhere, mediocre requirements resolution, and a lack of forced namespacing come to mind. Maybe it's a result of being used by people who are not primarily programmers.

That's my diagnosis. I've tried on and off since at least 2006 to affect the course of that culture, to make managing R packages more tractable.

I'd say the R dev community was then actively hostile to a culture change to support any model other than individual contributors working at their desktop.

Most R is written by people who are not (and mostly don't want to be) professional programmers. This is both a strength (industrial strength discipline specific tools) and a weakness (oh dear lord the code, my eyeeeeees).

It's also important to note that much of the original core of R is based on S, which was developed around the same time as C, so some baggage would be expected.

  > Unlike Excel and many other graphical user interface (GUI)-based programs, R’s reliance on text-based structure makes it straightforward to review at any time the commands used in a data processing pipeline to ensure that the correct steps were taken.
  > Furthermore, the ability to view the underlying commands facilitates transparency and reproducibility of analyses.

The article seems to be targeted at people with zero programming knowledge. The arguments here are valid, but don't rely on R. The title could just have been ".... Should Embrace a Programming Language".

I disagree. As a software engineer, R is a nuisance, it's a terrible language, and I hate doing complicated things in it.

But it's very powerful, it's exactly right for these use cases and its ecosystem is mindbogglingly huge. Also, it tends to be easier to grasp for folks who don't have prior programming knowledge (anecdotal, but I've seen people pick it up very quickly who struggled a lot with, say, Python. And Python is the only language/ecosystem that comes close to R.)

So, yeah, a lot of languages could be used for the use cases in TFA, but R is uniquely suited, weaknesses notwithstanding.

But, to focus on the original article, Clinical Labs, where data analysis is literally the basis for life-and-death decisions, is not a sensible use case.

I run operations for a company that relies heavily on R, and I'd strongly advise against using the language. R's package management system makes reproducing work difficult. We've had to rely on using renv, a snapshot of CRAN (the default source of R packages: some FTP servers), and a bunch of Docker to get vaguely reproducible installs. However, since R installing a package involves compiling that code that you just downloaded from a public FTP server, installs are extremely slow.

I'd recommend python based on the slightly-saner tooling. I've found that python with conda/pipenv/poetry results in mostly reproducible installs of the tools needed to run a computation.

So, I actually get what you mean here, and have used both R and Python in anger for a number of years.

This is all about tradeoffs. Fundamentally, if your package doesn't compile on the latest version of R, it gets removed from CRAN. This means that each version of R has a consistent set of packages that (mostly) work together.

Contrast with Python which does facilitate reproducible builds, because you can hack together ancient versions of Python and make them continue working. I could go into a massive rant here about pip, but it's trending in the right direction now and I don't want to discourage any of the people working on it.

R is better in terms of being able to ensure that for a given R version, any package you install will be compatible, Python is better for making sure that that one application built three years ago keeps working in the same fashion.

Also, it sounds like you're running a nix based system, have you considered (I'm sure you have) using the system packages. For example, the Debian/Ubuntu ones are pretty comprehensive, at the cost of using older versions. I believe that R-studio also have pre-built packages for Linux (but have not tested this) so that could also work.

To be fair, conda is pretty good as a package manager, because it handles the C++/C dependencies. But to your Docker point, that's how I handle the insanity that is python packaging, especially in the data science space, so it may just be an issue with the field itself.

Conda supports R and it gives you R binaries on any platform. We've used this setup for years at my old workplace, and it gives you sane reproducible builds.

I am a clinical laboratorian and i find this article very useful .. Thank you for sharing. Can you help me to explore this field ?

https://r4ds.had.co.nz/ you could use this to get started.

This seems like a reasonable place to start: https://online-learning.harvard.edu/subject/r

Tilman M. Davies’s book, The Book of R: A First Course in Programming and Statistics is a good place to start. See [1].

[1] https://www.amazon.com/Book-First-Course-Programming-Statist...

What do you currently use for data analysis?

I’ve taken courses on statistical computing in R and statistical computing in SAS in my statistics degree. We were always told that SAS is the standard for anything health care, pharmaceutical, or where regulation and publication comes into play.

Anecdotally, my friends who did PhDs in biochem and immunology all used SAS for their data analysis.

Have I been misled or is this up to individual preference?

Software Carpentry community [1] has a few very good tutorial guides and workshops for those who are new to R. Their main aim is for teaching basic laboratory skills for research computing. Others who are already proficient in R can utilize and adopt these materials for their own training and workshops.

The first guide is for clinical settings, doing data analysis for inflammation in patients who have been given a new treatment for arthritis [2]. Another is a general introduction to R for non-programmers using gapminder data for reproducible scientific analysis [3][4].

[1]https://software-carpentry.org/lessons/index.html

[2]http://swcarpentry.github.io/r-novice-inflammation/

[3]http://swcarpentry.github.io/r-novice-gapminder/

[4]https://www.gapminder.org/data/

This is more of a sales pitch for the general concept of programming rather than R in particular. R is as good a choice as any...

My impression is that people outside of maths and statistics are more likely to choose Python than R, because they're able to get started with it more easily.

Conventional programmers seem to be somewhat reluctant to learn R's syntax and adjust their programming model.

Non-programmer types think in maths even less so they like the python "straightforwardness".

R is used almost exclusively in stats. Most in maths use python, c++ (there's a surprising amount of hpc code, e.g. pde solvers and other stuff floating around in c++), matlab, etc.

No more fortran I guess?

From what I've seen, there is actually still people using FORTRAN for Applied Math. I had several professors who use it for CFD.

No.

R is hard to reproduce library setup. Unable to compile and static validation.

R, for all its strengths, seems to have quite a learning curve and a lot of syntax to remember. The other approach is to use a GUI based enviroment such as Easy Data Transform, Alteryx or Knime. These are never going to be quite as flexible as a language-based approach, but they are a lot easier to get started with - especially for people with no programming background.

It's interesting to observe that whenever R is discussed, someone talked that python is better than R in this or that area.

I am a clinical laboratorian and find this article very useful. Can you help me to explore this new field ?

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