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These patterns appear in many fields. I take it as a sign that the tooling in the field is underdeveloped. This leads to a split between domain problem solvers
by civilized 3y ago
These patterns appear in many fields. I take it as a sign that the tooling in the field is underdeveloped.
This leads to a split between domain problem solvers, who are driven to solve the field's actual problems at all costs (including unreliable code that produces false results) and software engineers, who keep things tidy but are too risk-averse to attempt any real problems.
I encourage folks with interests in both software and an area of application to look at what Hadley Wickham did for tabular data analysis and think about what it would look like to do that for your field.
- pas 3y agojournals, research universities/institutions, and grant orgs have the resources and gatekeeping role to encourage and enforce standards, train and support investigators in conducting real science not just pseudoscience, but these entities are actively disowning their responsibility in the name of empty "empowerment" (of course because rationally no one has a real chance of successfully pushing through a reform, so the smart choice is to just not rock the boat)
- fifilura 3y agoCan you elaborate on your thoughts regarding Wickham?
- MostlyStable 3y agoNot the person you are replying to, but here are my thoughts: He wrote the tidyverse package/group of packages which includes/is tightly associated with ggplot. It is an extensive set of tools for analyzing and plotting data. None of it is can't be done in base or or with existing packages, but it streamlined the process. It is an especially big improvement when doing grouped/apply functions, which, in my experience, is a huge part of scientific data analysis. For many R users (especially those trained in the past 5 years or so) tidyverse and ggplot are barely distinguishable as libraries as opposed to core R features. I personally don't like ggplot for plotting and do all my figures in base R graphics, but the rest of tidyverse has dramatically improved my workflow. Thanks to tidyverse, while my code is by no means perfect (I agree with all the aforementioned criticisms of academic coding, especially in biology/ecology), it is cleaner, more legible, and more reproducible in large part thanks to tidyverse.
- fifilura 3y agoMy interpretation: Good APIS, preferably declarative, allows the scientist to write concise code. Win.
- mannykannot 3y agoUnreliable code that produces false results does not solve the field's actual problems, and is likely to contribute to the reproducibility problem. It might solve the author's immediate problem of needing to publish something. Update: I guess I misinterpreted OP's intent here, with "unreliable code that produces false results" being part of the field's actual problems rather than one of the costs to be borne.
- civilized 3y agoI meant that the drive to solve problems at all costs can be self-defeating if you overextend yourself by making unreliable code that produces false results.
- noobermin 3y agoMay be biology (or really, may be not) but honestly it's just the nature of the beast. Literally fortran is the oldest language, it's just the attitude and spirit is different than that of software development.