Counting lines of code

Was asked recently about how many lines of python code was in my most recent project. A simple command line check, cd into your project directory and run:

find -type f -name "*.py" | xargs wc -l

(If on windows, you can download the GOW tools to be able to use these same tools by default available on unix/mac.) This will include whitespace and non-functional lines (like docstrings), but that I think is ok. Doing this for my current main project at Gainwell, I have about 30k lines of python code. Myself (and now about 4 other people) have been working on that code base for nearly a year.

For my first production project at (then) HMS, the total lines of python code are 20k, and I developed the bulk of that in around 7 months of work. Assuming 20 work days in a month, that results in around 20000/140 ~ 143 lines of code per workday. I did other projects during that time span, but this was definitely my main focus (and I was the sole developer/data scientist). I think that is high (more code is not necessarily better, overall code might have decreased as future development of this project happened over time), but is ballpark reasonable expectations for working data scientists (I would have guessed closer to around 100 per day). In the grand scheme of things, this is like 2 functions or unit tests per work day (when considering white space and docstrings).

Doing this for all of my python code on my personal machine is around 60k (I do around, as I am removing counts for projects that are just cloned). And for all the python code on my work machine is around 140k (for 3 years of work). (I am only giving fuzzy numbers, I have some projects joint work I am half counting, and some cloned code I am not counting at all.)

Doing this same exercise for R code, I only get around 40k lines of code on my personal machine. For instance, my ptools package has under 3k lines of "*.R" code total. I am guessing this is due to not only R code being more precise than python, but to take code into production takes more work. Maybe worth another blog post, but the gist of the difference between an academic project is that you need the code to run one time, whereas for a production project the code needs to keep running on a regular schedule indefinitely.

I have written much more SPSS code over my career than R code, but I have most of it archived on Dropbox, so cannot easily get a count of the lines. I have a total of 1846 sps files (note that this does not use xargs).

find -type f -name "*.sps" | wc -l

It is possible that the average sps file on my machine is 200 lines per file (it definitely is over 100 lines). So my recent python migration I don’t think has eclipsed my cumulative SPSS work going back over a decade (but maybe in two more years will).

Outputs vs Outcomes and Agile

For my criminal justice followers, there is a project planning strategy, Agile, that dominates software engineering. The idea behind Agile is to formulate plans in short sprints (we do two week sprints at my work). So we have very broad based objectives (Epics) that can span a significant amount of time. Then we have shorter goals (Stories) that are intended to take up the sprint. Within each story, we further break down our work into specific tasks that we can estimate how long they will take. So something at my work may look like:

  • Build Model to Predict Readmission for Heart Attacks (Epic)
    • Create date pipeline for training data (Story)
      • SQL functions to prepare data (Task, 2 days)
      • python code to paramaterize SQL (Task, 3 days)
      • Unit tests for python code (Task, 1 day)
    • Build ML Model (Story)
      • evaluate different prediction models (Task, 2 days)
    • Deploy ML Model in production (Story)

Etc. People at this point often compare Agile vs Waterfall, where waterfall is more longish term planning (often on say a quarterly schedule). And Agile per its name is suppossed to be more flexible, and modify plans on short term. Most of my problems with Agile could apply though to Waterfall planning as well – short term project planning (almost by its nature) has to be almost solely focused on outputs and not outcomes.

Folks with a CJ background will know what I am talking about here. So police management systems often contrast focusing on easily quantifiable outputs, such as racking up traffic tickets and low level arrests, vs achieving real outcomes, such as increased traffic safety or reducing violent crime. While telling police officers to never do these things does not make sense, you can give feedback/nudge them to engage in higher quality short term outputs that should better promote those longer term outcomes you want.

Agile boards (where we post these Epics/Stories/Tasks, for people to keep tabs on what everyone is doing) are just littered with outputs that have little to no tangible connection to real life outcomes. Take my Heart Attack example. It may be there is a current Heart Attack prediction system in place based on a simple scorecard – utility in that case would be me comparing how much better my system is than the simpler scorecard method. If we are evaluating via dollars and cents, it may only make sense to evaluate how effective my system is in promoting better health outcomes (e.g. evaluating how well my predictive system reduces follow up heart attacks or some other measure of health outcomes).

The former example is not a unit of time (and so counts for nothing in the Agile framework). Although in reality it should be the first thing you do (and drop the project if you cannot sufficiently beat a simple baseline). You don’t get brownie points for failing fast in this framework though. In fact you look bad, as you did not deliver on a particular product.

The latter example unfortunately cannot be done in a short time period – we are often talking about timescales of years at that point instead of weeks. People can look uber productive on their Agile board, and can easily accomplish nothing of value over broad periods of time.

Writing this post as we are going through our yearly crisis of “we don’t do Agile right” at my workplace. There are other more daily struggles with Agile – who defines what counts as meeting an objective? Are we being sufficiently specific in our task documentation? Are people over/under worked on different parts of the team? Are we estimating the time it takes to do certain tasks accurately? Does our estimate include actual work, or folds in uncertainty due to things other teams are responsible for?

These short term crises of “we aren’t doing Agile right” totally miss the boat for me though. I formulate my work strategy by defining end goals, and then work backwards to plan the incremental outputs necessary to achieve those end goals. The incremental outputs are a means to that end goal, not the ends themselves. I don’t really care if you don’t fill out your short term tasks or mis-estimate something to take a week instead of a day – I (and the business) cares about the value added of the software/models you are building. It isn’t clear to me that looking good on your Agile board helps accomplish that.

Over 10 years of blogging

I just realized the other day that I have been blogging for over 10 years (I am old!) First hello world post post was back in December 2011.

I would recommend folks in academia/coding to at a minimum do a personal webpage. I use wordpress for my blog (did a free wordpress for quite a long time). WordPress is 0 code to make a personal page to host your CV.

I treat the blog as mostly my personal nerd journal, and blog about things I am working on or rants on occasion. I do not make revenue off of the blog directly, but in terms of getting me exposure it has given quite a few consulting leads over the years. As well as just given my academic work a much wider exposure.

So I always have a few things I want to blog about in the hopper. But always feel free to ask me anything (similar to how Andrew Gelman answers emails), and if I get a chance I will throw up a blog post in response.

Some peer review ideas

I recently did two more reviews for Crime Solutions. I actually have two other reviews due, in which I jumped Crime Solutions up in my queue. This of course is likely to say nothing about anyone but myself and my priorities, but I think I can attribute this behavior to two things:

  1. CrimeSolutions pays me to do a review (not much, $250, IMO I think I should get double this but DSG said it was pre-negotiated with NIJ).
  2. CrimeSolutions has a pre-set template. I just have to fill in the blanks, and write a few sentences to point to the article to support my score for that item.

Number 2 in particular was a determinant in me doing the 2nd review CrimeSolutions forwarded to me in very short order. After doing the 1st, I had the template items fresh in my mind, and knew I could do the second with less mental overhead.

I think these can, on the margins, improve some of the current issues with peer reviews. #1 will encourage more people to do reviews, #2 will improve the reliability of peer reviews (as well as make it easier for reviewers by limiting the scope). (CrimeSolutions has the reviewers hash it out if we disagree about something, but that has only happened once to me so far, because the template to fill in is laid out quite nicely.)

Another problem with peer reviews is not just getting people to agree to review, but to also to get them to do the review in a timely manner. For this, I suggest a time graded pay scale – if you do the review faster, you will get paid more. Here are some potential curves if you set the pay scale to either drop linearly with number of days or a logarithmic drop off:

So here, if using the linear scale and have a base rate of $300, if you do the review in two weeks, you would make $170, but if you take the full 30 days, you make $10. I imagine people may not like the clock running so fast, so I also devised a logarithmic pay scale, that doesn’t ding you so much for taking a week or two, but after that penalizes you quite heavily. So at two weeks is just under $250.

I realize pay is unlikely to happen (although is not crazy unreasonable, publishers extract quite a bit of rents from University libraries to subscriptions). But standardized forms are something journals could do right now.

Reversion in the tech stack and why DS models fail

Hackernews recently shared a story about not using an IDE, and I feel mostly the same way. Hence the title in the post – so my current workflow for when I steal some time to work on my R package ptools my workflow looks like this, using Rterm from the shell:

I don’t have anything against RStudio, I just only have so much room in my brain. Sometimes conversations at work are like a foreign language, “How are we going to test the NiFi script from Hadoop to our Kubernetes environment” or “I can pull the docker image from JFrog, but I run out of room when extracting the image on our sandbox machine. But df says we have plenty of room on all the partitions?”.

If you notice at the top the (base) in front of the shell, that is because this is within the anaconda shell as well. So if you look at many of my past blog posts (see here for one example), I am just using the snipping tool in windows to take screenshots of the shell output in interactive mode.

I am typically just writing the code in Notepad++ (as well as this blog post) – and it is quite simple to switch between interactive copy this function/code and compiling entire scripts. Here is a screenshot of R unit tests for example.

So Notepad++ has some text highlight (for both R and python), and that is nice, but honestly not that necessary. Main thing I use is the selection of brackets to make sure they are balanced. I am sure I am missing out on some nice autocomplete features that would make me more productive, and function hints in Spyder are nice for pandas functions (I mostly use google still though for that when I need it).

I do use VS Code for development work on our headerless virtual machines at work. But that is more to replicate essentially the workflow on Windows with file explorer + Notepad++ + Shell (I am not a vim ninja – what is it esc + wq:, need to look that up everytime). I fucked up one of my git repos the other day using VS Code stuff tools, and I am just using git directly anymore. (Again this means I am the problem, not VS Code!)

Why data science projects fail?

Some more random musings, but the more I get involved and see what projects work and what don’t at work, pretty much all of the failures I have come across are due to what I will call “not modeling the right thing”. That potentially covers a bit, but quite a few are simply not understanding counterfactual reasoning and selection bias.

The modeling part (in terms of actually fitting models) is typically quite easy – you do some simple but slightly theoretically informed feature engineering and feed that info into a machine learning model that is very flexible. But maybe that is the problem, people can easily fool themselves into thinking a model looks good, but because they are modeling the wrong thing it does not result in better decision making.

Even in most of the failures I have seen, selection bias is surmountable (often just requires multiple models or models on different samples of data – reduced form for the win!). So learning how to train/test split the data, and feed your data into XGboost only takes a few classes to learn. How to know the right thing to model though takes a bit more thought.

A secondary part of the failure is not learning how to translate the model outputs into actionable decisions. But the not modeling the right thing is at the start, so makes any downstream decision not work out how you want.

Ask me anything

So I get cold emails probably a few times a month asking random coding questions (which is perfectly fine — main point of this post!). I’ve suggested in the past that folks use a few different online forums, but like many forums I have participated in the past they died out quite quickly (so are not viable alternatives currently).

I think going forward I will mimic what Andrew Gelman does on his blog, just turn my responses into blog posts for everyone (e.g. see this post for an example). I will of course ask people permission before I post, and omit names same as Gelman does.

I have debated over time of doing a Patreon account, but I don’t think that would work very well (imagine I would get 1.2 subscribers for $3 a month!). Ditto for writing books, I debate on doing a Data Science for Crime Analysts in Python or something along those lines, but then I write the outline and think that is too much work to have at best a few hundred people purchase the book in the end. I will do consulting gigs for folks, but the majority of questions people ask do not take long enough to justify running a tab for the work (and I have no desire to rack up charges for grad students asking a few questions).

So feel free to ask me anything.

CrimRxiv, Alt-Journal Contributions, and Mike Maltz’s Retrospective

As I’m sure followers of mine know, I am a big proponent of posting pre-prints. Spearheaded by Scott Jacques, he has started a specifically criminology focused pre-print server title CrimRxiv. It is still in beta but anyone can contribute a paper if they want.

One of the things me and Scott have been jamming about is how to leverage crimrxiv to make a journal that not only takes advantage of all the goodies on the internet, such as being able to embed interactive graphics or other rich media directly in a journal articles. But to really widen the scope of what ‘counts’ in terms of scholarly contribution. Why can’t things like a cool app, or a really good video lecture you edited, or a blog post illustrating code be put on the same level with journal articles?

Part of the reason I am writing this blog post is that I saw Michael Maltz recently publish a retrospective on his career on Academia.edu. This isn’t a typical journal article, but despite that there is no reason why you shouldn’t share such pieces. So I was able to convince Mike to post A Retrospective Look at My Professional Life to crimrxiv. When he first posted it on Academia.edu here was my response on how Mike (despite never having crossed paths) has influenced my career.


Hi Michael and thank you for sharing,

I’ve followed your work since a grad student at Albany. I initially got hooked on data viz based on Tufte’s book. When I looked for examples of criminologists discussing data viz you were the only one I found. That was sometime around 2010, so you had that chapter in the handbook of quantitative crim. You also had another article about drawing glyphs to illustrate life course transitions I was familiar with.

When I finished my classes at SUNY, I then worked at Troy as a crime analyst while finishing my dissertation. I doubt any of the coffee shops were the same from your time, but I did like walking over to Famous hotdogs for lunch every now and then.

Most of my work at the PD was making time series graphs and maps. No regression, so most of my stats training was not particularly useful. Even my mapping course I took focused on areal data analysis was not terribly relevant.

I tried to do similar projects to your glyph life-courses with interval censored crime data, but I was never really successful with that, they always ended up being too complicated with even moderately large crime datasets, see https://andrewpwheeler.com/2013/02/28/interval-graph-for-viz-temporal-overlap-in-crime-events/ and https://andrewpwheeler.com/2014/10/02/stacking-intervals/ for my attempts.

What was much more helpful was simply doing monitoring metrics over time, simple running means, and then I just inverted the PDF of the Poisson to give error bars, e.g. https://andrewpwheeler.com/2016/06/23/weekly-and-monthly-graphs-for-monitoring-crime-patterns-spss/. Then cases that were outside the error bands signified an anomalous pattern. In Troy there was an arrest of a single prolific person breaking into cars, and the trend went from a creeping 10 year high to a 10 year low instantly in those graphs.

So there again we have your work on the Poisson distribution and operations research in that JQC article. Also sometime in there I saw a comment you made on Andrew Gelman’s blog pointing to your work with error bands for BJS. Took that ‘fan chart’ idea later on and provided error bands for city level and USA level homicide trends, e.g. https://apwheele.github.io/MathPosts/FanChart_NewOrleans.html. Most of popular discussion of large scale crime trends is misguided over-interpreting short term noise in my opinion.

So all my degrees are in criminal justice, but I have been focusing more on linear programming over time borrowing from operations researchers as well, https://andrewpwheeler.com/2020/05/29/an-intro-to-linear-programming-for-criminologists/. I’ve found that taking outputs from a predictive model and then applying a decision analysis to specifically articulate strategies CJ agencies should take is much more fruitful than the typical way academic research is done.

Thank you again for sharing your story and best, Andy Wheeler

Deleted Twitter Account

I’ve decided to delete Twitter. It is for multiple reasons in the end.

Reason 1, I was definitely addicted to it. Checked it quite often during the daytime. Deleting off of my phone (and ditto for email) was a good first step, but I still checked it quite a bit when I was on my personal computer.

Reason 2 — there is a XKCD comic about staying up arguing with people on the internet. I was constantly tempted to do this on Twitter. It is never really worth it. Many of the examples that come to mind I did this — had a comment stream with Pete Kraska the other day about grant funding, and in the past Travis Pratt over pre-prints — Pete/Travis had an ounce of truth in their initial statements, but made sweeping generalizations that don’t describe the majority of people (which included me, hence my urge to respond). While they likely did not intend to say something directly about me, they did so in making general stereotyping comments.

I respect each as scholars, but they just have ill-informed opinions in those cases. You would think criminologists would be less likely to attribute the malice of a few to widespread groups of individuals, but so it goes. No doubt I have bad/wrong opinions all the time as well.

Reason 3, a former colleague the other day was upset I liked a tweet that was a critique of their work. This is just one example, but there are a million different things people could take offense to. I am not interested in even the potential of saying or doing something that would result in a sandbag onslaught I’ve seen several times on Twitter. I of course do not intentionally mean to hurt peoples feelings, but I do not feel like defending minor stuff like that either. Worrying about things like that is just not good for my mental health.

There are of course good things I will be missing out on. I initially joined Twitter to keep up on the news. Between Google Scholar and CrimPapers I can keep up on academic work. (Actual news I should definately not be getting my info from tweets!) But the biggest benefit in the end was there are several internet friends I only met on Twitter and would not have had the opportunity to meet without Twitter.

And of course it was nice to tweet a blog post and get a dozen likes (or say something snarky and get 30). So my work will have less exposure than before, but honestly it was not much to begin with. My last post had more likes (around a dozen) than referrals from Twitter (around half that!) Not like tweeting my blog posts resulted in 1000’s of views, more like a few dozen extra most of the time (and a few hundred extra in the best of times). So I will just continue to write blog posts, and they will have a few less views than before. I wish my blog had bigger reach but it is really just my place for creative output.

I encourage folks to always reach out and send me an email to keep in touch if you are one of my former Twitter friends. Academia can be a lonely place in normal times, and with isolating in the pandemic I can’t even imagine what it would be like without my family. I don’t think my time spent on Twitter was good for my personal well being though in the end, even though it did definitely help me be part of a larger community of colleagues and friends. 

Resources of interest for criminologists and crime analysts

I tend to get about one email per week asking for help. Majority of folks are either students asking for general research advice, or individuals who came across my webpage asking for advice about code.

This is great, and everyone should always feel open to send me an email. The utility of me answering these questions (for everyone) are likely greater than spending time working on a paper, so I do not mind at all. I can currently keep up with the questions given the volume (but not by much, and is dependent on how busy I am with other work/family things). Worst case I will send an email response that says sorry I cannot respond to this anytime soon.

Many times there are other forums though for people to post questions that are ultimately better. One, I participate in many of these, so it is not like sending an email just to me, it is like sending an email to me + 40 other people who can answer your question. Also from my perspective it is better to answer a question once in one of these forums, than repeat the same answer a dozen different times. (Many times I write a blog post if I get the same question multiple times.)

While the two groups overlap a bit, I separate out resources aimed at criminologists (as typically more interested in research and are current master/PhD students), whereas crime analysts are embedded in a criminal justice agency.

For Criminologists

For resources on where to ask questions, Jacob Kaplan recently created a slack channel, crimhelp.slack.com. It has been joined by a variety of criminologists, folks in think tanks/research institutes, current graduate students, and some working crime analysts. It is new, but you can go and peruse the topics so far, they are pretty wide in scope.

So that forum you can really ask about anything crim related, the remaining resources are more devoted towards programming/statistical analysis.

If you are interested in statistical or programming questions, I used to participate in StackOverflow, Cross Validated (the stats site), and the GIS site. They are good places to check out prior answers, and are worth a shot asking a question on occasion. For tricky python or R coding questions that are small in scope, StackOverflow is excellent. Anything more complicated it is more hit or miss.

Many programming languages have their own question boards. Stata and SPSS are ones I am familiar with and tend to receive good responses (I still actively participate in the SPSS board). If I’m interested in learning some new command/library in Stata, I often just search the forum for posts related to it to check it out in the wild.

For programming questions, it is often useful to create a minimal reproducible example to describe the problem, show what the input data looks like and how you want the output data to look like. (In fact on the forums I link to you will almost always be asked explicitly to do that.)

For Crime Analysts

In similar spirit to the crim slack channel, Police Rewired has a Discord group for crime analysts (not 100% sure who started it, Andreas Varotsis is one of the people involved though). So that was founded by some UK analysts, but there are US analysts participating as well (and the problems folks deal with are very similar, so no real point in making a distinction between US/UK).

For crime analysts in the US, you should likely join either the IACA or a local crime analyst network. Many of the local ones come bundled, so if you join the Texas analyst network TXLEAN you also automatically get an IACA membership. To join is cheap (especially for current students). IACA has also started a user question forum as well.

For folks looking to get an entry level gig, the IACA has a job board that is really good. So it is worth the $10 just for that. They have various other intro resources though as well. For current BA/Masters students who are looking to get a job, I also suggest applying to private sector analyst jobs as well. They are mostly exchangeable with a crime analyst role. (Think more excel jockey than writing detailed statistic programming.)

How I learn to code

What prompted this blog post is that I’ve gotten asked by maybe 5 different people in the past month or so asking for resources to learn about statistical programming. And honestly I do not have a good answer, I’ve never really sat down with a book and learned a statistical software (tried on a few occasions and failed). I’m always just project focused.

So I wanted to do an example conjunctive analysis, or deep learning with pytorch, or using conformal prediction intervals to generate synthetic control estimates, etc. So I just sat down and figured out how to do those specific projects using various resources around the internet. One of my next personal projects is going to estimate prediction intervals for logistic multilevel models using Julia (based on this very nice set of intros to the language). I also need to get a working familiarity with Tableau. (Both are related to projects I am doing at work.) So expect to see a Tableau dashboard on the blog sometime in the near future!

Also many statistical programming languages are pretty much exchangeable for the vast majority of tasks people do. You can see that I have example blog posts for Excel, Access/SQL, R, SPSS, Stata, python, and ArcGIS. Just pick one and figure it for a particular project.

For criminologists, I have posted my Phd research course materials, and for Crime Analysts I have posted my GIS Class and my Crime Analysis course materials (although the GIS course is already out of date, it uses Arc Desktop instead of ArcPro). I don’t suggest you sit down and go through the courses though page-by-page. What I more suggest is look at the table of contents, see if anything strikes your fancy, read that particular lecture/code, and if you want to apply it to your own projects try to work it out. (At least that is how I go about learning coding.)

If you want more traditional learning materials for learning how to do code (e.g. textbooks or online courses), I suggest you ask folks on those forums I mentioned. They will likely be able to provide much better advice than I would.

To end it is totally normal to want to ask questions, get advice, or get feedback. Both my experience in Academia and in Crime Analysis it can be very lonely (I was in a small department, so was the only analyst). Folks on these forums are happy to help and connect.

300 blog posts and public good criminology

This isn’t technically my 300th blog post, but the 300th page I’ve constructed on my blog (so e.g. it includes when I’ve made a page for a class). I’ve posted a spreadsheet of the titles and dates of the posts over time (and updating it I noticed I was at 300).

I typically get around 200~300 views per day. Most of these are probably bots, but unless say over 90% are bots this website gets way more views than the cumulative views of all my academic papers combined. Here is a screen shot of the stats wordpress gives to me. My downtick in 2019 I thought was going to spiral into very few views, but it is still holding on.

I kind of have three different types of blog posts. One are example code snippets/data analysis. Often these are things I have done multiple times, so I want to create a record for me to more easily search up later. For example making a hexbin map in ggplot, or a margins plot in Stata. I wrote a recent post because I was talking with a friend about crime weights, and I wanted an example of using regression in python and an error bar plot for my library. (Quite a few birds with that stone.)

Two are questions I repeatedly encounter by students. For example, I made a list of demographic variables I use in the census, and where to find or scrape crime generator variables. Consistently my most popular post is testing the equality of two regression coefficients.

The third are just more generic opinion pieces. For example my notes on (the now late) David Bayley’s writing on the police potential to reduce crime, or Jane Jacob’s take on neighborhoods, or that I don’t think latent trajectories are real things.

Some are multiple of these categories put together, particularly opinion pieces with example code snippets to illustrate the points I am making. Like a simulation of why I like to model individual delinquency items, or how to balance false positives in bail decisions.

On Public Good Criminology

None of these per se fit in the example framework of typical peer review output. So despite no peer review, I think things like deriving optimal treatment allocation with network spillovers, or that conformal predictions intervals for synthetic control estimates are much smaller than permutation tests are a substantive contribution to share!

So that brings me to the public good point. Most criminologists have a default of only valuing a closed peer review system. Despite my blog posts not being peer reviewed (ditto for the pre-prints I post at first), I hope folks can take the time to judge for themselves whether they are valuable or not. We would be much better off as a group if we did things like share code, share class preps, or failed projects by default.

Some of these posts I might write up if we had a short journal for our field akin to Economics Letters, but even that is a lot of work for very little value added to be frank. (If I had infinite time I also might turn my notes on Poisson/Negative Binomial regression into a little Sage green book.) Being a private sector data scientist now without the tenure boot on my neck, I don’t really have any need or desire to go through that process.

If all you value are getting the opinions of a handful of other academics than by all means keep your work close to the chest and only publish in peer reviewed journals. If you want to provide a public good though, your work actually needs to be public.