Structuring R projects

There are some things that I call Smith goods:1 things I want, nay, require, but hate doing. A clean room is one of these – I have a visceral need to have some semblance of tidiness around me, I just absolutely hate tidying, especially in the summer.2 Starting and structuring packages and projects is another of these things, which is why I’m so happy things like cookiecutter exist that do it for you in Python.

While I don’t like structuring R projects, I keep doing it, because I know it matters. That’s a pearl of wisdom that came occasionally at a great price.
I am famously laid back about structuring R projects – my chill attitude is only occasionally compared to the Holy Inquisition, the other Holy Inquisition and Gunny R. Lee Ermey’s portrayal of Drill Sgt. Hartman, and it’s been months since I last gutted an intern for messing up namespaces.3 So while I don’t like structuring R projects, I keep doing it, because I know it matters. That’s a pearl of wisdom that came occasionally at a great price, some of which I am hoping to save you by this post.

Five principles of structuring R projects

Every R project is different. Therefore, when structuring R projects, there has to be a lot more adaptability than there is normally When structuring R projects, I try to follow five overarching principles.

  1. The project determines the structure. In a small exploratory data analysis (EDA) project, you might have some leeway as to structural features that you might not have when writing safety-critical or autonomously running code. This variability in R – reflective of the diversity of its use – means that it’s hard to devise a boilerplate that’s universally applicable to all kinds of projects.
  2. Structure is a means to an end, not an end in itself. The reason why gutting interns, scalping them or yelling at them Gunny style are inadvisable is not just the additional paperwork it creates for HR. Rather, the point of the whole exercise is to create people who understand why the rules exists and organically adopt them, understanding how they help.
  3. Rules are good, tools are better. When tools are provided that take the burden of adherence – linters, structure generators like cookiecutter, IDE plugins, &c. – off the developer, adherence is both more likely and simpler.
  4. Structures should be interpretable to a wide range of collaborators. Even if you have no collaborators, thinking from the perspective of an analyst, a data scientist, a modeller, a data engineer and, most importantly, the client who will at the very end receive the overall product.
  5. Structures should be capable of evolution. Your project may change objectives, it may evolve, it may change. What was a pet project might become a client product. What was designed to be a massive, error-resilient superstructure might have to scale down. And most importantly, your single-player adventure may end up turning into an MMORPG. Your structure has to be able to roll with the punches.

A good starting structure

Pretty much every R project can be imagined as a sort of process: data gets ingested, magic happens, then the results – analyses, processed data, and so on – get spit out. The absolute minimum structure reflects this:

.
└── my_awesome_project
    ├── src
    ├── output
    ├── data
    │   ├── raw
    │   └── processed
    ├── README.md
    ├── run_analyses.R 
    └── .gitignore

In this structure, we see this reflected by having a data/ folder (a source), a folder for the code that performs the operations (src/) and a place to put the results (output/). The root analysis file (the sole R file on the top level) is responsible for launching and orchestrating the functions defined in the src/ folder’s contents.

The data folder

The data folder is, unsurprisingly, where your data goes. In many cases, you may not have any file-formatted raw data (e.g. where the raw data is accessed via a *DBC connection to a database), and you might even keep all intermediate files there, although that’s pretty uncommon on the whole, and might not make you the local DBA’s favourite (not to mention data protection issues). So while the raw/ subfolder might be dispensed with, you’ll most definitely need a data/ folder.

When it comes to data, it is crucial to make a distinction between source data and generated data. Rich Fitzjohn puts it best when he says to treat

  • source data as read-only, and
  • generated data as disposable.

The preferred implementation I have adopted is to have

  • a data/raw/ folder, which is usually is symlinked to a folder that is write-only to clients but read-only to the R user,4,
  • a data/temp/ folder, which contains temp data, and
  • a data/output/ folder, if warranted.

The src folder

Some call this folder R– I find this a misleading practice, as you might have C++, bash and other non-R code in it, but is unfortunately enforced by R if you want to structure your project as a valid R package, which I advocate in some cases. I am a fan of structuring the src/ folder, usually by their logical function. There are two systems of nomenclature that have worked really well for me and people I work with:

  • The library model: in this case, the root folder of src/ holds individual .R scripts that when executed will carry out an analysis. There may be one or more such scripts, e.g. for different analyses or different depths of insight. Subfolders of src/ are named after the kind of scripts they contain, e.g. ETL, transformation, plotting. The risk with this structure is that sometimes it’s tricky to remember what’s where, so descriptive file names are particularly important.
  • The pipeline model: in this case, there is a main runner script or potentially a small number. These go through scripts in a sequence. It is a sensible idea in such a case to establish sequential subfolders or sequentially numbered scripts that are executed in sequence. Typically, this model performs better if there are at most a handful distinct pipelines.

Whichever approach you adopt, a crucial point is to keep function definition and application separate. This means that only the pipeline or the runner scripts are allowed to execute (apply) functions, and other files are merely supposed to define them. Typically, folder level segregation works best for this:

  • keep all function definitions in subfolders of src/, e.g. src/data_engineering, and have the directly-executable scripts directly under src/ (this works better for larger projects), or
  • keep function definitions in src/, and keep the directly executable scripts in the root folder (this is more convenient for smaller projects, where perhaps the entire data engineering part is not much more than a single script).

output and other output folders

Output may mean a range of things, depending on the nature of your project. It can be anything from a whole D.Phil thesis written in a LaTeX-compliant form to a brief report to a client. There are a couple of conventions with regard to output folders that are useful to keep in mind.

Separating plot output

My personal preference is that plot output folders should be subfolders of output/, rather than top-tier folders, unless the plots themselves are the objective.
It is common to have a separate folder for plots (usually called figs/ or plots/), usually so that they could be used for various purposes. My personal preference is that plot output folders should be subfolders of output folders, rather than top-tier folders, unless they are the very output of the project. That is the case, for instance, where the project is intended to create a particular plot on a regular basis. This was the case, for instance, with the CBRD project whose purpose was to regularly generate daily epicurves for the DRC Zaire ebolavirus outbreak.

With regard to maps, in general, the principle that has worked best for teams I ran was to treat static maps as plots. However, dynamic maps (e.g. LeafletJS apps), tilesets, layers or generated files (e.g. GeoJSON files) tend to deserve their own folder.

Reports and reporting

For business users, automatically getting a beautiful PDF report can be priceless.
Not every project needs a reporting folder, but for business users, having a nice, pre-written reporting script that can be run automatically and produces a beautiful PDF report every day can be priceless. A large organisation I worked for in the past used this very well to monitor their Amazon AWS expenditure.5 A team of over fifty data scientists worked on a range of EC2 instances, and runaway spending from provisioning instances that were too big, leaving instances on and data transfer charges resulting from misconfigured instances6 was rampant. So the client wanted daily, weekly, monthly and 10-day rolling usage nicely plotted in a report, by user, highlighting people who would go on the naughty list. This was very well accomplished by an RMarkdown template that was ‘knit‘ every day at 0600 and uploaded as an HTML file onto an internal server, so that every user could see who’s been naughty and who’s been nice. EC2 usage costs have gone down by almost 30% in a few weeks, and that was without having to dismember anyone!7

Probably the only structural rule to keep in mind is to keep reports and reporting code separate. Reports are client products, reporting code is a work product and therefore should reside in src/.

Requirements and general settings

I am, in general, not a huge fan of outright loading whole packages to begin with. Too many users of R don’t realise that

  • you do not need to attach (library(package)) a package in order to use a function from it – as long as the package is available to R, you can simply call the function as package::function(arg1, arg2, ...), and
  • importing a package using library(package) puts every single function from that package into the namespace, overwriting by default all previous entries. This means that in order to deterministically know what any given symbol means, you would have to know, at all times, the order of package imports. Needless to say, there is enough stuff to keep in one’s mind when coding in R to worry about this stuff.

However, some packages might be useful to import, and sometimes it’s useful to have an initialisation script. This may be the case in three particular scenarios:

  • You need a particular locale setting, or a particularly crucial environment setting.
  • It’s your own package and you know you’re not going to shadow already existing symbols.
  • You are not using packrat or some other package management solution, and definitely need to ensure some packages are installed, but prefer not to put the clunky install-if-not-present code in every single thing.

In these cases, it’s sensible to have a file you would source before every top-level script – in an act of shameless thievery from Python, I tend to call this requirements.R, and it includes some fundamental settings I like to rely on, such as setting the locale appropriately. It also includes a CRAN install check script, although I would very much advise the use of Packrat over it, since it’s not version-sensitive.

Themes, house style and other settings

It is common, in addition to all this, to keep some general settings. If your institution has a ‘house style’ for ggplot2 (as, for instance, a ggthemr file), for instance, this could be part of your project’s config. But where does this best go?

I’m a big fan of keeping house styles in separate repos, as this ensures consistency across the board.
It would normally be perfectly fine to keep your settings in a config.R file at root level, but a config/ folder is much preferred as it prevents clutter if you derive any of your configurations from a git submodule. I’m a big fan of keeping house styles and other things intended to give a shared appearance to code and outputs (e.g. linting rules, text editor settings, map themes) in separate – and very, very well managed! – repos, as this ensures consistency across the board over time. As a result, most of my projects do have a config folder instead of a single configuration file.

It is paramount to separate project configuration and runtime configuration:

  • Project configuration pertains to the project itself, its outputs, schemes, the whole nine yards. For instance, the paper size to use for generated LaTeX documents would normally be a project configuration item. Your project configuration belongs in your config/ folder.
  • Runtime configuration pertains to parameters that relate to individual runs. In general, you should aspire to have as few of these, if any, as possible – and if you do, you should keep them as environment variables. But if you do decide to keep them as a file, it’s generally a good idea to keep them at the top level, and store them not as R files but as e.g. JSON files. There are a range of tools that can programmatically edit and change these file formats, while changing R files programmatically is fraught with difficulties.

Keeping runtime configuration editable

A few years ago, I worked on a viral forecasting tool where a range of model parameters to build the forecast from were hardcoded as R variables in a runtime configuration file. It was eventually decided to create a Python-based web interface on top of it, which would allow users to see the results as a dashboard (reading from a database where forecast results would be written) and make adjustments to some of the model parameters. The problem was, that’s really not easy to do with variables in an R file.

On the other hand, Python can easily read a JSON file into memory, change values as requested and export them onto the file system. So instead of that, the web interface would store the parameters in a JSON file, from which R would then read them and execute accordingly. Worked like a charm. Bottom line – configurations are data, and using code to store data is bad form.

Dirty little secrets

Everybody has secrets. In all likelihood, your project is no different: passwords, API keys, database credentials, the works. The first rule of this, of course, is never hardcode credentials in code. But you will need to work out how to make your project work, including via version control, while also not divulging credentials to the world at large. My preferred solutions, in order of preference, are:

  1. the keyring package, which interacts with OS X’s keychain, Windows’s Credential Store and the Secret Service API on Linux (where supported),
  2. using environment variables,
  3. using a secrets file that is .gitignored,
  4. using a config file that’s .gitignored,
  5. prompting the user.

Let’s take these – except the last one, which you should consider only as a measure of desperation, as it relies on RStudio and your code should aspire to run without it – in turn.

Using keyring

keyring is an R package that interfaces with the operating system’s keychain management solution, and works without any additional software on OS X and Windows.8 Using keyring is delightfully simple: it conceives of an individual key as belonging to a keyring and identified by a service. By reference to the service, it can then be retrieved easily once the user has authenticated to access the keychain. It has two drawbacks to be aware of:

  • It’s an interactive solution (it has to get access permission for the keychain), so if what you’re after is R code that runs quietly without any intervention, this is not your best bet.
  • A key can only contain a username and a password, so it cannot store more complex credentials, such as 4-ple secrets (e.g. in OAuth, where you may have a consumer and a publisher key and secret each). In that case, you could split them into separate keyring keys.

However, for most interactive purposes, keyring works fine. This includes single-item secrets, e.g. API keys, where you can use some junk as your username and hold only on to the password.

For most interactive purposes, keyring works fine. This includes single-item secrets, e.g. API keys.
By default, the operating system’s ‘main’ keyring is used, but you’re welcome to create a new one for your project. Note that users may be prompted for a keychain password at call time, and it’s helpful if they know what’s going on, so be sure you document your keyring calls well.

To set a key, simply call keyring::key_set(service = "my_awesome_service", username = "my_awesome_user). This will launch a dialogue using the host OS’s keychain handler to request authentication to access the relevant keychain (in this case, the system keychain, as no keychain is specified), and you can then retrieve

  • the username: using keyring::key_list("my_awesome_service")[1,2], and
  • the password: using keyring::key_get("my_awesome_service").

Using environment variables

The thing to remember about environment variables is that they’re ‘relatively private’: everyone in the user session will be able to read them.
Using environment variables to hold certain secrets has become extremely popular especially for Dockerised implementations of R code, as envvars can be very easily set using Docker. The thing to remember about environment variables is that they’re ‘relatively private’: they’re not part of the codebase, so they will definitely not accidentally get committed to the VCS, but everyone who has access to the particular user session  will be able to read them. This may be an issue when e.g. multiple people are sharing the ec2-user account on an EC2 instance. The other drawback of envvars is that if there’s a large number of them, setting them can be a pain. R has a little workaround for that: if you create an envfile called .Renviron in the working directory, it will store values in the environment. So for instance the following .Renviron file will bind an API key and a username:

api_username = "my_awesome_user"
api_key = "e19bb9e938e85e49037518a102860147"

So when you then call Sys.getenv("api_username"), you get the correct result. It’s worth keeping in mind that the .Renviron file is sourced once, and once only: at the start of the R session. Thus, obviously, changes made after that will not propagate into the session until it ends and a new session is started. It’s also rather clumsy to edit, although most APIs used to ini files will, with the occasional grumble, digest .Renvirons.

Needless to say, committing the .Renviron file to the VCS is what is sometimes referred to as making a chocolate fireman in the business, and is generally a bad idea.

Using a .gitignored config or secrets file

config is a package that allows you to keep a range of configuration settings outside your code, in a YAML file, then retrieve them. For instance, you can create a default configuration for an API:

default:
    my_awesome_api:
        url: 'https://awesome_api.internal'
        username: 'my_test_user'
        api_key: 'e19bb9e938e85e49037518a102860147'

From R, you could then access this using the config::get() function:

my_awesome_api_configuration <- config::get("my_awesome_api")

This would then allow you to e.g. refer to the URL as my_awesome_api_configuration$url, and the API key as my_awesome_api_configuration$api_key. As long as the configuration YAML file is kept out of the VCS, all is well. The problem is that not everything in such a configuration file is supposed to be secret. For instance, it makes sense for a database access credentials to have the other credentials DBI::dbConnect() needs for a connection available to other users, but keep the password private. So .gitignoreing a config file is not a good idea.

A dedicated secrets file is a better place for credentials than a config file, as this file can then be wholesale .gitignored.
A somewhat better idea is a secrets file. This file can be safely .gitignored, because it definitely only contains secrets. As previously noted, definitely create it using a format that can be widely written (JSON, YAML).9 For reasons noted in the next subsection, the thing you should definitely not do is creating a secrets file that consists of R variable assignments, however convenient an idea that may appear at first. Because…

Whatever you do…

One of the best ways to mess up is creating a fabulous way of keeping your secret credentials truly secret… then loading them into the global scope. Never, ever assign credentials. Ever.

You might have seen code like this:

dbuser <- Sys.getenv("dbuser")
dbpass <- Sys.getenv("dbpass")

conn <- DBI::dbConnect(odbc::odbc(), UID = dbuser, PWD = dbpass)
Never, ever put credentials into any environment if possible – especially not into the global scope.
This will work perfectly, except once its done, it will leave the password and the user name, in unencrypted plaintext (!), in the global scope, accessible to any code. That’s not just extremely embarrassing if, say, your wife of ten years discovers that your database password is your World of Warcraft character’s first name, but also a potential security risk. Never put credentials into any environment if possible, and if it has to happen, at least make it happen within a function so that they don’t end up in the global scope. The correct way to do the above would be more akin to this:

create_db_connection <- function() {
    DBI::dbConnect(odbc::odbc(), UID = Sys.getenv("dbuser"), PWD = Sys.getenv("dbpass")) %>% return()
}

Concluding remarks

Structuring R projects is an art, not just a science. Many best practices are highly domain-specific, and learning these generally happens by trial and pratfall error. In many ways, it’s the bellwether of an R developer’s skill trajectory, because it shows whether they possess the tenacity and endurance it takes to do meticulous, fine and often rather boring work in pursuance of future success – or at the very least, an easier time debugging things in the future. Studies show that one of the greatest predictors of success in life is being able to tolerate deferred gratification, and structuring R projects is a pure exercise in that discipline.

Structuring R projects is an art, not just a science. Many best practices are highly domain-specific, and learning these generally happens by trial and error.
At the same time, a well-executed structure can save valuable developer time, prevent errors and allow data scientists to focus on the data rather than debugging and trying to find where that damn snippet of code is or scratching their head trying to figure out what a particularly obscurely named function does. What might feel like an utter waste of time has enormous potential to create value, both for the individual, the team and the organisation.

As long as you keep in mind why structure matters and what its ultimate aims are, you will arrive at a form of order out of chaos that will be productive, collaborative and useful.
I’m sure there are many aspects of structuring R projects that I have omitted or ignored – in many ways, it is my own experiences that inform and motivate these commentaries on R. Some of these observations are echoed by many authors, others diverge greatly from what’s commonly held wisdom. As with all concepts in development, I encourage you to read widely, get to know as many different ideas about structuring R projects as possible, and synthesise your own style. As long as you keep in mind why structure matters and what its ultimate aims are, you will arrive at a form of order out of chaos that will be productive, collaborative and mutually useful not just for your own development but others’ work as well.

My last commentary on defensive programming in R has spawned a vivid and exciting debate on Reddit, and many have made extremely insightful comments there. I’m deeply grateful for all who have contributed there. I hope you will also consider posting your observations in the comment section below. That way, comments will remain together with the original content.

References   [ + ]

1.As in, Adam Smith.
2.It took me years to figure out why. It turns out that I have ZF alpha-1 antitrypsin deficiency. As a consequence, even minimal exposure to small particulates and dust can set off violent coughing attacks and impair breathing for days. Symptoms tend to be worse in hot weather due to impaired connective tissue something-or-other.
3.That’s a joke. I don’t gut interns – they’re valuable resources, HR shuns dismembering your coworkers, it creates paperwork and I liked every intern I’ve ever worked with – but most importantly, once gutted like a fish, they are not going to learn anything new. I prefer gentle, structured discussions on the benefits of good package structure. Please respect your interns – they are the next generation, and you are probably one of their first example of what software development/data science leadership looks like. The waves you set into motion will ripple through generations, well after you’re gone. You better set a good example.
4.Such a folder is often referred to as a ‘dropbox’, and the typical corresponding octal setting, 0422, guarantees that the R user will not accidentally overwrite data.
5.The organisation consented to me telling this story but requested anonymity, a request I honour whenever legally possible.
6.In case you’re unfamiliar with AWS: it’s a cloud service where elastic computing instances (EC2 instances) reside in ‘regions’, e.g. us-west-1a. There are (small but nonzero) charges for data transfer between regions. If you’re in one region but you configure the yum repo server of another region as your default, there will be costs, and, eventually, tears – provision ten instances with a few GBs worth of downloads, and there’ll be yelling. This is now more or less impossible to do except on purpose, but one must never underestimate what users are capable of from time to time!
7.Or so I’m told.
8.Linux users will need libsecret 0.16 or above, and sodium.
9.XML is acceptable if you’re threatened with waterboarding.

Assignment in R: slings and arrows

Having recently shared my post about defensive programming in R on the r/rstats subreddit, I was blown away by the sheer number of comments as much as I was blown away by the insight many displayed. One particular comment by u/guepier struck my attention. In my previous post, I came out quite vehemently against using the = operator to effect assignment in R. u/guepier‘s made a great point, however:

But point 9 is where you’re quite simply wrong, sorry:

never, ever, ever use = to assign. Every time you do it, a kitten dies of sadness.

This is FUD, please don’t spread it. There’s nothing wrong with =. It’s purely a question of personal preference. In fact, if anything <- is more error-prone (granted, this is a very slight chance but it’s still higher than the chance of making an error when using =).

Now, assignment is no doubt a hot topic – a related issue, assignment expressions, has recently led to Python’s BDFL to be forced to resign –, so I’ll have to tread carefully. A surprising number of people have surprisingly strong feelings about assignment and assignment expressions. In R, this is complicated by its unusual assignment structure, involving two assignment operators that are just different enough to be trouble.

A brief history of <-

IBM Model M SSK keyboard with APL keys
This is the IBM Model M SSK keyboard. The APL symbols are printed on it in somewhat faint yellow.

There are many ways in which <- in R is anomalous. For starters, it is rare to find a binary operator that consists of two characters – which is an interesting window on the R <- operator’s history.

The <- operator, apparently, stems from a day long gone by, when keyboards existed for the programming language eldritch horror that is APL. When R’s precursor, S, was conceived, APL keyboards and printing heads existed, and these could print a single ← character. It was only after most standard keyboard assignments ended up eschewing this all-important symbol that R and S accepted the digraphic <- as a substitute.

OK, but what does it do?

In the Brown Book, the underscore was actually an alias for the arrow assignment operator.
In the Brown Book (Richard A. Becker and John M. Chambers (1984). S: An Interactive Environment for Data Analysis and Graphics), the underscore was actually an alias for the arrow assignment operator! Thankfully, this did not make it into R.
<- is one of the first operators anyone encounters when familiarising themselves with the R language. The general idea is quite simple: it is a directionally unambiguous assignment, i.e. it indicates quite clearly that the right-hand side value (rhs, in the following) will replace the left-hand side variable (lhs), or be assigned to the newly created lhs if it has not yet been initialised. Or that, at the very least, is the short story.

Because quite peculiarly, there is another way to accomplish a simple assignment in R: the equality sign (=). And because on the top level, a <- b and a = b are equivalent, people have sometimes treated the two as being quintessentially identical. Which is not the case. Or maybe it is. It’s all very confusing. Let’s see if we can unconfuse it.

The Holy Writ

The Holy Writ, known to uninitiated as the R Manual, has this to say about assignment operators and their differences:

The operators <- and = assign into the environment in which they are evaluated. The operator <- can be used anywhere, whereas the operator = is only allowed at the top level (e.g., in the complete expression typed at the command prompt) or as one of the subexpressions in a braced list of expressions.

If this sounds like absolute gibberish, or you cannot think of what would qualify as not being on the top level or a subexpression in a braced list of expressions, welcome to the squad – I’ve had R experts scratch their head about this for an embarrassingly long time until they realised what the R documentation, in its neutron starlike denseness, actually meant.

If it’s in (parentheses) rather than {braces}, = and <- are going to behave weird

To translate the scriptural words above quoted to human speak, this means = cannot be used in the conditional part (the part enclosed by (parentheses) as opposed to {curly braces}) of control structures, among others. This is less an issue between <- and =, and rather an issue between = and ==. Consider the following example:

x = 3

if(x = 3) 1 else 0
# Error: unexpected '=' in "if(x ="

So far so good: you should not use a single equality sign as an equality test operator. The right way to do it is:

> if(x == 3) 1 else 0
[1] 1

But what about arrow assignment?

if(x <- 3) 1 else 0
# [1] 1

Oh, look, it works! Or does it?

if(x <- 4) 1 else 0
# [1] 1

The problem is that an assignment will always yield true if successful. So instead of comparing x to 4, it assigned 4 to x, then happily informed us that it is indeed true.

The bottom line is not to use = as comparison operator, and <- as anything at all in a control flow expression’s conditional part. Or as John Chambers notes,

Disallowing the new assignment form in control expressions avoids programming errors (such as the example above) that are more likely with the equal operator than with other S assignments.

Chain assignments

One example of where  <- and = behave differently (or rather, one behaves and the other throws an error) is a chain assignment. In a chain assignment, we exploit the fact that R assigns from right to left. The sole criterion is that all except the rightmost members of the chain must be capable of being assigned to.

# Chain assignment using <-
a <- b <- c <- 3

# Chain assignment using =
a = b = c = 3

# Chain assignment that will, unsurprisingly, fail
a = b = 3 = 4
# Error in 3 = 4 : invalid (do_set) left-hand side to assignment

So we’ve seen that as long as the chain assignment is logically valid, it’ll work fine, whether it’s using <- or =. But what if we mix them up?

a = b = c <- 1
# Works fine...

a = b <- c <- 1
# We're still great...

a <- b = c = 1
# Error in a <- b = c = 1 : could not find function "<-<-"
# Oh.

The bottom line from the example above is that where <- and = are mixed, the leftmost assignment has to be carried out using =, and cannot be by <-. In that one particular context, = and <- are not interchangeable.

A small note on chain assignments: many people dislike chain assignments because they’re ‘invisible’ – they literally return nothing at all. If that is an issue, you can surround your chain assignment with parentheses – regardless of whether it uses <-, = or a (valid) mixture thereof:

a = b = c <- 3
# ...
# ... still nothing...
# ... ... more silence...

(a = b = c <- 3)
# [1] 3

Assignment and initialisation in functions

This is the big whammy – one of the most important differences between <- and =, and a great way to break your code. If you have paid attention until now, you’ll be rewarded by, hopefully, some interesting knowledge.

= is a pure assignment operator. It does not necessary initialise a variable in the global namespace. <-, on the other hand, always creates a variable, with the lhs value as its name, in the global namespace. This becomes quite prominent when using it in functions.

Traditionally, when invoking a function, we are supposed to bind its arguments in the format parameter = argument.1 And as we know from what we know about functions, the keyword’s scope is restricted to the function block. To demonstrate this:

add_up_numbers <- function(a, b) {
    return(a + b)
}

add_up_numbers(a = 3, b = 5)
# [1] 8

a + b
# Error: object 'a' not found

This is expected: a (as well as b, but that didn’t even make it far enough to get checked!) doesn’t exist in the global scope, it exists only in the local scope of the function add_up_numbers. But what happens if we use <- assignment?

add_up_numbers(a <- 3, b <- 5)
# [1] 8

a + b
# [1] 8

Now, a and b still only exist in the local scope of the function add_up_numbers. However, using the assignment operator, we have also created new variables called a and b in the global scope. It’s important not to confuse it with accessing the local scope, as the following example demonstrates:

add_up_numbers(c <- 5, d <- 6)
# [1] 11

a + b
# [1] 8

c + d
# [1] 11

In other words, a + b gave us the sum of the values a and b had in the global scope. When we invoked add_up_numbers(c <- 5, d <- 6), the following happened, in order:

  1. A variable called c was initialised in the global scope. The value 5 was assigned to it.
  2. A variable called d was initialised in the global scope. The value 6 was assigned to it.
  3. The function add_up_numbers() was called on positional arguments c and d.
  4. c was assigned to the variable a in the function’s local scope.
  5. d was assigned to the variable b in the function’s local scope.
  6. The function returned the sum of the variables a and b in the local scope.

It may sound more than a little tedious to think about this function in this way, but it highlights three important things about <- assignment:

  1. In a function call, <- assignment to a keyword name is not the same as using =, which simply binds a value to the keyword.
  2. <- assignment in a function call affects the global scope, using = to provide an argument does not.
  3. Outside this context, <- and = have the same effect, i.e. they assign, or initialise and assign, in the current scope.

Phew. If that sounds like absolute confusing gibberish, give it another read and try playing around with it a little. I promise, it makes some sense. Eventually.

So… should you or shouldn’t you?

Which raises the question that launched this whole post: should you use = for assignment at all? Quite a few style guides, such as Google’s R style guide, have outright banned the use of = as assignment operator, while others have encouraged the use of ->. Personally, I’m inclined to agree with them, for three reasons.

  1. Because of the existence of ->, assignment by definition is best when it’s structured in a way that shows what is assigned to which side. a -> b and b <- a have a formal clarity that a = b does not have.
  2. Good code is unambiguous even if the language isn’t. This way, -> and <- always mean assignment, = always means argument binding and == always means comparison.
  3. Many argue that <- is ambiguous, as x<-3 may be mistyped as x<3 or x-3, or alternatively may be (visually) parsed as x < -3, i.e. compare x to -3. In reality, this is a non-issue. RStudio has a built-in shortcut (Alt/⎇ + ) for <-, and automatically inserts a space before and after it. And if one adheres to sound coding principles and surrounds operators with white spaces, this is not an issue that arises.

Like with all coding standards, consistency is key. Consistently used suboptimal solutions are superior, from a coding perspective, to an inconsistent mixture of right and wrong solutions.

References   [ + ]

1.A parameter is an abstract ‘slot’ where you can put in values that configure a function’s execution. Arguments are the actual values you put in. So add_up_numbers(a,b) has the parameters a and b, and add_up_numbers(a = 3, b = 5) has the arguments 3 and 5.

Automagic epi curve plotting: part I

As of 24 May 2018, the underlying data schema of the Github repo from which the epi curve plotter draws its data has changed. Therefore, a lot of the code had to be adjusted. The current code can be found here on Github. This also plots a classical epi curve.

One of the best resources during the 2013-16 West African Ebola outbreak was Caitlin RiversGithub repo, which was probably one of the best ways to stay up to date on the numbers. For the current outbreak, she has also set up a Github repo, with really frequent updates straight from the WHO’s DON data and the information from DRC Ministry of Public Health (MdlS) mailing list.1 Using R, I have set up a simple script that I only have to run every time I want a pre-defined visualisation of the current situation. I am usually doing this on a remote RStudio server, which makes matters quite easy for me to quickly generate data on the fly from RStudio.

Obtaining the most recent data

Using the following little script, I grab the latest from the ebola-drc Github repo:

# Fetch most recent DRC data.
library(magrittr)
library(curl)
library(readr)
library(dplyr)

current_drc_data <- Sys.time() %>%
  format("%d%H%M%S%b%Y") %>%
  paste("raw_data/drc/", "drc-", ., ".csv", sep = "") %T>%
  curl_fetch_disk("https://raw.githubusercontent.com/cmrivers/ebola_drc/master/drc/data.csv", .) %>%
  read_csv()

This uses curl (the R implementation) to fetch the most recent data and save it as a timestamped2 file in the data folder I set up just for that purpose.3 Simply sourcing this script (source("fetch_drc_data.R")) should then load the current DRC dataset into the environment.4

Data munging

We need to do a little data munging. First, we melt down the data frame using reshape2‘s melt function. Melting takes ‘wide’ data and converumnts it into ‘long’ data – for example, in our case, the original data had a row for each daily report for each health zone, and a column for the various combinations of confirmed/probable/suspected over cases/deaths. Melting the data frame down creates a variable type column (say, confirmed_deaths and a value column (giving the value, e.g. 3). Using lubridate,5 the dates are parsed, and the values are stored in a numeric format.

library(magrittr)
library(reshape2)
library(lubridate)

current_drc_data %<>% melt(value_name = "value", measure.vars = c("confirmed_cases", "confirmed_deaths", "probable_cases", "probable_deaths", "suspect_cases", "suspect_deaths", "ruled_out"))
current_drc_data$event_date <- lubridate::ymd(current_drc_data$event_date)
current_drc_data$report_date <- lubridate::ymd(current_drc_data$report_date)
current_drc_data$value <- as.numeric(current_drc_data$value)

Next, we drop ruled_out cases, as they play no significant role for the current visualisation.

current_drc_data <- current_drc_data[current_drc_data$variable != "ruled_out",]

We also need to split the type labels into two different columns, so as to allow plotting them as a matrix. Currently, data type labels (the variable column) has both the certainty status (confirmed, suspected or probable) and the type of indicator (cases vs deaths) in a single variable, separated by an underscore. We’ll use stringr‘s str_split_fixed to split the variable names by underscore, and join them into two separate columns, suspicion and mm, the latter denoting mortality/morbidity status.

current_drc_data %<>% cbind(., str_split_fixed(use_series(., variable), "_", 2)) %>% 
                 subset(select = -c(variable)) %>% 
                 set_colnames(c("event_date", "report_date", "health_zone", "value", "suspicion", "mm"))

Let’s filter out the health zones that are being observed but have no relevant data for us yet:

relevant_health_zones <- current_drc_data %>% 
                         subset(select = c("health_zone", "value")) %>% 
                         group_by(health_zone) %>% 
                         summarise(totals = sum(value, na.rm=TRUE)) %>% 
                         dplyr::filter(totals > 0) %>% 
                         use_series(health_zone)

This gives us a vector of all health zones that are currently reporting cases. We can filter our DRC data for that:

current_drc_data %<>% dplyr::filter(health_zone %in% relevant_health_zones)

This whittles down our table by a few rows. Finally, we might want to create a fake health zone that summarises all other health zones’ respective data:

totals <- current_drc_data %>% group_by(event_date, report_date, suspicion, mm) 
                           %>% summarise(value = sum(value), health_zone=as.factor("DRC total"))

# Reorder totals to match the core dataset
totals <- totals[,c(1,2,6,5,3,4)]

Finally, we bind these together to a single data frame:

current_drc_data %<>% rbind.data.frame(totals)

Visualising it!

Of course, all this was in pursuance of cranking out a nice visualisation. For this, we need to do a couple of things, including first ensuring that “DRC total” is treated separately and comes last:

regions <- current_drc_data %>% use_series(health_zone) %>% unique()
regions[!regions == "DRC total"]
regions %<>% c("DRC total")

current_drc_data$health_zone_f <- factor(current_drc_data$health_zone, levels = regions)

I normally start out by declaring the colour scheme I will be using. In general, I tend to use the same few colour schemes, which I keep in a few gists. For simple plots, I prefer to use no more than five colours:

colour_scheme <- c(white = rgb(238, 238, 238, maxColorValue = 255),
                   light_primary = rgb(236, 231, 216, maxColorValue = 255),
                   dark_primary = rgb(127, 112, 114, maxColorValue = 255),
                   accent_red = rgb(240, 97, 114, maxColorValue = 255),
                   accent_blue = rgb(69, 82, 98, maxColorValue = 255))

With that sorted, I can invoke the ggplot method, storing the plot in an object, p. This is so as to facilitate later retrieval by the ggsave method.

p <- ggplot(current_drc_data, aes(x=event_date, y=value)) +

  # Title and subtitle
  ggtitle(paste("Daily EBOV status", "DRC", Sys.Date(), sep=" - ")) +
  labs(subtitle = "(c) Chris von Csefalvay/CBRD (cbrd.co) - @chrisvcsefalvay") +
  
  # This facets the plot based on the factor vector we created ear 
  facet_grid(health_zone_f ~ suspicion) +
  geom_path(aes(group = mm, colour = mm, alpha = mm), na.rm = TRUE) +
  geom_point(aes(colour = mm, alpha = mm)) +

  # Axis labels
  ylab("Cases") +
  xlab("Date") +

  # The x-axis is between the first notified case and the last
  xlim(c("2018-05-08", Sys.Date())) +
  scale_x_date(date_breaks = "7 days", date_labels = "%m/%d") +

  # Because often there's an overlap and cases that die on the day of registration
  # tend to count here as well, some opacity is useful.
  scale_alpha_manual(values = c("cases" = 0.5, "deaths" = 0.8)) +
  scale_colour_manual(values = c("cases" = colour_scheme[["accent_blue"]], "deaths" = colour_scheme[["accent_red"]])) +

  # Ordinarily, I have these derive from a theme package, but they're very good
  # defaults and starting poinnnnnntsssssts
  theme(panel.spacing.y = unit(0.6, "lines"), 
        panel.spacing.x = unit(1, "lines"),
        plot.title = element_text(colour = colour_scheme[["accent_blue"]]),
        plot.subtitle = element_text(colour = colour_scheme[["accent_blue"]]),
        axis.line = element_line(colour = colour_scheme[["dark_primary"]]),
        panel.background = element_rect(fill = colour_scheme[["white"]]),
        panel.grid.major = element_line(colour = colour_scheme[["light_primary"]]),
        panel.grid.minor = element_line(colour = colour_scheme[["light_primary"]]),
        strip.background = element_rect(fill = colour_scheme[["accent_blue"]]),
        strip.text = element_text(colour = colour_scheme[["light_primary"]])
  )
DRC EBOV outbreak, 22 May 2018. The data has some significant gaps, owing to monitoring and recording issues, but some clear trends already emerge from this simple illustration.

The end result is a fairly appealing plot, although if the epidemic goes on, one might want to consider getting rid of the point markers. All that remains is to insert an automatic call to the ggsave function to save the image:

Sys.time() %>%
  format("%d%H%M%S%b%Y") %>%
  paste("DRC-EBOV-", ., ".png", sep="") %>%
  ggsave(plot = p, device="png", path="visualisations/drc/", width = 8, height = 6)

Automation

The cronR package has a built-in cron scheduler add-in for RStudio, allowing you to manage all your code scheduling needs.

Of course, being a lazy epidemiologist, this is the kind of stuff that just has to be automated! Since I run my entire RStudio instance on a remote machine, it would make perfect sense to regularly run this script. cronR package comes with a nice widget, which will allow you to simply schedule any task. Old-school command line users can, of course, always resort to ye olde command line based scheduling and execution. One important caveat: the context of cron execution will not necessarily be the same as of your R project or indeed of the R user. Therefore, when you source a file or refer to paths, you may want to refer to fully qualified paths, i.e. /home/my_user/my_R_stuff/script.R rather than merely script.R. cronR is very good at logging when things go awry, so if the plots do not start to magically accumulate at the requisite rate, do give the log a check.

The next step is, of course, to automate uploads to Twitter. But that’s for another day.

References   [ + ]

1.Disclaimer: Dr Rivers is a friend, former collaborator and someone I hold in very high esteem. I’m also from time to time trying to contribute to these repos.
2.My convention for timestamps is the military DTG convention of DDHHMMSSMONYEAR, so e.g. 7.15AM on 21 May 2018 would be 21071500MAY2018.
3.It is, technically, bad form to put the path in the file name for the curl::curl_fetch_disk() function, given that curl::curl_fetch_disk() offers the path parameter just for that. However, due to the intricacies of piping data forward, this is arguably the best way to do it so as to allow the filename to be reused for the read_csv() function, too.
4.If for whatever reason you would prefer to keep only one copy of the data around and overwrite it every time, quite simply provide a fixed filename into curl_fetch_disk().
5.As an informal convention of mine, when using the simple conversion functions of lubridate such as ymd, I tend to note the source package, hence lubridate::ymd over simply ymd.

Installing RStudio Server on Debian 9

Oh, wouldn’t it be just wonderful if you could have your own RStudio installation on a server that you could then access from whatever device you currently have, including an iPad? It totally would. Except it’s some times far from straightforward. Here’s how to do it relatively painlessly.

Step 1: Get a server

Choose a suitable (and affordable) server, pick a location near you in the drop-down menu on the bottom, and press Add this Linode! to set up your first Linode.

I use Linode,1 and in general, their 4096 server is pretty good. Linodes can be very easily resized, so this should not be a worry.

Step 2: Set up the server

Once your Linode is up, it will turn up on your dashboard with a random name (linode1234567, typically). If you click on it, you will see your Linode is ‘Brand New’, which means you need to configure it. I usually keep them in groups depending on purpose: blog servers, various processing servers, hosts, research servers. Each of them then gets a name. Choose whatever nomenclature fits your needs best.

Give your Linode a name you can recognise it by, and assign it to a category.

Next, click on the Rebuild tab, and configure the root password, the operating system (we’ll be using Debian 9), the swap disk size (for R, it’s a good idea to set this as large as you can) and finally, set the deployment disk size. I usually set that for 66%.

Step 3: Install R

The Remote Access field shows the SSH access command, complete with the root user, as well as public IPs, default gateways and other networking stuff.

SSH into your Linode and log in as root. You will find your Linode’s IP address and other interesting factoids about it under the Remote access tab. I have obscured some information as I don’t want you scallywags messing around with my server, but the IP address is displayed both in the SSH link (the one that goes ssh [email protected] or something along these lines) and below under public IPs.

Using vim, open /etc/apt/sources.list and add the following source:

# CRAN server for Debian stretch (R and related stuff)
deb http://cran.rstudio.com/bin/linux/debian stretch-cran34/

Save the file, and next install dirmngr (sudo apt-get install dirmngr). Then, add the requisite GPG key for CRAN, update the repository and install r-base:

sudo apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'

sudo apt update
sudo apt install r-base

At this point, you can enter R to test if your R installation works, and try to install a package, like ggplot2. It should work, but may ask you to select an installation server. If all is well, this is what you should be getting:

[email protected]:~# R

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

In the prompt, enter install.packages("ggplot2"). Select a server if requested. Otherwise, watch ggplot2 (and a bazillion other packages) install. Then, quit R by calling q().

Step 4: Downgrade libssl

For some inscrutable reason, RStudio is currently set up to work with libssl1.0.0, whereas Debian 9 comes with libssl1.1.0 out of the box. Clearly that’s not going to work, so we’ll have to roll back our libssl. We’ll do so by creating a file called /etc/apt/sources.list.d/jessie.list using vim. And we’ll fill it with the following:

deb http://httpredir.debian.org/debian jessie main contrib non-free
deb-src http://httpredir.debian.org/debian jessie main contrib non-free

deb http://security.debian.org/ jessie/updates main contrib non-free
deb-src http://security.debian.org/ jessie/updates main contrib non-free

In case you’re curious: this creates a sources list called jessie, and allows you to draw from Debian Jessie. So let’s have apt get with the program (sudo apt update), and install libssl1.0.0 (sudo apt install libssl1.0.0). Ift may be prudent to also install the openssl tool corresponding to the libssl version (sudo apt install openssl/jessie).

Step 5: Time to install RStudio Server!

First, install gDebi, a package installer, by typing sudo apt-get install gdebi. Next, we’ll be grabbing the latest RStudio version using wget, and installing it using gDebi. Make sure you either do this in your home directory or in /tmp/, ideally. Note that the versions of RStudio tend to change – 1.1.442 was the current version, released 12 March 2018, at the time of writing this post, but may by now have changed. You can check the current version number here.

wget https://download2.rstudio.org/rstudio-server-1.1.442-amd64.deb
sudo gdebi rstudio-server-1.1.442-amd64.deb

If all is well and you said yes to the dress question about whether you actually want to install RStudio Server (no, you’ve been going through this whole pain in the rear for excrement and jocularity, duh) , you should see something like this:

(Reading database ... 55651 files and directories currently installed.)
Preparing to unpack rstudio-server-1.1.442-amd64.deb ...
Unpacking rstudio-server (1.1.442) ...
Setting up rstudio-server (1.1.442) ...
groupadd: group 'rstudio-server' already exists
rsession: no process found
Created symlink /etc/systemd/system/multi-user.target.wants/rstudio-server.service → /etc/systemd/system/rstudio-server.service.
● rstudio-server.service - RStudio Server
   Loaded: loaded (/etc/systemd/system/rstudio-server.service; enabled; vendor preset: enabled)
   Active: active (running) since Sat 2018-03-31 21:59:25 UTC; 1s ago
  Process: 16478 ExecStart=/usr/lib/rstudio-server/bin/rserver (code=exited, status=0/SUCCESS)
 Main PID: 16479 (rserver)
    Tasks: 3 (limit: 4915)
   CGroup: /system.slice/rstudio-server.service
           └─16479 /usr/lib/rstudio-server/bin/rserver

Mar 31 21:59:25 localhost systemd[1]: Starting RStudio Server...
Mar 31 21:59:25 localhost systemd[1]: Started RStudio Server.

Now, if all goes well, you can navigate to your server’s IP at port 8787, and you should behold something akin to this:

The login interface. Technically, you could simply log in with your root password and root as the username. But just don’t yet.

There are a few more things you wish to install at this point – these are libraries that will help with SSL and other functionality from within R. Head back to the terminal and install the following:

sudo apt-get install libssl-dev libcurl4-openssl-dev libssh2-1-dev

Step 6: Some finishing touches

The login screen will draw on PAM, Unix’s own authentication module, in lieu of a user manager. As such, to create access, you will have to create a new Unix user with adduser, and assign a password to it. This will grant it a directory of its own, and you the ability to fine-tune what they should, and what they shouldn’t, have access to. Win-win! This will allow you to share a single installation among a range of people.

Step 7: To reverse proxy, or to not reverse proxy?

There are diverging opinions as to whether a reverse proxy such as NGINX carries any benefit. In my understanding, they do not, and there’s a not entirely unpleasant degree of security by obscurity in having a hard to guess port (which, by the way, you can change). It also makes uploads, on which you will probably rely quite a bit, more difficult. On the whole, there are more arguments against than in favour of a reverse proxy, but I may add specific guidance on reverse proxying here if there’s interest.

References   [ + ]

1.Using this link gives me a referral bonus of $20 as long as you remain a customer for 90 days. If you do not wish to do so, please use this link. It costs the same either way, and I would be using Linode anyway as their service is superbly reliable.