Recently an R user tweeted sardonically,
I want to replace the value in a cell in something the kids are calling a 'tibble'. In baseR, it was a simple 1 liner for a dataframe:
df[column#,row#]=newvalue
What's the Tidy version?
The stark answer is that there really is no good Tidy way to do this very basic, fundamental operation in R, something that a base-R course would treat in the first lesson or two. Clearly:
There is something very wrong with the Tidy(-only) approach to teaching R learners.
The context of this essay is how to teach R to students without prior coding background. These learners typically come from the social sciences, business, or the humanities, sometimes from the life sciences.
I believe that teaching R via the Tidyverse is counterproductive for this group of learners.
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The Tidyverse is more complex and abstract than base-R, hence harder to learn, directly antithetical to Tidy's stated goal of making R accesible to a broader community.
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Tidy-based courses must therefore restrict coverage to a small set of operations, mainly a few dplyr verbs. The students may be happy but they are unprepared to use R productively in their work, as exemplified in the above tweet,
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Accordingly, noncoder learners should be taught a mix of base-R and Tidy, starting first with base-R. "Graduates" of mixed courses are then equipped to apply whichever tool they find most convenient in any given application.
Note: By "base-R" I mean array indices, loops, if-then-else and so on. I do NOT advocate a slow, boring approach in which, for instance, one starts with "R data can be real, character or logical..." My own online course has students doing useful operations starting in the very first lesson.
What informs my views here?
I teach in the Computer Science Dept. at UC Davis (though again, my focus here is on noncoder learners of R, not CS majors). I formerly was a Professor of Statistics at that university. I am an award-winning textbook author, and am also the recipient of university awards for teaching and public service.
Specifically in terms of R, I have been an R user and developer since near the beginning, having used R's predecessor S before that. I've published several books that use R, and have served as the Editor-in-Chief of the R Journal, as well as Associate Editor for the Journal of Statistical Software. My abovementioned R tutorial for beginners, fasteR, has become my most popular GitHub repo, with nearly 700 GitHub stars.
But it goes far beyond that; I really am intensely interested in how people learn, from children to middle-aged adults. Among other things, I've taught English As a Second Language to working-class adults from China, and have taught a short course on probability to sixth-graders.
See my full bio
Note that in discussing teaching in this essay, I am taking the target audience here to be nonprogrammers who wish to use R for data analysis.
RStudio's presentation of ggplot2 as part of the Tidyverse is misleading. That package predates Tidy, and the package is widely used by both base-R advocates and Tidy proponents alike. RStudio's marketing of Tidy as including ggplot2 only came later.
This is important, since many who praise Tidy cite ggplot2 as their first reason for being pro-Tidy in teaching. This obfuscates the real problems with Tidy as I see them:
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focus on dplyr, purrr and pipes, and
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a ban/near ban on the use of loops, the '$' sign, brackets
More details later in this document.
I believe that R learners should be taught both base-R and Tidy, base-R first. Many R teachers feel the same way. But there are some who:
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Refuse to teach any base-R.
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Ban the use of $, [, loops, the apply() family and so on.
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Treat dplyr as the go-to tool for almost any R action, including challenging ones, ignoring that base-R might lead to a simpler solution. Again, the example in the Prologue above illustrates this.
(As of July 2022, RStudio changed its name to Posit, but in this document I will use the original, more familiar name.)
I like and admire the RStudio people, including the Tidyverse originator, Hadley Wickham, and have always supported them, both privately and publicly. They and I have been interacting from the beginning, when the firm consisted only of founder JJ Allaire and ace developer Joe Cheng. I highly praise the firm to my students, and I use and recommend Hadley's (NON-Tidyverse) packages ggplot2 and stringr. On occasion his devtools has been an absolute lifesaver for me. Hadley was the internal reviewer for my book, The Art of R Programming, and I was one of the internal reviewers for Hadley's Advanced R (2nd. ed.). RStudio's Quarto package is an exciting new development for the R community.
Nevertheless, I believe that RStudio took a wrong turn when it decided to promote the Tidyverse for beginning learners who have no prior coding background. Tidy makes it more difficult for noncoders to learn R, and leaves them less able to use it productively.
RStudio has always been a very public-spirited firm (they eventually changed to Public Benefit Corporation legal status), In this light, it is very unfortunate that RStudio did not consult with the broader R community in developing this new "dialect" of R.
As noted in my background summary above, I have been quite active in the R movement, so all this is quite troubling to me. Hence the document you are now reading.
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Again, my focus here is on teaching R to those with little or no coding background. I am not discussing teaching Computer Science students.
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Tidy was consciously designed to equip learners with just a small set of R tools. The students learn a few dplyr verbs well, but that equips them to do much less with R than a standard R beginners course would teach. That leaves the learners less equipped to put R to practical use, compared to "graduates" of standard base-R courses.
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Tidy teachers of R claim great success, but these "testimonials" are misleading. The "success" is due to watering down the material (and conflation with ggplot2). The students learn to mimic a few example patterns and may be happy, but they are not equipped to use R beyond superficial operations.
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The Tidyers' refusal to teach the '[' and [ '$' operators, and the lack of coverage of R vectors, are major handicaps for Tidy "graduates" to making use of most of R's statistical functions and statistical packages.
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Tidy's is too abstract for noncoder beginners, due to the philosophy of functional programming (FP). The latter is popular with many sophisticated computer scientists, but is difficult even for computer science students, let alone the nontech learners that form our focus here. Tidy is thus unsuited as the initial basis of instruction for nonprogrammer students of R. FP should be limited and brought in gradually. The same statement applies to base-R's own FP functions.
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The Tidy FP philosophy replaces straightforward, easily grasped, loops with abstract use of functions. Since functions are the most difficult aspect for noncoder R learners, FP is clearly not the right path for such learners. Indeed, even many Tidy advocates concede that it is in various senses often more difficult to write Tidy code than base-R. Even Hadley says, for instance, "it may take a while to wrap your head around [FP]."
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A major problem is Tidy's cognitive overload: The basic operations contain myriad variants. Though of course one need not learn them all, one needs some variants even for simple operations, e.g. pipes on functions of more than one argument.
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The obsession among many Tidyers that one must avoid writing loops, the '$' operator, brackets and so on often results in obfuscated code. Once one goes beyond the simple mutate/select/filter/summarize pattern, Tidy programming can be of low readability. The much-vaunted "English-like" theme of Tidy becomes an obstacle rather than an aid.
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Tidy advocates also concede that debugging Tidy code is difficult, especially in the case of pipes. Yet noncoder learners are the ones who make the most mistakes, so it makes no sense to have them use a coding style that makes it difficult to track down their errors.
In summary, Tidy uses unnecessarily complicated machinery, an obvious drawback for teaching beginners, and yet only equips students to perform a narrow set of operations. It would be like teaching English As a Second Language as follows: The instructor teaches the students to say "Good Morning," by providing them with a template like,
It is my fervent wish that you find your morning unusually fulfilling.
The students would be told to substitute morning with afternoon or evening. But they would have no idea what the other words mean, and it would not generalize much. The students may even rave about these English "lessons," but they won't have learned much at all.
Case study: delayed learning (I)
Let's look at an example in my online R tutorial, fasteR. Consider, for instance, an innocuous line like
> hist(Nile)i.e. drawing a simple histogram of R's built-in Nile River dataset.
This is in the very first lesson in my tutorial. Easy! By contrast, the Tidy crowd forbids use of base-R plots, insisting on using ggplot2. I also prefer ggplot2 to base-R graphics (though again it should not be considered part of the Tidyverse), but here we have a much more important goal--to give students an actual useful application of R right from the start. Tidy greatly impedes that goal.
To be Tidy the instructor would have to do something like
> library(ggplot2)
> dn <- data.frame(Nile)
> ggplot(dn) + geom_histogram(aes(Nile),dn)Here the instructor would have a ton of things to explain -- packages, data frames, ggplot(), the aes argument, the role of the '+' (it's not addition here) and so on -- and thus she could definitely NOT present it in the first lesson.
(Things would be simpler for Tidy instructors if they were to use qplot() in the ggplot2 package, but as far as I know, few if any Tidy courses do this.)
Also in my very first lesson, I do
> mean(Nile[80:100])printing the mean Nile River flow during a certain range of years. Incredibly, not only would this NOT be in a first lesson with Tidy, the students in a Tidy course may actually never learn how to do this. Typical Tidyers don't consider vectors very important for learners, let alone vector subscripts.
As a concrete example of this Tidy point of view, consider the book Getting Started with R, by Beckerman et al, Oxford University Press, second edition, 2017. The book makes a point of being "Tidyverse compliant". In 231 pages, vectors are mentioned just briefly, with no coverage of subscripts. Hadley, in his Tidy "bible," R for Data Science", actually does cover vectors--but not until Chapter 20. Again, typical Tidy courses don't cover vectors at all.
In other words, even after one lesson, the base-R learner would be way ahead of her Tidy counterparts.
Case study: delayed learning (II)
A researcher tweeted in December 2019 that an introductory statistics book by Peter Dalgaard is "now obsolete," because it uses base-R rather than Tidy. Think of what an "update" to use of Tidy would involve, how much extra complexity it would impose on the students. Here is an early lesson from the book:
> thue2 <- subset(thuesen,blood.glucose < 7)This could easily be in the base-R instructor's second lesson, if not the first. For Tidy, though, this would have to be changed to
> library(dplyr)
> thue2 <- thuesen %>% filter(blood.glucose < 7)Here the instructor would first have to teach the pipe operator '%>%', again extra complexity. And in so doing, she would probably emphasize the "left to right" flow of pipes, but the confused students would then wonder why, after that left-to-right flow, there is suddenly a right-to-left flow, with the '<-'. (For some reason, the Tidy people don't seem to use R's '->' op.)
Again, the Tidyverse is simply too complex for R learners without coding background. It slows down their learning process.
Case study: tapply() (I)
One of the most commonly-used functions in base-R is tapply(). It's quite easy to teach beginners, by presenting its call form to them:
tapply(what to split, how to split it,
what to apply to the resulting chunks)However, for some reason Tidy advocates deeply resent this function. Indeed, to them tapply() epitomizes what's wrong with base-R.
When the Tidyverse was first developed, Prof. Roger Peng gave a thoughtful keynote talk, Teaching R to New Users--from tapply to the Tidyverse, also presented as a Web page. Oddly, tapply() is not mentioned in Dr. Peng's talk or in the printed version, but the title says it all: One should teach Tidy, not tapply().
Surprisingly, though, in making his comparison of Tidy to base-R, his base-R example is aggregate(), not tapply(). The complexity of aggregate() function makes for an unfair comparison, a straw man; tapply() is much simpler, and perfect for R beginners, and thus the proper comparison as the title of the talk seems to agree.
Below is an example from the Peng talk, using the built-in R dataset airquality. We find the mean ozone level by month:
group_by(airquality, Month) %>%
summarize(o3 = mean(Ozone, na.rm = TRUE))Here is the base-R version offered by Dr. Peng:
aggregate(airquality[, “Ozone”],
list(Month = airquality[, “Month”]),
mean, na.rm = TRUE)Indeed, that base-R code would be difficult for R beginners. But here is the far easier base-R code, using tapply():
tapply(airquality$Ozone,airquality$Month,mean,na.rm=TRUE)This fits clearly into our tapply call form shown above:
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What to split: Ozone
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How to split it: by Month
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What to apply to the resulting chunks: mean
The Tidy version requires two function calls rather than one for base-R. The Tidy code is a bit wordier, and requires that one do an assignment (to o3). All in all, the base-R version is simpler, and thus easier for noncoder beginners.
Case study: tapply() (II)
Of course, one can find instances in which each approach, base-R and Tidy, is simpler to use than the other. Indeed, I have strongly advocated that noncoder R learners should pick up some of both. (Much more on this point below.) But I think it's worth repeating how simple it is for R learners to solve many basic problems using tapply().
Consider this example, a bit more advanced, that I like to use to motivate linear regression models. We wish to predict human weight from height, and wish to first check approximate linearity.
The dataset, involving heights and weights of professional baseball players, mlb, is from my regtools package. For each height value, there are various players of that height, so we plot mean weight against height, checking for a linear pattern.
Base-R:
htsAndWts <- tapply(mlb$Weight,mlb$Height,mean)
plot(htsAndWts)Tidy (plus ggplot2):
mlb %>%
group_by(Height) %>%
summarize(weights = mean(Weight)) %>%
ggplot(aes(x=Height,y=weights)) + geom_point() Two major dplyr functions, pipes, and a somewhat sophisticated usage of ggplot2! It would be out of the question to use this example early in a Tidy course, far too much machinery to cover. But easy to do so in a course using base-R, in the first or second lesson. That should be the goal, empowering students to work on real problems, early on.
Most people, on most issues, avoid extremes. But some teachers of R have gone polemic, with dogmatic calls for "purity," with a Tidy-only approach.
I did suggest a mixed approach to RStudio founder and CEO JJ Allaire when we met (at his request) in 2019. Unfortunately, JJ did not like the idea either, on the grounds that RStudio should not be telling people how to teach. But of course, that is exactly what RStudio has been doing in promoting Tidy.
I'll take for my examples here from the Educator's Perspective article, written by a number of prominent Tidy advocates. The authors' viewpoint is commonplace in the US.
The Tidyers believe that two of the most basic operations in R, the $ sign and bracketing, are harmful. For instance, consider an example in Educator's Perspective.
The dataset is loan data available in the openintro package. Here is the Tidy code to preprocess the data:
loans <- openintro::loans_full_schema %>%
mutate(
homeownership = str_to_title(homeownership),
bankruptcy = if_else(public_record_bankrupt >= 1, "Yes", "No")
) %>%
filter(annual_income >= 10)
In base-R:
loans <- openintro::loans_full_schema
loans$bankruptcy <- ifelse(loans$public_record_bankrupt >= 1, "Yes", "No")
subset(loans,annual_income >= 10)
One should not conflate conciseness with clarity. But here the base-R code is both more concise and more straightforward. The Tidyers might even agree, except that they would object to the code's usage of '$'. As the article puts it:
When using base R the variables in that data frame are commonly accessed with the $ operator (e.g., loans$loan amount to access the variable called loan amount in the data frame loans). Often, students are tempted to access the loan amount variable in this example by referring to it simply as loan amount and not specifying the name of the data frame in which it lives. This results in a frustrating error: object 'loan amount' not found.
The simple solution to this "problem" is to explain it to students, and have them watch for it. It would be impossible to have students avoid all possible errors, and again, this one is easy to remedy with proper advance warning. Isn't this preferable to saddling learners with a more complex, less direct coding paradigm? Don't "throw the baby out with the bath water"!
And the argument "Coding style X often results in errors by beginners, so we should replace X by other machinery" of course works both ways. A common error among Tidy beginners is failure to reassign the result of something like mutate(). The above argument would imply that the base-R approach of simply tacking on the new variable to the given data frame is superior, as we did in the code above,
loans$bankruptcy <- ifelse(loans$public_record_bankrupt >= 1, "Yes", "No")
Tidy essentially ignores vectors. Consider this very simple example: Say we wish to add to the mtcars data a column consisting of the horsepower-to-weight ratio.
In base-R, it is extremely simple:
mtcars$hwratio <- mtcars$hp / mtcars$wtWant to add a column to a data frame? Hey, just add it!
But in Tidy:
mtcars %>% mutate(hwratio=hp/wt) -> mtcarsStill not terribly complex, but again we're invoking some machinery -- piping, a function call, and reassigning to the original data frame The base-R version is simple and straightforward, thus easier for R beginners to grasp.
The Tidyers oppose teaching loops to beginners, again on the grounds that loop coding is error-prone. That is open to debate, but the point is that loops are easier to debug; the sophisticated machinery that Tidyers want in lieu of loops, FP, is NOT easy to debug (more on this below). Here the Tidyers' "cure is worse than the disease.".
The article is so purist that it even recommends against teaching lm(). Use broom, they say. What's next, a Tidy wrapper for sqrt()?
The Tidyers become so focused on Tidy that they try to solve every problem by using that tool. The result is seen in "How do I do such-and-such using Tidy?" queries in Twitter, Stack Overflow and so on.
In many cases, the problem has a simple and direct base-R solution, but those who submit the queries are so fixated on dplyr, that they are incapable of taking that easier path.
Case study: Hadley recommends tapply()!
As noted earlier, many who learned R from a Tidyer are surprised to learn that ggplot2 makes liberal use of tapply(). It shouldn't be surprising, as ggplot2 is pre-Tidy, but many of the more ardent Tidyers have portrayed tapply() as the epitome of "What's wrong with R."
The tragic error of the "dplyr or bust" obsession is shown in the following Twitter exchange.
David Robinson, a well-known Tidy advocate, tweeted
dplyr #rstats pattern I use constantly:
%>% group_by(...) %>% mutate(n = n()) %>% ungroup()
Do others? Would a shortcut be helpful?
Hadley correctly replied, in the same thread, that one should use base-R functions here, ave() or tapply().
An R Core member, commenting on this phenomenon (but not this incident) cited a saying, "Sometimes the followers are holier than the prophet."
As noted, R courses using the Tidyverse often do rather little beyond their canonical data %>% group_by %>% mutate %>% summarize paradigm. That leaves the learners less equipped to put R to practical use, compared to "graduates" of standard base-R courses.
Even more important, once one gets past that simple paradigm, Tidy runs into real problems.
Again, let's use an mtcars example taken from an online tutorial. Here the goal is to regress miles per gallon against weight, calculating R2 for each cylinder group. Here's the Tidy solution, from the online help page for map():
mtcars %>%
split(.$cyl) %>%
map(~ lm(mpg ~ wt, data = .)) %>%
map(summary) %>%
map_dbl("r.squared")
# output
4 6 8
0.5086326 0.4645102 0.4229655There are several major points to note here:
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The R learner here must learn two different FP map functions for this particular example. This is an excellent example of Tidy's cognitive overload problem. Actually, the Tidyverse FP package, purrr, has 52 different map functions! (See below.)
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That "Tidy" code is a nightmare to read. For instance, the first '~' in that first map call is highly nonintuitive. This is starkly counter to the Tidyers' claim that Tidy is more intuitive and English-like.
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Tidy, in its obsession to avoid R's standard '$' symbol, is causing all kinds of chaos and confusion here.
The hapless student would naturally ask, "Where does that expression 'summary' come from?" It would appear that map() is being called on a nonexistent variable, summary. In actuality, base-R's summary() function is being called on the previous computation behind the scenes. Again, highly nonintuitive, and NOT stated in the online help page.
The poor student is further baffled by the call to map_dbl(). Where did that 'r.squared' come from? Again, Tidy is hiding the fact that summary() yields an S3 object with component r.squared. Yes, sometimes it is helpful to hide the details, but not if it confuses beginners.
The fact is, R beginners would be much better off writing a loop here, avoiding the conceptually more challenging FP. But even if the instructor believes the beginner must learn FP, the base-R version is far easier:
lmr2 <- function(mtcSubset) {
lmout <- lm(mpg ~ wt,data=mtcSubset)
summary(lmout)$r.squared
}
u <- split(mtcars,mtcars$cyl)
sapply(u,lmr2)Here lmr2() is defined explicitly, as opposed to the Tidy version, with its inscrutable '~' within the map() call.
In a Twitter discussion of the above example, a Tidy advocate protested that the above purrr code was not appropriate for learners:
Sure, but my original tweet was about teaching newbies. Your example is not really relevant to that because it's about a VERY complex concept.
Exactly my point! Newbies should write this as a plain loop, NOT using purrr or even base-R's FP constructs. Then it won't be advanced at all.
But the Tidy promoters don't want learners to use loops. So the instructor using Tidy simply would avoid giving students such an example, whereas it would be easy for the base-R instructor to do so.
Granted, loops can lose their clarity if they are nested. This can be ameliorated by using good comment lines and indenting, but it's fine to use functions---not in FP format, but simply as calls. For learners, Use the format
for (outer loop specs) {
...
w <- f(whatever)
...
}
f <- function(something)
{
# the work of what would have been the inner loop goes here
}rather than say, one of the apply() or purrr functions.
Again, Tidy has a serious problem of cognitive overload. Tidyverse students are being asked to learn a much larger volume of material. This is ironic, in that the goal in developing Tidy for teaching was to limit a course to just a few verbs. The problem is that the verbs have dozens of variants. This is clearly bad pedagogy.
Tidy advocates say the uniformity of interface in all those functions makes learning them easier. Uniform syntax is nice, yes, but the fact remains that users must learn the semantics of the functions, i.e. what operations they perform. What, for example, is the difference between summarize(), summarize_each(), summarize_at() and summarize_if()? Under which circumstances should each be used? The user must sift through this.
As Matt Dowle, creator of data.table, pointed out about dplyr,
It isn't one function mutate that you combine in a pipe. It's mutate, mutate_, mutate_all, mutate_at, mutate_each, mutate_each_, mutate_if, transmute, transmute_, transmute_all, transmute_at and transmute_if. And you're telling me [because of consistency of the user interfaces] you don't need a manual to learn all those?
Having a common syntax thus does not compensate for this dizzying complexity.
And students who need to go further will find a daunting task. See "The Tidyverse Curse", in which the author says inter alia that he uses "only" 60 Tidyverse functions -- 60! The "star" of the Tidyverse, dplyr, consists of 263 functions.
While a user initially need not use more than a small fraction of those 263 functions, the high complexity is clear. Every time a user needs some variant of an operation, she must sift through those hundreds of functions for one suited to her current need.
By contrast, if the user knows base-R (not difficult), she can handle any situation with just a few simple operations. The old adage applies: "Give a man a fish, and he can eat for a day. Teach him how to fish, and he can eat for a lifetime."
Note that the above example uses the "dot notation," used when the output of a pipe is fed into a multi-argument function. Here is the advice given at the official Tidyverse site:
Placing lhs elsewhere in rhs call
Often you will want lhs to the rhs call at another position than the first. For this purpose you can use the dot (.) as placeholder. For example, y %>% f(x, .) is equivalent to f(x, y) and z %>% f(x, y, arg = .) is equivalent to f(x, y, arg = z).
This phrasing is likely beyond the comprehension of many R beginners. Seeing a few examples would help them, of course. but it is yet another example of how Tidy causes cognitive overload for learners.
As noted above, some Tidyers even oppose teaching lm(). Instead, they recommend using the broom wrapper. The wrapper is indeed useful, but students need to learn the basics. And of course, it is unreasonable to ask that the hundreds of R statistical operations, and the thousands of packages, all have Tidy wrappers.
Consider the Tidyers' opposition to teaching the '$' and brackets operations. This is an obvious impediment to using R's statistical operations.
Most of the R statistical functions return S3 objects, i.e. lists, accessible via '$'. Similarly, statistical operations in R are mainly vector- and matrix-oriented. (A matrix is a special case of a vector.) I would find it difficult to teach a course in linear regression, principal components, log-linear models and so on to students who did not have solid prior experience with '$' and vectors.
Thus we immediately see a problem with Tidy: It creates a barrier to use of R as a statistical tool by Tidy "graduates."
Here is an example of bridging the gap between Tidy and statistics, by Claus Wilke, who begins by reporting, "I’ve finally figured out how to perform a PCA using the tidyverse." His word "finally" shows that there is indeed a gap. His answer is to use the broom package. As it was, even that package did not quite work, he said, though the development version did. And what about the thousands of CRAN packages that return S3 objects? Is broom going to provide a Tidy interface to each one? That of course would be unrealistic.
A fundamental problem, from my point of view, is that the RStudio people are not primarily statisticians. Their focus is on developing software, primarily for data wrangling and graphics. They do this quite well, but they are not the types who sit around debating, for example, the propriety of p-values. Statistics is not foremost on their radar screens, and this sad gap between Tidy and statistics is a result.
Here is an example from Text Mining with R, by Julia Silge of RStudio, and the aforementioned David Robinson. It's a great introduction to the text analysis field, and I myself have found the book useful.
This example, which may be found here, is a bit more involved than the previous ones, and thus better illustrates my concerns about debugging Tidy code. Courses that teach using Tidy do very well for simple examples; this one is more complex, possibly in terms of writing the code, and definitely in terms of debugging.
Debugging is something I've given a fair amount of thought to. I even wrote a book on it, The Art of Debugging (NSP, 2008). As noted earlier, noncoder R learners are the ones most in need of debugging skills, as they make the most errors. Thus the example here is of high importance.
The R package janeaustenr brings in full corpuses of six Austen novels:
> library(janeaustenr)
> books <- austen_books()
> str(books)
Classes ‘tbl_df’, ‘tbl’ and 'data.frame': 73422 obs. of 2 variables:
$ text: chr "SENSE AND SENSIBILITY" "" "by Jane Austen" "" ...
$ book: Factor w/ 6 levels "Sense & Sensibility",..: 1 1 1 1 1 1 1 1 1 1 ...
...
> books$text[22225]
[1] "drink to our good journey."
The authors' first goal is to put all the books together, one row per line of a book, with line and chapter number. Here are a couple of typical rows in the desired result:
"children, the old Gentleman's days were comfort… Sense & Sens… 25 1
...
"As we went along, Kitty and I drew up the blind… Pride & Prej… 7398 39Here is the solution given by the authors:
original_books <- austen_books() %>%
group_by(book) %>%
mutate(line = row_number(),
chapter = cumsum(str_detect(text, regex("^chapter [\\divxlc]",
ignore_case = TRUE)))) %>%
ungroup()A base-R version within reach of R beginners would begin with split(), to group by books, followed by loop over books. A more advanced base-R coder might use FP, first with lapply() and then with Reduce() to concatenate the data frames.
The R beginners version may be unfancy, even old-fashioned, but again suitable for beginners -- especially from the point of view of debugging, a key point for noncoder R learners, as noted, and my main point in this section. Even the base-R FP version would be quite debuggable (providing the function called by lapply() is named).
By contrast, this example epitomizes the problems with debugging Tidy code. Suppose, for instance, that the user had accidentally typed 'sum' rather than 'cumsum' in the above code. The output would look like this:
> original_books
text book line chapter
<chr> <fct> <int> <int>
1 "SENSE AND SENSIBILITY" Sense & Sensibility 1 50
2 "" Sense & Sensibility 2 50
3 "by Jane Austen" Sense & Sensibility 3 50
4 "" Sense & Sensibility 4 50
5 "(1811)" Sense & Sensibility 5 50
6 "" Sense & Sensibility 6 50
7 "" Sense & Sensibility 7 50
8 "" Sense & Sensibility 8 50
9 "" Sense & Sensibility 9 50
10 "CHAPTER 1" Sense & Sensibility 10 50
with 73,412 more rows
The 'chapter column' should read 1, not 50. But there is not error message, hence no clue as to what the problem might be.
If the code had not used pipes, one could use the R debug() or browser() functions, or the RStudio IDE debugging tool. Even use of print() statements, which I do not recommend in general, would still be effective of the code had been nonpiped. (Details below in the special section on pipes.) But it won't work in the Tidy, i.e. piped, version.
For instance, consider the code
debug(group_by)
mtcars %>% group_by(cyl)This produces
debugging in: group_by(., cyl)
debug: {
UseMethod("group_by")
}
Dealing with this is far beyond the skillset of R beginners.
Pipes are fundamentally unsuitable for use of debugging tools, and even just using print() statements is impossible.
One partial remedy is the clever pipecleaner package for debugging pipes. It works only up to a point, and is probably a bit too involved for R beginners. Most signifcantly, the package writeup also notes that
Occasionally it is necessary to restructure code from a piped to an unpiped form.
This makes it clear that pipes (both the Magrittr pipes in Tidy, and that later native pipes added to base-R), were simply not designed with debugging in mind. As the package author says, sometimes the only solution is to convert the code to ordinary unpiped form. (The package has an aid for this.)
Pipes play a central role in the Tidy paradigm. According to the Tidy advocates, the claimed alternative--function composition--is confusing for those without coding background. That point is debatable, but once again, the Tidy people are presenting us with a false choice, pipes or function composition.
There is a "third way"--breaking a sequence of function calls into separate, intermediate results. In other words, instead of
y <- h(g(f(x))) # functional compositionor
y <- x %>% f %>% g %>% h # pipeswrite
a <- f(x)
b <- g(a)
y <- h(b)The Tidyers do sometimes mention this Third Way, but immediately dismiss it. Hadley, for instance, in R for Data Science feels that it creates "cluttered" code. Well, OK, each person has his/her own aesthetic values, but really that should pale in comparison to code writability, readability and debuggability.
For example, consider the Jane Austen novels example above.
original_books <- austen_books() %>%
group_by(book) %>%
mutate(line = row_number(),
chapter = cumsum(str_detect(text, regex("^chapter [\\divxlc]",
ignore_case = TRUE)))) %>%
ungroup()A non-piped version (but still using dplyr) would be, say,
austens <- austen_books()
booksGrouped <- tibble(group_by(austens,book))
chapterNumbers <-
cumsum(str_detect(booksGrouped$text, regex("^chapter [\\divxlc]",
ignore_case = TRUE)))
mutated <- mutate(booksGrouped,line = row_number(),chapter=chapterNumbers)
original_books <- ungroup(mutated)Now, suppose the user had accidentally typed 'sum' instead of 'cumsum'. In the unpiped version, the user could run this code one line at a time, pausing to check the result at each step, either via a debugging tool or just using print(). She would quickly determine that the line in which chapterNumbers is assigned is the culprit. This is the essence of debugging--first narrow down where the error arises.
As noted, one could not do this with the piped version. Indeed, the user would likely convert to the non-piped version for debugging!
So why not do this in the first place? I assert that it would be easier to write nonpipe code to begin with. During the writing of the code, the breaking down the overall action into simple intermediate steps make it easier for the author to plan out the trajectory of the code. Each intermediate step allows the author to "catch one's breath."
For the same reasons, I assert that such code is easier to write and debug, but also easier for others to read.
Isn't this worth a little bit of clutter?
Even I, with several decades of programming experience in numerous languages, almost never use functional composition (other than a nesting depth of 2). Nor do I use pipes. I use separate intermediate statements, as discussed above. It's just clearer. And yes, worth the bit of clutter!
I wrote at the outset of this document that ggplot2 (GGP2) should not be considered part of the Tidyverse. I'll go into detail below, but first, why does it matter?
The answer is that, among the many people I've interacted with regarding Tidy, often the first reaaon they cite for liking Tidy is the ease with which one can code nice graphics. I fully agree that GGP2 is excellent, and I use and teach it myself -- but it's not the Tidyverse. My point, then, is they are endorsing Tidy because of something that is not part of Tidy. Indeed, GGP2 is widely used by base-R and Tidy advocates alike.
RStudio is a business. Its job, rightly so, is to promote its products. The GGP2 package had been enormously popular well before Tidy came along. Clearly, RStudio saw that, and thus saw that a good way to sell the Tidyverse was to include the popular GGP2 in the definition of Tidy. The message was, "Look how much easier it is do graphics in Tidy vs. in base-R."
GGP2 does make graphics easier. But it is misleading to speak of GGP2 as justification for using the Tidyverse, especially in teaching. A listing of the chronology clarifies the matter:
-
The GGP2 package was Hadley Wickham's PhD project, which implemented Lee Wilkinson's grammar of graphics ideas. Hadley completed his dissertation in 2008, well before Tidy.
-
The pre-Tidy nature of GGP2 is exemplified by the fact that in the GGP2 code, Hadley has SEVEN instances of calls to tapply()--the function the Tidiers "love to hate."
-
GGP2 uses the '+' operator to modify a plot, rather than the Tidy way, which would be to use a pipe. In fact, Hadley has noted that he would use a pipe if he were designing GGP2 today.
Again, GGP2 is a wonderful package. RStudio has the right to define the Tidyverse however they feel appropriate. But RStudio's naming freedom does not justify burdening and handicapping R learners with Tidy, i.e. FP, dplyr, purrr and so on.
If there is one aspect of the Tidy-vs.-base-R debate that in my opinion demonstrates the problem with Tidy, it's that Tidy advocates want R beginners to avoid loops. Indeed, many of those advocates do not even teach loops at all.
The Tidyers want R beginners to use functional programming (FP) instead of loops. But even the Tidyers agree that the concept of functions is one of the hardest for beginners to learn. Thus it makes no sense to force beginners to use a the tough concept of FP in lieu of the much more natural loops approach. FP does have its place, but it should be taught as an advanced topic.
An anti-loops mentality has become the Tidy advocates' test of whether one is a "true believer" in the Tidy philosophy. I've seen Twitter posts in which R learners actually apologize for using loops.
It is worth noting that top university Computer Science Departments have shifted away from teaching their introductory programming courses using the FP paradigm, in favor of the more traditional Python, as they deem FP to be more abstract and challenging.
An interesting discussion of the topic is in Charavarty and Keller. Though they support using FP in introductory programming classes for CS majors, the authors' goals are antithetical to those of R learners. The authors list three goals, one of which is to teach theoretical computer science, certainly not desirable for teaching R in general, let alone for teaching R to those with no coding experience. They also concede that a key concept in FP, recursion, is a "signficant obstacle" even for CS students.
If FP is tough for CS students, it makes no sense to have nonprogrammer learners of R use it.
Even Hadley, in R for Data Science, says:
The idea of passing a function to another function is extremely powerful idea, and it’s one of the behaviours that makes R a functional programming language. It might take you a while to wrap your head around the idea, but it’s worth the investment.
Actually, most non-FP languages allow passing one function to another, but yes it is a powerful tool, worth the investment of time -- for the experienced R programmer. But again, it's wrong to force nonprogrammer learners of R to "wrap their heads around" FP.
And it is much more than just a matter of banning loops. The '$' and '[' operators must also be banned, as they allow side effects. In the example in our Prologue at the top of this essay, the base-R solution
df[column#,row#] = newvaluecauses df to change, a side effect. FP prohibits side effects, hence the proscribing of '['. The same problem arises with '$'.
Due to a catchy name, a charismatic developer (Hadley), the Bandwagon Effect, and highly aggressive marketing by a dominant commercial entity, Tidy now is a major force in the R world.
It has even brought a "pop culture" to R. One prominent Tidy advocate (and coauthor of the Educator Perspective article) even sells "Tidy merchandise" -- bags, mugs, and shoes. A popular Tidy Tuesday series has arisen on Twitter. At times, it has even veered into the realm of cult. There are many who equate Hadley Wickham with R itself. He is treated like a rock star by R "groupies." What a difference from the staid R community of yore! We who have been in R since the early days applaud RStudio for spreading the word, but it has come at major costs to the well-being of the language.
Putting the hero worship aside, at the very least one can say that many if not most in that huge Tidy following view R to consist mainly as
R = dplyr + ggplot2 + RStudio IDE + Rmarkdown
As noted, an article on the teaching of R argues against teaching a mix of base-R and Tidy to beginners, and RStudio founder JJ Allaire has refused to recommend teaching a mix.
To us longtime R advocates, this is a tragic irony. On the one hand, again RStudio is to be congratulated for greatly increasing the worldwide count of R users. But the tragedy is that those users tend to be ill-equipped to actually use R productively, compared to "graduates" of standard base-R courses -- and without Tidy being easier to learn.
The danger of being wrapped up in hoopla and crusade, of course, is that one can lose sight of reality. In my view, this is what has happened with Tidy.
Equally important is the impact on the R language itself. In his aforementioned keynote address, Prof. Peng asked,
It will be interesting to see how things evolve, and whether the community can sustain multiple ways of programming. I think that it can, but that's my opinion.
I am indeed worried that R will split into two different "dialects. Though Peng's speculation may be correct if one views R strictly as a programming language, R is a statistical tool. As explained earlier in this document, Tidy is at odds with the most R statistical packages. Though packages like broom might be developed to bridge the gap in some specific instances, there obviously are far too many packages for this to be realistic. It is here that the divide between the Tidy and base-R worlds may be mostly keenly manifest.
Sadly, that divide has occasionally become personal. For instance, there was harsh public criticism from some in RStudio and the firm's allies, toward the base-R-favoring R/Finance Conference in 2018, accusing the conference organizers of being insensitive to gender diversity. In my view, this was quite unfair, and it was my first exposure to a bitter base/Tidy divide. It was also my first real exposure to Twitter. Shortly after the conference, an RStudio employee asked me, "What do you think of the tweetstorm about the conference?", total news to me. I was shocked by the vitriol.
Some in RStudio have Twitter-blocked some of the Tidy critics, abruptly ending frank but civil conversation. In my case, one major RStudio developer made quite a show of it, tweeting a screen shot in which "You have blocked this user" is repeated dozens of times. There was also tension between RStudio and Matt Dowle, author of data.table, a technically superior competitor to dplyr.
But the good news is that both sides have been making attempts at reconciliation. Especially notable is that the R Core Group, a body that controls the development of base-R, recently added a native pipe to the language. I doubt many in that group actually use it, but it is an impressive olive branch. The R Foundation now includes a number of pro-Tidy members.
RStudio, including Hadley, has also made various conciliatory public remarks. Indeed, my meeting with RStudio CEO JJ Allaire in 2019 came at JJ's suggestion. Around that time, JJ also met with Matt Dowle. Also in 2019, RStudio stopped viewing data.table as a rival, and announced the release of dtplyr, a Tidy-syntax front end to data.table. Since data.table is much faster on large datasets than dplyr, this was a win-win for the entire R community.
Hopefully we will be seeing more of these positive trends in the coming years. As I explained in that meeting with JJ, the best form of reconciliation on RStudio's part would be to encourage instructors in the Tidy community to teach a mixture of Tidy and base-R.
It should be noncontroversial that R learners should be given a choice of tools, and that they themselves should decide what is the best one to use in any given setting. And if for example some thus-empowered useR feels that
mtcars$hwratio <- mtcars$hp / mtcars$wtis more convenient than
mtcars %>% mutate(hwratio=hp/wt) -> mtcarsso be it. There will be other cases in which the graduates of mixed instruction find the Tidy solution more appealing. Rest assured, Tidy is here to stay.