Archive for C

ten computer codes that transformed science

Posted in Books, Linux, R, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , on April 23, 2021 by xi'an

In a “Feature” article of 21 January 2021, Nature goes over a poll on “software tools that have had a big impact on the world of science”. Among those,

the Fortran compiler (1957), which is one of the first symbolic languages, developed by IBM. This is the first computer language I learned (in 1982) and one of the two (with SAS) I ever coded on punch cards for the massive computers of INSEE. I quickly and enthusiastically switched to Pascal (and the Apple IIe) the year after and despite an attempt at moving to C, I alas kept the Pascal programming style in my subsequent C codes (until I gave up in the early 2000’s!). Moving to R full time, even though I had been using Splus since a Unix version was produced. Interestingly, a later survey of Nature readers put R at the top of the list of what should have been included!, incidentally including Monte Carlo algorithms into the list (and I did not vote in that poll!),

the fast Fourier transform (1965), co-introduced by John Tukey, but which I never ever used (or at least knowingly!),

arXiv (1991), which was started as an emailed preprint list by Paul Ginsparg at Los Alamos, getting the current name by 1998, and where I only started publishing (or arXiving) in 2007, perhaps because it then sounded difficult to submit a preprint there, perhaps because having a worldwide preprint server sounded more like bother (esp. since we had then to publish our preprints on the local servers) than revolution, perhaps because of a vague worry of being overtaken by others… Anyway, I now see arXiv as the primary outlet for publishing papers, with the possible added features of arXiv-backed journals and Peer Community validations,

the IPython Notebook (2011), by Fernando Pérez, which started by 259 lines of Python code, and turned into Jupyter in 2014. I know nothing about this, but I can relate to the relevance of the project when thinking about Rmarkdown, which I find more and more to be a great way to work on collaborative projects and to teach. And for producing reproducible research. (I do remember writing once a paper in Sweave, but not which one…!)

why does rbinom(1,1) differ from sample(0:1,1) with the same seed?

Posted in Statistics with tags , , , , , , , , , on February 17, 2021 by xi'an
> set.seed(1)
> rbinom(10,1,0.5)
 [1] 0 0 1 1 0 1 1 1 1 0

> set.seed(1) > sample(c(0,1), 10, replace = TRUE) [1] 0 1 0 1 0 0 1 0 1 1

This rather legitimate question was posted on X validated last week, the answer being that the C codes behind both functions do not use pseudo-random generators in the same manner. For instance, rbinom does get involved beyond a mean value of 30 (and otherwise resorts to the inverse cdf approach). And following worries about sample biases, sample was updated in 2019 (and also seems to resort to the inverse cdf when the mean is less than 200). However, when running the above code on my machine, still using the 2018 R version 3.4.4!, I recover the same outcome:

> set.seed(1)
> rbinom(10,1,0.5)
 [1] 0 0 1 1 0 1 1 1 1 0

> set.seed(1)
> sample(c(0,1), 10, replace = TRUE)
 [1] 0 0 1 1 0 1 1 1 1 0

> set.seed(1) > qbinom(runif(10),1,0.5) [1] 0 0 1 1 0 1 1 1 1 0
> set.seed(1) > 1*(runif(10)>.5) [1] 0 0 1 1 0 1 1 1 1 0


Posted in Books, Kids, R with tags , , , , , , , , , on March 28, 2019 by xi'an

One challenge on code golf is to find the shortest possible code to identify whether or not an integer belongs to the binary cyclops numbers which binary expansion is 0, 101, 11011, 1110111, 111101111, &tc. The n-th such number being

a(n) = 2^{2n + 1} - 2^n - 1 = 2\,4^n - 2^n - 1 = (2^n - 1)(2\,2^n + 1)

this leads to the above solution in R (26 bits). The same length as the C solution [which I do not get]


And with shorter versions in many esoteric languages I had never heard of, like the 8 bits Brachylog code


or the 7 bits Jelly


As a side remark, since this was not the purpose of the game, the R code is most inefficient in creating a set of size (x+1), with most terms being Inf.

València summer school

Posted in Kids, pictures, R, Running, Statistics, Travel, University life, Wines with tags , , , , , , , , on January 31, 2018 by xi'an

In another continuation of the summer of Bayesian conferences in Europe, the Universidat de Valencià is organising a summer school on Bayesian statistics, from 16 July till 20 July, 2018. Which thus comes right after our summer school on computational statistics at Warwick. With a basic course on Bayesian learning (2 days). And a more advanced course on Bayesian modeling with BayesX. And a final day workshop.

Extending R

Posted in Books, Kids, R, Statistics with tags , , , , , , , , , , , , , , , , , on July 13, 2016 by xi'an

As I was previously unaware of this book coming up, my surprise and excitement were both extreme when I received it from CRC Press a few weeks ago! John Chambers, one of the fathers of S, precursor of R, had just published a book about extending R. It covers some reflections of the author on programming and the story of R (Parts 2 and 1),  and then focus on object-oriented programming (Part 3) and the interfaces from R to other languages (Part 4). While this is “only” a programming book, and thus not strictly appealing to statisticians, reading one of the original actors’ thoughts on the past, present, and future of R is simply fantastic!!! And John Chambers is definitely not calling to simply start over and build something better, as Ross Ihaka did in this [most read] post a few years ago. (It is also great to see the names of friends appearing at times, like Julie, Luke, and Duncan!)

“I wrote most of the original software for S3 methods, which were useful for their application, in the early 1990s.”

In the (hi)story part, Chambers delves into the details of the evolution of S at Bells Labs, as described in his [first]  “blue book” (which I kept on my shelf until very recently, next to the “white book“!) and of the occurrence of R in the mid-1990s. I find those sections fascinating maybe the more because I am somewhat of a contemporary, having first learned Fortran (and Pascal) in the mid-1980’s, before moving in the early 1990s to C (that I mostly coded as translated Pascal!), S-plus and eventually R, in conjunction with a (forced) migration from Unix to Linux, as my local computer managers abandoned Unix and mainframe in favour of some virtual Windows machines. And as I started running R on laptops with the help of friends more skilled than I (again keeping some of the early R manuals on my shelf until recently). Maybe one of the most surprising things about those reminiscences is that the very first version of R was dated Feb 29, 2000! Not because of Feb 29, 2000 (which, as Chambers points out, is the first use of the third-order correction to the Gregorian calendar, although I would have thought 1600 was the first one), but because I would have thought it appeared earlier, in conjunction with my first Linux laptop, but this memory is alas getting too vague!

As indicated above, the book is mostly about programming, which means in my case that some sections are definitely beyond my reach! For instance, reading “the onus is on the person writing the calling function to avoid using a reference object as the argument to an existing function that expects a named list” is not immediately clear… Nonetheless, most sections are readable [at my level] and enlightening about the mottoes “everything that exists is an object” and “everything that happens is a function” repeated throughout.  (And about my psycho-rigid ways of translating Pascal into every other language!) I obviously learned about new commands and notions, like the difference between

x <- 3


x <<- 3

(but I was disappointed to learn that the number of <‘s was not related with the depth or height of the allocation!) In particular, I found the part about replacement fascinating, explaining how a command like

diag(x)[i] = 3

could modify x directly. (While definitely worth reading, the chapter on R packages could have benefited from more details. But as Chambers points out there are whole books about this.) Overall, I am afraid the book will not improve my (limited) way of programming in R but I definitely recommend it to anyone even moderately skilled in the language.