What is R, what it was, and what it will become

Roger Peng provides a lesson on the roots of R and how it got to where it is now:

Chambers was referring to the difficulty in naming and characterizing the S system. Is it a programming language? An environment? A statistical package? Eventually, it seems they settled on “quantitative programming environment”, or in other words, “it’s all the things.” Ironically, for a statistical environment, the first two versions did not contain much in the way of specific statistical capabilities. In addition to a more full-featured statistical modeling system, versions 3 and 4 of the language added the class/methods system for programming (outlined in Chambers’ Programming with Data).

I’m starting feel my age, as some of the “history” feels more like recent experience.

You can also watch Peng’s keynote in the video version.

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My father on D-Day: 75 years ago

Today is the 75th anniversary of D-Day—the day British, Canadian, and American troops landed on the beaches of Normandy.1

For us baby boomers it always meant a day of special significance for our parents. In my case, it was my father who took part in the invasions. That's him on the right as he looked in 1944. He was an RAF pilot flying rocket-firing typhoons in close support of the ground troops. His missions were limited to quick strikes and reconnaissance during the first few days of the invasion because Normandy was at the limit of their range from southern England. During the second week of the invasion (June 14th) his squadron landed in Crepon, Normandy and things became very hectic from then on with several close support missions every day [see Hawker Hurricanes and Typhoons in World War II].

I have my father's log book and here are the pages from June 1944 (below). The red letters on June 6 say "DER TAG." It was his way of announcing D-Day. On the right it says "Followed SQN across channel. Saw hundreds of ships ... jumped by 190s. LONG AWAITED 2nd FRONT IS HERE." Later that day they shot up German vehicles south-east of Caen where there was heavy fighting by British and Canadian troops. The next few weeks saw several sorties over the allied lines. These were mostly attack missions using rockets to shoot up German tanks, vehicles, and trains.

The photograph on the right shows a crew loading rockets onto a typhoon based just a few kilometers from the landing beaches in Normandy. You can see from the newspaper clipping in my father's log book that his squadron was especially interested in destroying German headquarter units and they almost got Rommel. It was another RAF squadron that wounded Rommel on July 17th.

The colorized photo on the left is my father in his Typhoon.

The log book entry (above) for June 10th says, "Wizard show. Recco area at 2000' south west of Caen F/S Moore and self destroyed 2 flak trucks, 2 arm'd trucks, and 1 arm'd command vehicle, Every vehicle left burning but one. Must have been a divisional headquarters? No casualties."

Here's another description of that rocket-firing typhoon raid [Air Power Over the Normandy Beaches and Beyond].
Intelligence information from ULTRA set up a particularly effective air strike on June 10. German message traffic had given away the location of the headquarters of Panzergruppe West on June 9, and the next evening a mixed force of forty rocket-armed Typhoons and sixty-one Mitchells from 2 TAF struck at the headquarters, located in the Chateau of La Caine, killing the unit's chief of staff and many of its personnel and destroying fully 75 percent of its communications equipment as well as numerous vehicles. At a most critical point in the Normandy battle, then, the Panzer group, which served as a vital nexus between operating armored forces, was knocked out of the command, control, and communications loop; indeed, it had to return to Paris to be reconstituted before resuming its duties a month later.

My father was awarded the Distinguished Flying Cross (DFC) for his efforts during the war.

(This article was first posted on June 6, 2014.)

1. The British landed at Sword Beach and Gold Beach, the Canadians at Juno Beach, and American troops landed at Omaha and Utah Beaches.

The role of cartography in early global explorations

For Lapham’s Quarterly, Elizabeth Della Zazzera turns back the clock to maps used for navigation, starting with the 1300s and through 1720:

From the fifteenth to the eighteenth century, European powers sent voyagers to lands farther and farther away from the continent in an expansionist period we now call the Age of Exploration. These journeys were propelled by religious fervor and fierce colonial sentiment—and an overall desire for new trade routes. They would not have been possible without the rise of modern cartography. While geographically accurate maps had existed before, the Age of Exploration saw the emergence of a sustained tradition of topographic surveying. Maps were being made specifically to guide travelers. Technology progressed quickly through the centuries, helping explorers and traders find their way to new imperial outposts—at least sometimes. On other occasions, hiccups in cartographic reasoning led their users even farther astray.

I particularly liked the part where in fourteen hundred ninety two, Columbus sailed the ocean blue — and made miscalculations because he misread the units on a map and ended up in the wrong part of the world.

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A phylogenetic network outside science

I have written before about the presentation of historical information using the pictorial representation of a phylogeny (eg. Phylogenetic networks outside science; Another phylogenetic network outside science). These diagrams are often representations of the evolutionary history of human artifacts, and so a phylogeny is quite appropriate. They are of interest because:
  • they are usually hybridization networks, rather than divergent trees, because the artifact ideas involve horizontal transfer (ideas added) and recombination (ideas replaced);
  • they are often not time consistent, because ideas can leap forward in time, so that the reticulations do not connect contemporary artifacts (see Time inconsistency in evolutionary networks); and
  • they are sometimes drawn badly, in the sense that the diagram does not reflect the history in a consistent way.
The latter point often involves poor indication of the time direction (see Direction is important when showing history), or involves subdividing the network into a set of linearized trees.

One particularly noteworthy example that I have previously discussed is of the GNU/Linux Distribution Timeline, which illustrates the complex history of the computer operating system. The problems with this diagram as a phylogeny are discussed in the blog post section History of Linux distributions.

In this new post I will simply point out that there is a more acceptable diagram, showing the key Unix and Unix-like operating systems. I have reproduced a copy of it below.

Click to enlarge.

This version of the information correctly shows the history as a network, not a series of linearized trees (each with a central axis). It also draws the reticulations in an informative manner, rather than having them be merely artistic fancies.

It is good to know that phylogenetic diagrams can be drawn well, even outside biology and linguistics.

Draft of talk, for comment

I will be presenting this talk in Brisbane in a few weeks. Have a look and make suggestions.

Corals — a new metaphor for phylogenetic diagrams

A year ago I mentioned a published discussion of the different branching diagrams that have been used for phylogenetic relationships (Tree metaphors and mathematical trees). If we consider the form of the relationship and whether time is involved, we get the following four possible diagram types:

Most current phylogenetic diagrams claim to show sister-group relationships (which means that ancestors are inferred only), with a time-order to the branching sequence. There is a broad range of diagram types in use, both mathematical and metaphorical. For example, the top four in this next diagram are mathematical and the bottom four are metaphorical variants of the above 2x2 table:

The connection between these different diagrams has both conceptual and practical problems, although these seem to be overlooked by most practitioners. This issue as been addressed by János Podani in a paper that is now online:
The Coral of Life. Evolutionary Biology (2019).
To quote from the Abstract:
The Tree of Life (ToL) has been of central importance in the biological sciences, usually understood as a model or a metaphor, and portrayed in various graphical forms to summarize the history of life as a single diagram. If it is seen as a mathematical construct — a rooted graph theoretical tree or, as more recently viewed, a directed network, the Network of Life (NoL) — then its proper visualization is not feasible, for both epistemological and technical reasons. As an overview included in this study demonstrates, published ToLs and NoLs are extremely diverse in appearance and content ... Metaphorical trees are even less useful for the purpose, because ramification is the only property of botanical trees that may be interpreted in an evolutionary or phylogenetic context. This paper argues that corals, as suggested by Darwin in his early notebooks, are superior to trees as metaphors, and may also be used as mathematical models. A coral diagram is useful for portraying past and present life because it is suitable: (1) to illustrate bifurcations and anastomoses, (2) to depict species richness of taxa proportionately, (3) to show chronology, extinct taxa and major evolutionary innovations, (4) to express taxonomic continuity, (5) to expand particulars due to its self-similarity, and (6) to accommodate a genealogy-based, rank-free classification.
It is worth checking out this paper, even if only for the new Coral of Life diagram that is presented in its Figure 3, which synthesizes much of our current knowledge.

John Ray

This has been submitted as an entry in the Encyclopedia of Evolutionary Psychological Science, and it is offered here for your delectation and delight… Title of entry: John Ray Synonyms: John Wray; Joanne Raio, Joannis Raii [Lat.] Life John Ray (1627/8–1705, known as Wray until 1670) was an English clergyman whose work in natural history […]

Lucretius and the papal secretary

In 1417, during the Council of Constance that reunited the Catholic Church in the west, a papal secretary took advantage of the location in Germany to visit some libraries, while the papacy was vacant. He was hunting manuscripts, but not the newly written ones. Instead Gian Francesco Poggio was seeking ancient manuscripts. A humanist inspired […]

CSI Tromsø: Where Forensics meets Vikings

  CSI Tromsø: Where Forensics meets Vikings   Posted August 22, 2018 by post-info Insect remains have their own tale to tell in the mystery that surrounds the Øsknes Viking burial boat, as Eva Pangiotakopulu

What was Darwin’s Origin actually called

So, I got caught parroting half-remembered factoids, to Down House no less, that the Origin dropped the “On” from the start of the title with the fourth edition. In my defence, I was making use of Darwin Online, the Cambridge University site that collates all of Darwin’s publications and a whole lot more, in their list […]