All posts by admin

Software

How to scrape a website with R II: WYSIWYG

Part II

Although Rselenium allows a screenshot of the current browser window

library(RSelenium)
remDr <- remoteDriver(
  remoteServerAddr = "localhost",
  port = 4444,
  browserName = "Chrome"
)
remDr$open()
remDr$navigate("http://google.com")
remDr$screenshot(display = T) # remDr$screenshot(file="screen.jpg")

I found it extremely difficult to control a webbrowser running in a Docker container – looking up the DOM tree, injecting javascript etc is a lot of guess work.

So we need also a VNC server in the docker container as found at github.

After starting in the terminal

docker run -d -p 4444:4444 -p 5900:5900 -v /dev/shm:/dev/shm selenium/standalone-chrome:4.0.0-beta-1-prerelease-20210207

we can watch live at vnc://127.0.0.1:5900 what’s going on.

 

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Allergy, Philosophy

Mass rebellion?

Richard Smith about “Peer reviewers-time for mass rebellion?” citing a colleague

"I never peer review. Why would I waste my time reviewing crummy research when I can be doing my own research? What's more, I'm funded to do research and am rewarded for it. Nobody either funds me to review or rewards me for doing it."

As always an excellent opinion piece. Didn’t medRxiv and bioRxiv show in 2020 that we don’t need pre publication review anymore?

 

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Philosophy

Isolated vertical or horizontal lines in gel images are not jpg compression artifacts

I frequently find the PubPeer excuse of compression artifacts in doctored images.

So lets have a look at that issue using the jpegoptim (manpage) and also jpeginfo (manpage). These are the usual effects

  • Ringing – high contrast areas with waves
  • Contouring, Banding, Pposterisation – extreme brightness changes
  • Staircase noise – along curving edges
  • Blockiness in “busy” regions – may mimick duplications
  • Gibbs phenomenon – small highlighted area of large contrast
  • Alias, MoirĂ©, frequent color/brightness change

Now let’s have a look at the compression artifacts in descending quality (BTW this also good exercise for the upcoming 125kB Content Upload Filter, I am therefore adding filesize also)

 

original image 893kB

Continue reading Isolated vertical or horizontal lines in gel images are not jpg compression artifacts →

 

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Noteworthy

A museum of diverse intellectual pathologies

There is a super interesting 1992 paper of Jacobson/Feinstein oxygen as a cause of blindness in premature infants: “autopsy” of a decade of errors in clinical epidemiologic research While it is quite obvious to recognize such an epidemic at a late stage (as in the thalidomide scandal) it needs quite a lot of oversight at the early phase.

it took more than a decade-1942 to 1954-to end an iatrogenic epidemic in which high-dose oxygen therapy led to retrolental fibroplasia (RLF) in premature infants, blinding about 10,000 of them. The autopsy revealed a museum of diverse intellectual pathology. When first noted, RLF was regarded as neither a new disease nor a postnatal effect. In early investigations, the ophthalmologists did not establish explicit criteria for diagnosis and confused RLF with malformations previously seen in full-term infants. Because the patients were not referred until months after birth, the ophthalmologists assumed that the lesion, which resembled an embryologic structure, must have occurred prenatally.

Even with the current COVID-19 we can see “live on stage” blinded experts. Maybe the “early intubation epidemic” is another example with new data published in the ERJ.

 

CC-BY-NC Science Surf , accessed 23.08.2026
Software

Sometimes it is better to switch bikes not gears

My 3 favorite programs? R, Bookends and Exposure.

The first choice is Rstudio (since 2012, being a long time SAS user). Here is the most recent JJ Allaire keynote

 

I was a bit with late with Bookends in 2018 (being a long time Sente user) but here is an introduction by Jon Ashwell.

 

And I am currently migrating to Exposure (after having used Lightroom for 13 years) by Jeff Butterworth

 

Life changes every day while it is sometimes better to switch bikes not gears.

 

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Software

Breaking up long chains in R’s dplyr/magrittr code and calling sub functions

Having several long and redundant chains in R ‘s magittr code, I have now figured out how to pipe into named and unnamed functions

f1 <- function(x) {
  x %>% count() %>% print()
}
f2 <- function(x) {
  x %>% tibble() %>% print()
}

So we have now two named functions with code blocks that can be inserted in an unnamed function whenever needed

iris %>%
  # do any select, mutate ....
  # before running both functions
  (function(x) {
    x %>% select(Species) %>% f1() %>% print()
    x %>% f2() %>% print()
  })

We can make a variable global from inside a function using <<- assignment but I have not found a way to continue the dplyr chain with any returned variable. So we are trapped inside the function

iris %>%
  (function(x) {
    result <<- x %>% head(1)
  })

 

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Philosophy

Re-Check your references before submission

I think it is now mandatory to check all references if there any PubPeer notes or if the references even has been retracted.

A recent Nature News highlights the issue

Most of the papers that cite discredited COVID research in The Lancet and The New England Journal of Medicine don't mention that the studies have been retracted. The infamous studies relied on health-record analyses from a company, Surgisphere, that declined to share its raw data for an audit. Science looked at 200 academic articles that cite the Surgisphere papers and found that 52.5% - including some in prominent journals - failed to mention the retractions.

 

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Philosophy

Facebook Epidemiology

By Adrian Gerard Barnett in “Epidemiology”

Some scientists hastily pivoted to epidemiologic modeling, including many with no qualifications or experience. This effort was likely from a desire to help, but it gummed up the scientific machinery with hundreds of new modeling papers needing expert peer review, while the real experts were busy on the models that mattered.
In the future, for such nationally important models, I would like to have two independent groups of official model- ers who would transparently report their results to the gov- ernment and the public. There are lots of uncertainties and scientific decisions that go into these models, and two expert groups coming to the same conclusion would greatly increase confidence for the decision makers…

I would like that also.

 

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Philosophy

Der Tanz auf dem Vulkan

Virologie und Epidemiologie sind der Eindämmung der Pandemie verpflichtet (Viren und ihre Ausbreitung kann man wissenschaftlich untersuchen).

Politik in der Demokratie ist der Mehrheitsfindung verpflichtet (mit Viren selbst kann man ja nicht verhandeln).

Juristen bedienen sich der Hermeneutik bestehender Gesetzestexte (auch wenn da eher wenig zu Viren steht).

Der “dance” wurde damit in den westlichen Demokratien zum groĂźen Tanz auf dem Vulkan. Auch wenn die Zahlen langsam sinken, der Abstieg ist nun genauso mĂĽhsam und gefährlich wie der Aufstieg.

Quelle: https://www.pngegg.com/de/png-ddgel/download und https://ourworldindata.org/coronavirus/country/germany?country=~DEU

Den fĂĽr mich unerwarteten zweiten groĂźen Absturz in der Corona Pandemie hat Heribert Prantl vor 2 Tagen im Hangar-7 hingelegt. Bei Artikel 2 GG hat Prantl offensichtlich nur den ersten Halbsatz von (1) gelesen:

(1) Jeder hat das Recht auf die freie Entfaltung seiner Persönlichkeit, soweit er nicht die Rechte anderer verletzt und nicht gegen die verfassungsmäßige Ordnung oder das Sittengesetz verstößt.

(2) Jeder hat das Recht auf Leben und körperliche Unversehrtheit. Die Freiheit der Person ist unverletzlich. In diese Rechte darf nur auf Grund eines Gesetzes eingegriffen werden.

 

CC-BY-NC Science Surf , accessed 23.08.2026
Noteworthy

COVID-19 Mortalität V: Vergleich Schweiz/Österreich

Hier noch ein Vergleich der Case Fatality Rate in Deutschland mit Ă–sterreich und der Schweiz.

Beide Länder haben in der ersten Phase offensichtlich dazu gelernt, wie man besser (nicht) beatmet, Deutschland hat eher nichts dazugelernt.

 

Quellen: RKI (Deutschland) https://experience.arcgis.com/experience/478220a4c454480e823b17327b2bf1d4 AGES (Österreich) https://covid19-dashboard.ages.at/dashboard.html sowie Dashboard (Schweiz) https://www.covid19.admin.ch/de/overview Download am 24.1.2021. CFR im gleitenden Mittel aus Fällen 14 Tage vor und Todesfällen 14 Tage nach dem Indextag. Letzter berichteter Wert 15.12.2020
Zeitungsausriss 29.10.2021, ĂĽberprĂĽft am 24.1.2021, Quelle https://wien.orf.at/stories/3073495/

 

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Philosophy

Uri Geller in Nature

Alle Nature Artikel in meinem engeren Arbeitsgebiet lagen daneben. Warum es aber trotzdem als höchste Auszeichnung gilt, einen Artikel dort veröffentlicht zu haben? Wo doch die allermeisten Artikel nicht einmal besonders häufig zitiert werden?
Und das mit Kosten für den deutschen Steuerzahler in Höhe von 9,500€?

Vielleicht sollte man doch mal an einen der legendärsten Artikel in Nature erinnern – die Studie zu Uri Geller (James Randi der den Geller Betrug aufgeklärt hat ist gerade erst verstorben).

The establishment of ESP [extrasensory perception] could conceivable require a paradigm shift (in Kuhn’s sense) of the most fundamental kind and our concepts of mind-brain relationships and cobsciousness would need radical alteration.

Es ist dabei nicht so sehr ein einzelner Artikel (den man natürlich hätte veröffentlichen können) sondern der monatelange Hype, der hier befeuert wurde.

Doch zurück zu den 9,500€ von den kein Reviewer einen Cent sieht. Undark hat eine vernichtende Analyse des Geschäftsmodells

But Springer Nature's announcement also exposes a deep structural problem in scientific publishing. The proposed author fee, known as an article processing charge, or APC, is several times higher than what other publishers charge; it will likely be out of reach for researchers working outside of the world's top institutions. Viewed in that light, Springer Nature's move to open access seems less like a step toward equity and more like a corporation taking advantage of an uneven scientific funding landscape to increase its profits.

 

 

CC-BY-NC Science Surf , accessed 23.08.2026
Philosophy

Wissenschaftsjournalismus in Deutschland

Die Defizite des Wissenschaftsjournalismus in Deutschland sind ja offensichtlich von vielen Kommentaren hier etwa zur NO2 Berichterstattung,
zu den Crispr Cas Zwillingen oder auch zu COVID-19.

Aber gibt es eine mehr systematische Exploration?

Die folgenden Literaturhinweise verdanke ich Carsten Reinmann

Die Qualität der Berichterstattung über Wissenschaft

Zu dem Thema auch

Senja Post (2015) http://doi.org/10.1177/1464884914541067
Summ/Volpers (2016) http://doi.org/10.1177/0963662515583419
Guenther et al. (2019) https://doi.org/10.1080/1461670X.2017.1353432

Völlig unbeirrt hagelt es nun Preise.

Mai Thi Nguyen-Kim ist "medium magazin" Journalistin des Jahres 2020.

Dazu die Recherchekooperation "Pillenkick" von Correctiv und ARD-Dopingredaktion: Jonathan Sachse, Arne Steinberg (Correctiv) und Hajo Seppelt, Wigbert Löer, Josef Opfermann, Patricia Corniciuc, Jörg Mebus, Shea Westhoff (ARD).

Und Volker Stollorz, Science Media Center.

 

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