Tag Archives: system

Rstudio, knitr (Rmarkdown2) and bash

5.01.2015 admin

I couldn’t find any example online how to revise my R code getting the exif data from pictures

fn <- c("/usr/local/bin/exiftool /Users/wjst/Desktop/white.tif")
info <- system(fn,inter=TRUE,wait=TRUE)

when moving now to knitr. So here is what worked for me as a replacement including the parsing
of exiftool output.

```{r, engine='bash', echo=FALSE}
/usr/local/bin/exiftool /Users/wjst/Desktop/white.tif >/Users/wjst/Desktop/white.txt
```
```{r Exif, echo=FALSE}
fn <- '/Users/wjst/Desktop/white.txt'
info <- paste(readLines(fn))
info <- strsplit(info,"[:]{1}[ ]{1}")
info <- matrix(data=unlist(info), ncol = 2, byrow = TRUE)
info <- gsub("(^[[:space:]]+|[[:space:]]+$)", "", info)
```
*Exif*
`r kable(info)`

Allergy, Philosophy

An epidemic of nonsense

2.10.2014 admin

13 € for a paperback, this is “An Epidemic of Absence. A new way of understanding allergies and autoimmune disease”. It is written by Moises Velasquez-Manoff , a journalist otherwise working for the “The Christian Science Monitor”. As his online bio reports “he dreamed of writing novels”. I would wish he would done so.

The outset is rather clear – Velasquez-Manoff wants to find a cure for his own autoimmmune disease. While this may be a legitimate justification for collecting information about a given topic, the method by Velasquez-Manoff is not. At a first glance, it looks like a serious book, well written, interesting facts presented in a coherent manner followed by numerous references. Maybe that made such an impression on the (numerous) positive reviewers. Maybe all the positive reviewers are experienced science journalists that judged by the overall impression plus some common sense plus some specific knowledge. But, Velasquez-Manoff did never hear the other side (on p.310, he even admits who has read and commented on sections of the manuscript: exclusively scientists in favor of the hygiene hypothesis). To recognize that you need to be a scientist – journalists would not notice that.

I compiled a long list the errors but feel now, that it would be too time consuming to write that down here. As far as it concerns me (p. 99) there was no grant to win in Munich as the study Velasquez-Manoff is talking about was a commissioned study. And sorry (p.100) I wrote the full grant application comparing East and West Germany children and did large part of the field study. Furthermore, I am not convinced (p.101) that the East West German differences ever supported the hygiene hypothesis, it is something different. And it was not in 2000 (p.102) that someone published on day care (p. 102), we wrote that already in 1999. Audiatur et altera pars, yea, yea.

Theology

The science market bubble

9.02.2010 admin

Wikipedia describes the last year’ financial crisis as “an economic bubble (sometimes referred to as a speculative bubble, a market bubble, a price bubble, a financial bubble, or a speculative mania) as a â€œtrade in high volumes at prices that are considerably at variance with intrinsic values”. A new and excellent Embo Report (thanks to WK) arrives at the same description of current science, a

dangerous cocktail of short-term gains prevailing over long-term interests, herding, increasing pressure to deliver results, the absence of effective oversight, and blind trust that the system would regulate itself Continue reading The science market bubble →