Please assign informative names to downloaded PDFs!

Bravo for the journals that assign human-readable informative names to the PDF versions of articles downloaded from their web sites.  For example, these naming schemes are very nice:

Hum. Mol. Genet.-2015-Simpkin-3752-63.pdf
PNAS-2005-Storey-12837-42.pdf
Int. J. Epidemiol.-2015-Sharp-1288-304.pdf


Boo for the journals that assign non-informative names to their PDF files.  For example, these naming schemes are not informative to me (even though the DOI is part of the name of the first two):

art%3A10.1186%2Fgb-2013-14-5-r42.pdf
art%3A10.1007%2Fs11357-016-9927-9.pdf
ijerph-12-14461.pdf

Simple parallelization using 'sem' of the GNU parallel package

If you have a multiprocessor computer, you can easily use the ‘sem’ part of the GNU Parallel system to run processes in parallel.   

It was really simple to use and worked as intended.  And this was much easier to install and get working than the other approach I was contemplating, which was installing grid engine software.

See:

https://www.gnu.org/software/parallel/sem.html

Below is my parallelized script, which ran a whole set of “HaploPS” commands in parallel using 12 of my processors.  I have bolded the two 'sem' commands that made this script execute in parallel.

$ more run_haploPS_parallel.sh 

#!/bin/bash

for (( chr=1;chr<=22;chr=chr+1)) {

     cd $chr

     for (( i=95 ; i>=5 ; i=i-5)) {

        freq=$(echo "scale=2;$i/100"|bc)

        date

        echo "Starting HaploPS run on chromosome " $chr " with freq = " $freq

        sem -j12 HaploPS -geno selscan.hap -legend selscan.map -freq 0$freq -out ../haploPS/haploPS_0${freq}_chr${chr}.txt 

        echo "Run completed."

        date

}

      cd ..

}

sem --wait

##############It will automatically run haploPS at 5 to 95 percent frequencies.

#################################################################

The difference between mathematics and statistics

"Mathematics is about whether the conclusions follow from the assumptions. By contrast, statistics is about whether the assumptions have anything to do with the real world." 

Jay Kadane, Leonard J. Savage Professor of Statistics, Emeritus, Carnegie-Mellon University

rsync

As part of transitioning from using an old desktop to a new desktop (while both are still active), I found the 'rsync' command to be very useful.  Here is the options I ended up using to accomplish my goal of copying over (old) files from the old machine to the new without wiping out any new files on the new machine:

rsync -avzuhP --log-file=/destination/dir/rsync_log.txt -e ssh remoteuser@remotehost:/source/dir /destination/dir/

Here's what the options do:
-a archive
-v verbose
-z compress
-u update  <= Do Not Overwrite the Modified Files at the Destination
-h human-readable
-P progress bar/partial transfers

Note that these options are turned on in '-a' archive mode:
        -r, --recursive             recurse into directories
        -l, --links                 copy symlinks as symlinks
        -p, --perms                 preserve permissions
        -t, --times                 preserve times
        -g, --group                 preserve group
        -o, --owner                 preserve owner (super-user only)
        -D                          same as --devices --specials

Hiding 'answer' slides in student handouts using Beamer

After adding 'Question' slides, followed by 'Answer' slides, to my Beamer presentation, I wondered if there was an easy way to remove the 'Answer' slides from the handout version of the slides that I will give to the students.

It turns out that there is, as described in this link:  just add <handout:0> right after the \begin{frame}

When 'handout' is added to the document class, all those slides marked with <handout:0> are automatically excluded.

This is wonderful!

The wonderful 'endfloat' LaTeX package

With LaTeX (or LyX), one can work on a manuscript while placing the tables and figures in their natural places, and then, with the addition of a single line to the preamble:

\usepackage[nolists,tablesfirst]{endfloat}

the tables and figures are magically moved to the end, as is required at submission by many journals.  

The 'endfloat' package even inserts markers like "[Table 1 about here]" in the main text.

Now I just need to persuade my colleagues to start writing their manuscripts in LaTeX...

Here is an amazing set of photographs of C.C. Li, who was the founder of the Division of Human Genetics within the Department of Biostatistics at the University of Pittsburgh.