Using RStudio, it is very easy to create Beamer slides using R Markdown. RStudio also supports LaTeX, so this enables even more flexibility.
Using the template shared here:
https://github.com/DanielEWeeks/Beamer-Rmd-Notes-Slides
one can also insert 'note slides' that can easily be all included or all excluded from the generated set of slides, just by toggling one word in the LaTeX header.
This allows one to use a more concise set of slides, without the notes, in class while providing the students a more comprehensive set that contains all the notes.
It could also be used to hide 'answer' slides from the students' slide set when posing questions in class. When posing questions in class, I prefer that the students don't have the 'answer' slides right in front of them. Then, after class, I make the slide set that contains the 'answer' slides available.
I previously shared instructions on a different approach for doing this when generating Beamer slides using LaTeX or LyX - see:
http://deweeks.blogspot.com/2014/08/hiding-answer-slides-in-student.html
Daniel E. Weeks' Blog
Dr. Weeks is a Professor of Human Genetics and Biostatistics at the University of Pittsburgh. His research focuses on statistical human genetics in the area of mapping susceptibility loci involved in complex human diseases. The content on this blog is for informational purposes only - use at your own risk!
Friday, December 23, 2016
Friday, November 11, 2016
Optical character recognition
Here is a script that uses the 'tesseract' optical character recognition software to extract recognizable text from a PDF file:
#!/bin/bash
# Purpose:
# To carry out OCR on a PDF file
if [[ $# -ne 1 ]]; then
echo "This script expects one argument."
echo " This argument is the name of the pdf file"
echo " including the .pdf extension"
echo "Usage: $0 file.pdf "
else
filename=$(basename "$1")
filename="${filename%.*}"
echo "Converting $1 to a tiff file named $filename.tiff"
echo "... "
convert -density 300 $1 -depth 8 -strip -background white -alpha off $filename.tiff
echo "Carrying out OCR on $filename.tiff to create $filename.txt"
tesseract $filename.tiff $filename
echo "The recognizable text in $1 has been output to the $filename.txt file."
fi
For information on how to install the needed software, see this web page.
Friday, October 28, 2016
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
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
Tuesday, March 22, 2016
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.
#################################################################
Tuesday, August 18, 2015
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
Jay Kadane, Leonard J. Savage Professor of Statistics, Emeritus, Carnegie-Mellon University
Monday, February 23, 2015
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
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
Thursday, August 28, 2014
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!
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!
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