Year: 2013

To submission

The goal before being really back to work is to finish the corrections of a manuscript, so as to submit it in first days of January. Then I’ll focus on writing my final thesis. My Christmas reading of ggplot2 gave me a lot of nice ideas.

I also have to finish the introduction course to R that I’ll give to colleagues next week. It’s going to be funny!

Posted by Benjamin in Publications, 0 comments

Christmas Holidays

Since exactly two years, I write a summary once a week to keep track of what’s happening, mostly about work matters, but occasionally about personal events also. I decided to write them here instead, as a public short lab notebook.

But, there is no much to say currently! I tried to achieved many things during the last days to get ready for Christmas Holidays. I’m finally back in France for two weeks, but you can still reach me by email 😉 More will come in the next weeks. In the meantime, I’m getting better with Illustrator.

Posted by Benjamin in Lab Notes, 0 comments

Convert BP and BC/AD times

This Alfred workflow converts BP times (Before Present) to BC/AD years, and reversely. The BC times have to be given as negative years. The result is copied to the clipboard, and alternatively as “cal. BP” or “cal. BC” when holding the action modifier Alt.

Posted by Benjamin in Software, 0 comments

Calculate mean and error

I often need to calculate the mean and ± error of two numbers, like for instance of a radiocarbon date. Here is a workflow (and below the AppleScript it includes) to calculate these two parameters based on two numbers input in Alfred.

set FirstNumber to first word of q as integer
set SecondNumber to second word of q as integer

set NumbersAverage to (FirstNumber + SecondNumber) / 2 as integer
set NumbersError to (SecondNumber - FirstNumber) / 2 as integer

set q to NumbersAverage & "±" & NumbersError as text
Posted by Benjamin in Software, 0 comments


PolyCounter is an amazing free software to count microfossils (or anything else) by Takeshi Nakagawa. It comes with a clean and intuitive user interface. You just need few minutes to get used to it and know how to set it. It provides counting alarms, real-time accumulation curve, and instant diagrams. Data are directly available in your directory as a csv file.

I strongly recommend it to whoever needs to analyze pollen samples!

Posted by Benjamin in Software, 0 comments

Clam Starter

Clam is one my favorite piece of software. Designed by Maarten Blaauw, it allows to draw age-depth model of stratigraphic cores, using the software R. It uses a csv file containing your radiocarbon dates’ results, stored in a specific folder. To avoid mistake and save time, I wrote an AppleScript to use with Alfred (my favorite Mac app!).

Continue reading →
Posted by Benjamin in Software, 0 comments

Scholarship in Sweden

I spent one month from mid-January to mid-February 2013 at the University of Kalmar (Sweden) to learn the theory of quantitative reconstruction of past vegetation. It consisted in courses and practical work to get used to the models developed by Shinya Sugita (including the models REVEAL and LOVE, as well as the Landscape Reconstruction Algorithm). This was the opportunity to apply these models to my data and represent so far the first attempt in the Alps.

Continue reading →
Posted by Benjamin in Lab Notes, 0 comments

Make a so-called csv a real csv

When you create csv files from the same systems than those which are not able to properly open them, you might need afterward to clean it up. I often find myself annoyed by so-called csv files that are actually delimited by semicolons, and commas are used as decimal separators. Here is a code to first replace commas by periods, then replace semicolons by commas.

tell application "Finder" to set FileToEdit to selection as string
set AccessToFile to open for access file FileToEdit with write permission
set CSVContent to read file FileToEdit
to switchText from t to r instead of s
set d to text item delimiters
set text item delimiters to s
set t to t's text items
set text item delimiters to r
tell t to set t to item 1 & ({""} & rest)
set text item delimiters to d
end switchText
switchText from CSVContent to "." instead of ","
set FirstStepText to result
switchText from FirstStepText to "," instead of ";"
set TextToWrite to result
set eof of file FileToEdit to 0
write TextToWrite to AccessToFile
close access AccessToFile

Credit goes to member kai (

Posted by Benjamin in Software, 0 comments