Software

A new era for the documentation of pollen counting data

As many of you already know, I’m a big fan of PolyCounter from Takeshi Nakagawa (find it here if you haven’t yet: http://polsystems.rits-palaeo.com/). PolyCounter introduced a modern way to acquiring data of Quaternary-palaeo-ecological samples, replacing the old-fashioned pen and paper by your computer. With PolyCounter, your counting data are instantly accumulated and stored in a numeric file, which is just what you need before you can actually visualise your data, and eventually apply fancy statistics on them.

https://giphy.com/embed/DHqth0hVQoIzS

Some potential users, however, have a (legitimate) fear of loosing data. Well, I would first argue that backing up data is one’s self duty, and actually a most-recommened practise for any kind of numerical data. But, regarding these counting data, I would mostly tell about particular features of PolyCounter.

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Posted by Benjamin in Lab Notes, Software, 0 comments

ggdiag

Last week was a short one. Thursday was off, and in such circumstances, people here usually also take the Friday off, and enjoy a looooong week-end. More explanations about this phenomenon in this video: https://www.youtube.com/embed/0-6sM0vo9Tk

I took this opportunity to work on a rather big project I’m truly dreaming of since years: plotting palynological diagrams with R! Since my Master studies, I’m using Tilia, which I became good at. I can produce complete, elegant diagrams, from scratch, in only a few hours. https://giphy.com/embed/CDJo4EgHwbaPS

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Learning Python

This month I’ve attended the seminar organised by the Laboratory of Maths of Besançon about Scientific informatics. There was nothing about directly related to my research topics but I was curious and thought I would eventually get interesting pieces of information. I did. The talks about rights and ownership of data and databases provided me useful insights regarding a personal project of mine (I hope I can write more about this very soon). There were a couple of talks about Python as well. Python is a language I want to get familiar with since long (more information here), and these talks motivated me. The syntax is similar to R, actually. I’m currently writing a little converter, slowly learning. I’ll probably use it with Alfred for punctual needs, but I’ll do larger scale conversions with R, and I’ll share it as it’s ready 😉

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PolyCounter and Windows 10

Great news, PolyCounter (this amazing software from Takeshi Nakagawa) works fine on Windows 10! More precisely, it works fine on the current Technical Preview of Windows 10 (final version available at the end of July). It actually works better than on Windows 8.1, since all sound files now play nicely.

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AppleScript to instant sort Tilia-ready data

The software Tilia, well known from palaeoecologists, needs the user to specify a group code for each taxa. The obvious question after that, is to sort all these data so that taxa with the same group code are gathered together. One could use the custom sort fonction from Excel, or use this AppleScript:

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Freeze Excel panes, with AppleScript

Browsing large dataset in Excel can be tricky sometimes, as one almost always wants to refer to row and column names. Excel provides a feature for this, called “freeze panes”, but the interface is not practical at all (Microsoft…). Here is a handy AppleScript to activate/deactivate on-the-go this feature. Just select the cell from which you want to freeze the panes, and run the script [I would suggest, from Alfred 🙂 ].

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Tilia Ergonomics – Generate taxa codes and groups

Many palaeoecologists and other scientists working with stratigraphical data use Tilia as a software for production and visualization of quality time-series graph. This software from Eric C. Grimm needs you to present your data in a particular way, so as to work properly. There is nothing difficult here, just something to pay attention about.

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I got an IDEA

I’m starting an exciting and elegant new personal project. You’ll know more about this in the next weeks/months, but here is something I can tell you already. One of the major prerequisite for this project is something I named Interactive and Dynamic Event Assessment, and Julien is currently “cracking the code” for this.

Otherwise, you probably heard about my new online paper. Next are coming soon!

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