Monday 7 November 2016

Catania Workshop

We held a workshop in Catania, sicily, from the 26th to the 30th of September of this year. It was convened, and beautifully organized, by P. Fiannacca and R. Cirrincione at Università degli Studi di Catania. With 20+ participants, including a sizeable group from Brazil, we think the workshop was quite a success (better ask the participants, though !).

Mt Etna, viewed from the hotel where we stayed (Jeff's balcony, to be specific)...
For the first time, we introduced during the workshop the set of modelling routines that we've been promising for years. Although there is no GUI to them now, they work nicely in command line. The next step is to actually release them... We also chanced upon a fantastic R package called gWidgets2, that may well take care of most of our GUI requirments (and, in the process, provide a way forwards for a modelling GUI).
The organizers of the workshop: Patrizia Fiannacca, Jeff, Vojta, Rosolino Cirrincione.

The real highlight of the week, however, was clearly not the code but the Wednesday trip to Mount Etna. Despite a somewhat cloudy weather, we enjoyed a great trip to the Valle del Bove, under the wise guidance of C. Ferlito.
Descending into the Valle del Bove

Listening to Carmelo !

Monday 26 September 2016

Hello Catania !

Good morning to all,

If you're sitting in the Catania workshop and are curious whether the adress Vojta just mentions is actually live -- where, yes it is !
Happy GCDkit-ing...

Thursday 14 July 2016

What have we been working on?

Mikulov - a lovely town in southern Moravia

Sampling local production in Mikulov

GCDkit is a permanent work in progress, and lots of things evolve! In May 2016, we (Vojtech and Jeff) met for a week in Moravia, locked ourselves in a room and coded from morning to evening. A pity considering the touristic resources, and the view from our room (rest assured that we did sample some of the better options however), but a huge success in terms of writing code!

So, here is a quick list of what we've been up to: you may regard it as a list of features that will be included in GCDkit, sooner or latter (to be honest, latter is more likely than sooner).

Interfaces and connections

  • We spent some effort towards making GCDkit truly platform independent. As we all know, GCDkit so far is a purely Windows-specific application; this is largely (only) due to the choice of using Windows-specific menu and interface functions (the menus that appear at the top of the R console). With help and incentive from some correspondents (Jesse Reimink, then at U. Alberta and now at DTM), we worked hard to make GCDkit usable under other systems. To some point, this can now be done. Jesse had GCDkit running under MacOS, and we had it functional in Linux (well, in an emulator). Of course, you should not expect it to be perfectly stable, and probably not 100% functional either. And obviously the menu system is missing; you have to run it purely from command line. Still, it works and it may be included in the distributed version in the not-so-far future.

GCDkit Development in Linux (Ubuntu)

  • As soon as GCDkit will become (mostly) platform independent and (mostly) usable without the Windows R GUI, nothing should theoretically stop us (or you) from developing other user interfaces. We explored the possibility, for instance, to run a Python application that would call R/GCDkit. Don't hold your breath, though.
  • An additional benefit of a Python/R connection is that QGIS -- the main open source alternative for GIS -- supports Python plugins. There is therefore a long-term possibility for calling a fully interactive GCDkit session from QGIS, and therefore do GCDkit processing on geographic data.
  • A simpler aternative is to use QGIS processing toolbox. As a proof of concept we managed, for instance, to load a shapefile (a geographic layer containing points with analyses) into GCDkit, calculate a CIPW norm, and return another geographic layer containing the normative values that you may then use in normal GIS way (for instance colour by proportion of a normative mineral, etc).

Running a GCDkit "geo-algorithm" from QGIS.


One of our main goals was to work on the long overdue modelling code. After several false starts, we had something to show during the last workshop in Krakow. This time, we totally overhauled the code, and now wrote something we believe is a rather flexible and powerful framework. From a user perspective, you'll be able to do something like that (don't try it on your system, it is not distributed, and it is very likely to change anyway!):

######## Direct melting of an avg Archaean basalt

# Define the mineral proportions
min.props.mod1<-c(0.6,0.4) # sum must be = 1

# Calculate the model
mod1<-pmDirectBatch(c0.lab="avg Arch basalt",min.prop=min.props.mod1,ff=0.7,"mins",mjr.set=mjrs,"kds",trc.set=trcs)

# Add more info (calculating every 0.1 here)
petroCalc(mod1,0.1) # Calculate every 0.1

# Extract the data for plotting

# Prepare a plot (just the real data)

# Add the model curve
Under the hood, we have defined a "PetroModel" class that stores all the information on a model, and several functions to calculate it. With such an object-oriented approach, the nice thing is that we can very easily expand the possibilities. Since we defined the "overplot" function for the main class for instance, we need no additional work to plot a model curve on a graph -- and this will remain true for direct or reverse models, or even for more complex ones including accessories saturation, variable D values, etc., should we decide to include these at some point.

There is no user interface so far, and no real plans to develop one. At the moment one has to resort to the command line and type the functions in, but it is not so difficult. Eventually, we will think of something perhaps using Python (cf. above), or Shiny.

Again, this is not released. It is our next main goal, but will take a bit more time to polish and package (and probably publish !).

Phase equilibria

During the Prague Goldschmidt conference last year, we presented an abstract demonstrating how we could read a PERPLE_X output and further process it to calculate trace elements compositions in the melt. Actually, this is a long standing idea (I [Jeff] started working on it using a monster of an Excel spreadsheet back in 2005, and we started writing this code during a chilly spring in Southern France in 2013). We did spend some work on that, too, tweaking and fixing the code once more (this nasty monazite saturation routine...), and thinking about a publication -- you're not likely to see this code soon and certainly not before we publish.

And more...

Well, we also spent some time discussing grant applications for funding our efforts, and celebrating the success of "ouR" book... We also considered plans to link our work with the very nice job done by Matt Mayne on something called RCrust. And, indeed, we enjoyed a lovely walk in the woods around Valtice.

Book Review

ou"R" book has been reviewed by H. Rollinson, who wrote this essentially nice piece in "Elements". We are very grateful for the positive feedback !

Tuesday 12 July 2016

Troubles with Windows 10

We have been recently flooded by  email reports of those of you who could not start the GCDkit installer on Windows 10. Strangely, the other versions of the system seem unaffected. We have examined the problem and, as it seems, it consists in the sudden change in security policy of Microsoft, requiring all installation programs to have a valid security certificate.

While we are working on the remedy, the only way on Win 10 seems to use the "advanced" setup taking advantage of the R library mechanism.  

There is no need to be afraid of this,  The procedure is as follows:
  • download and install the R 3.2.1 for Windows
  • download the library
  • run the R console in a SDI mode
  • install the library from the R console (Menu Packages > Install package(s) from local zip files...)
  • install the R2HTML, RODBC and sp libraries (Menu Packages > Install package(s)...) [working Internet connection is required]
  • load the GCDkit library (Menu Packages > Load package > GCDkit or type library(GCDkit) into the R Console)
The last step is to be repeated every time you start R GUI a new. 

Alternatively, you can make an shortcut at your Desktop with a text similar to mine (do take care of the correct path):

"C:\R\R-3.2.1\bin\i386\Rgui.exe" --silent --no-save --sdi

Please do note the quotation marks, they should be there.

Setting the directory to that with R libraries. In my case it is:


I hope that this will help. Please let us know if there are any further problems. 


Tuesday 23 February 2016

What is new in GCDkit 4.1 (Chlopskie jadlo)?

On 10 February has been released a new version of GCDkit. Apart from numerous bug fixes, and a great deal of editing to enable running the GCDkit scripts in a batch mode, it brings several new features. Arguably the most interesting include: 
Switching between datasets
  • Datasets can be stored using the function pokeDataset. Or it is done automatically, like for data freshly loaded into the system using the functions loadData and accessVar. Technically they always become components of a list WRCube.
  • Later, the previous datasets can be restored by functions peekDataset or selectDataset.
  • The WRCube can be cleared anytime using the function purgeDatasets; only the most recent copy of the current dataset survives this operation.
  • Function selectAll has been completely rewritten using the dataset switching, i.e. backup copy of data  stored in the WRCube. Variables WR.bak,WRanh.bak,milli.bak and labels.bak are thus not needed anymore.
  • New function figOverplot allows overplotting a reference dataset onto any Figaro-compatible binary plots, ternary plots, or spiderplots. The reference dataset, stored in an arbitrary global variable, can contain either real-world data or a numeric matrix  spanning from petrogenetic modelling.
Futher important changes
  • figCex, plateCex accept now the value NA (no quotes) that means no plotting  of symbols (most useful on spiderplots if only lines are desired).
  • figAddReservoirs checked and reprogrammed; it newly does work for ternary plots,  and is Figaro-compatible for binaries, ternaries and spiders. It also includes a lot of new arguments, mainly plotting parameters.
  • New functions oxide2ppm and ppm2oxide to recast wt.% of the given oxide to ppm of cations
  • Platform-independent functions tk_winDialog and tk_winDialogString written in Tcl/Tk.
  • calcCore does not require global variables anymore, but can use also those from the parental environment.
  • accessVar does not utilize Windows clipboard to transfer data into variables WR and labels anymore

We trust that you will find this new release useful and reasonably stable.

Good luck, Vojtech