Saturday, 14 April 2018

Version 5.0 has been just released!

On March 28, 2018 has been released a new version of GCDkit 5.0. It was developed in R 3.4.3 and code-named El Chupacabra. The most important changes are summarised below.

Towards a platform-independent version
  • It is well-known that the GCDkit has been originally designed as a Windows-only package. From the current version it is possible to install  and run it also on operation systems other than Windows,  most notably Linux or Mac OSX.  
  • So far, this concerns command-line/batch mode only. 
  • The platform-independent graphical user interface (menus, dialogue boxes...) written in Tcl/Tk language  is ready and just being tested. If you are feeling unadventurous, and work on Linux and/or Mac, please do get in touch and you can become one of the beta testers. 

New Windows installer
  • As we hope, we have fixed the long-standing problems with the installation of GCDkit on Windows 10, and people without administrative rights.
  • The new GUI installer, based on the Tcl/Tk  language,  is started by simply dragging the file @INSTALL.r from the temporary installation directory onto the R Console window. 
  • his file can be also located manually and loaded using the  File|Source R code...'  menu. See the download page for more details. 
  • Please note that this installer relies on a live Internet connection to download the missing packages required by the GCDkit. 

User-defined templates
  • User-defined templates for stand-alone Figaro plots or their plates. They can be uploaded into the  directory Diagrams/User and then employed for standard plotting (i.e. not classification)  purposes. This mechanism allows easy and fully automatic expansion of the plotting capabilities  of the GCDkit system. For further info, see the file @README.txt in the directory in question.
  • There are five examples of user-defined templates provided: three binary plots for discrimination of lavas from destructive plate boundaries (Pearce 1982), ternary plot for classification of A-type granites (Grebennikov 2014) and binary plot of Paulick et al. (2006) to portray the mantle peridotite fertility.  

Overplotting two or more datasets on a single diagram (or plate)
  • Functions allowing overplotting new datapoints onto standard single binary plots, ternary plots,
    spiderplots or multiple plots, including the diagram templates (overplotDataset, underplotDataset) linked to the menu system. 
  • In addition, there are functions figOverplot and figOverplotDiagram but these are meant mostly for internal use. 
  • For plotting serves a reference dataset, either real-world data (say compiled from literature) or a numeric  matrix spanning, for instance, from petrogenetic modelling.
  • See the example of overplotting the atacazo over sazava dataset on De la Roche et al. (1980) plot.
  • Very attractive feature should be the new possibility of obtaining dataset by online search of the database. The search can be performed directly from the menu GCDkit|Online search  It invokes a graphical front-end, written By Oscar Laurent (ETH, Zurich) that allows to enter the desired search criteria. On Windows, it also includes a primitive, and still rather slow, possibility of selecting a polygon of interest from a map of the World. 

Further new features/important changes
  • New plugin 'disclosure' for log-transformation of compositional data.
  • New geotectonic/general purpose diagrams
    • La/Yb vs. Nb/La and La/Yb vs. Th/Nb of Hollocher et al. (2012)
    • La/10-Y/15-Nb/8 of Cabanis and Lecolle (1989)
    • Zr/Y-Th/Yb of Ross and Bedard (2009)
    • YbN vs. LaN/YbN of Martin (1986) to distinguish adakites and TTGs
    • F-M-W diagram (Ohta and Arai 2007) for chemical weathering of igneous rocks
  • calcAnomaly, a function for calculating a magnitude of any anomaly on any spiderplot, based on concentrations of selected neighbouring (not necessarily adjacent) elements.
  • Spanish translation of the classification plots (courtesy of Tomas Grijalva,  Geology Department of UNAM, Mexico).
  • New zircon saturation model of Boehnke et al. (2013).
  • New training dataset giving the whole-rock major- and trace-element contents,   together with Sr and Nd isotopic compositions of lavas from two volcanic complexes in Ecuador: the Atacazo and the Ninahuilca (Hidalgo 2006; Hidalgo et al. 2008).   This dataset, kindly provided by Silvana Hidalgo, is used in a worked example (chapter 25) of Janousek et al.’s book (2016).
  • Another new training dataset from the Central Bohemian Plutonic Complex, Czech Republic  (Janousek et al. 2000, 2010). It could be, together with already present, used to test dataset switching etc.
  • New function figFixLim() extends the scales of both axes of a binary plot automatically  if necessary to accommodate all the data points.
  • new training dataset from the Central Bohemian Plutonic Complex, Czech Republic (Janousek et al. 2000, 2010). It could be, together with already present, used to test   dataset switching etc.
  •  New function figFixLim()extends the scales of both axes of a binary plot automatically  if necessary to accommodate all the data points.
  • New normalization scheme of Anders and Grevesse (1989) for chondrite-normalized REE spiderplots.
  • Better behaviour of many functions in batch mode (in RTerm, Jupyter, on Linux/Mac etc.)......

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

    Good luck, Vojtech


  1. Hello ... can anyone help me?
    I have been using CGDkit for some time and I can not install the new version in Windows 10, because when I unzip the folder, it does not have the Run RGUI file, 32 bit version (shortcut labeled R i386).

    1. Hello, yes, the installation philosophy has changed completely - and you should read Instructions at our download page, Have you installed R first? GCDkit is just a library for R.

    2. Hello, thank you for replying. Yes, I have read and followed the instructions. The R was installed, however from "Run RGUI, 32 bit version (shortcut labeled R i386)" was not possible.

    3. Hello,
      to be concerete, the shortcut to 32-bit R on my desktop is named R i386 3.4.3. Can you find it and start it?

  2. Hi!

    The new version of the GCDkit is really nice but I can't select the elements when I want to do a spider plot. There is another way to do it in this new version? In the previous GCDkit versions it was possible to do it.


  3. Hello,
    I am not sure what are you after - if it is introducing your own normalizing scheme for spiderplot, or modifying an existing one, please refer to:

    Or please provide more details.

    1. Hi,
      Sorry for the late reply. That link really helped.
      Thank you for the help.

  4. This comment has been removed by the author.

  5. Hi! Thanks for all the tips in the blog. They really help. I was used to GCDkit in PC, but now I managed to install XQuartz, R 3.5.1, the packages ("R2HTML","RODBC","XML","sp") and load GCDkit on HighSierra 10.13.6. When I load the library with library(GCDkit) there is an error message:

    Error reading the GCDkit config file!
    Sticking to defaults....

    Patching.... please wait

    Initializing the EarthChem interface....
    Testing - on Non-Windows system - skipping Eartchem interface

    #but after it, there is the normal GCDkit message followed by:
    "Ready 2 go - Enjoy!"

    I set the working directory, but when I try to loadData, if it is an .xlsx file, the following message appears:
    Excel 2007 file...WARNING: MS Excel import is not available on 64bit systems! Quitting...
    File reading error

    #.xls files also do not load

    #And if I try a .csv file, the message is:
    CSV file...loading...
    Error in file(file, "rt") : não é possível abrir a conexão
    File reading error
    Error in sqlQuery(channel, paste("SELECT * FROM [", which.table, "]", :
    objeto 'channel' não encontrado

    Is there any component I didn't install? If it is the case to run R in 32 bits, how can I change it in ios?


    1. Ola Isabela,
      obrigadinho for your bug report. It seems that there are some problems with the RODBC library used to read Excel and CSV files. I am not working on Mac but I suspect that the ODBC drivers are available only on Windows, and then only on 32 bit systems. To be on the safe side, you can stick to text files (just copy and paste from you Excel). Meanwhile, let us to examine the problem further.


    2. Olá Vojtech, thank you for your reply!
      I also tried GCDkit 4.1 in R 3.2.1 and the error messages are:

      GCDkit-> loadData("teste1.xlsx")
      Excel 2007 file...Error in try(switch(suffix, ROC = { :
      não foi possível encontrar a função "odbcConnectExcel2007"
      File reading error
      Error in inherits(channel, "RODBC") : objeto 'channel' não encontrado
      GCDkit-> loadData("teste3.csv")
      CSV file...loading...
      Error in kde[, f] : índice fora de limites
      File reading error
      Error in inherits(channel, "RODBC") : objeto 'channel' não encontrado

      But as you suggested, copying with ctrl+c and pasting with ctrl+v was supposed to work? Because it is not. I'm getting error message of unexpected numeric constant for the numbers in the columns.
      Is there a special command for "Paste Data from Clipboard" instead of ctrl+v?
      Sorry, but I am new at not having the GUI.


    3. Dear Isabela,
      [1] You should be able to switch on the GUI on Mac by typing in the Console window:

      [2] Try to load the sample data file

      [3] No, Ctrl-V will not work, you have to invoke "Paste data from clipboard" from the menu

      Please let me know, how you are getting on.

    4. Hi Vojtech,
      [1] I was able o switch on the GUI with menuet(), but there is a message "Error in menuOff() : object 'schema.db' not found" once I do it . Options inside each tab of the GUI are not available to click. Only "Load data file" and "Paste data from clipboard". And there are error messages also when I try to use them. But...

      [2]I successfully loaded the sazava.txt using the batch mode and then I managed to load my own data. I must have done something wrong in formatting tables the other day.

      I will work with that! Thank you very much.

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  7. Hi!

    I am trying to install the 5.0 version on my win10 but when I load the package it always suggested that something is wrong with line 216 in"EarthChemFUN.r". I checked the file and find that there is a strange character under UTF-8 ("zzz=="something not correctly shown"", seems to be a \hat{A} but only shown under Windows-1252). I commented this line out and now it seems to work fine.

    I am using the Chinese version of win10 with English language pack and this might cause the encoding problem. So I wonder if I need to install another language pack? Or commenting this line out would not affect the program?

    Jiacheng Tian

    1. Hello,
      you are not the first Chinese user reporting this problem with encoding in the EartChem module. But you can perhaps try us to test a remedy for us. Could you please replace the offending line of code in the file ErathChemFUN.r by:

      if(.Platform$OS.type=="windows") zzz[zzz==intToUtf8(0x00c2)]<-NA

      Please let me know whether it has worked. If so, we will add it to the next release.

    2. Hi Vojtech,

      After changing the code I could load gcdkit package and use it now. But as I don't use Earthchem module, I don't know whether it also works well after the change.

      Thank you for your help!
      Jiacheng Tian

    3. Dear Jiacheng Tian,
      I am pleased, thank you for letting me know.

  8. how can I use Logarthmic axis please ?

  9. Simply use the menu Plots|Binary plot, and when asked to specify which of the axes should be logarithmic, reply x, y, or xy. See also indication in the relevant dialogue box.

  10. Hello
    I'd like to add a new normalization sceme to the spiderplots.
    How can I do that using the 5.0 version?

  11. It is the same like before, see

    1. Mr Janousek, thanks for replying.
      I was having difficulties to find the file, but now I got it. Thank you again.