Monday, 9 November 2015

GCDkit 4.0 (Great October Revolution) just released!

We are pleased to announce that the new stable version of GCDkit has been just released!
Primarily, it is aimed to accompany our freshly published book (see the previous post). Of course, this brought about numerous small changes to the code, especially in the batch mode.

But there also further important improvements, even though many are hiding behind the bonnet.

  •  At last, the package has got its NAMESPACE, which means that it became available for R 3.2 and higher.
  •  Hopefully fixed were the notorious problems with installation pointed out by several users even on this forum. They were apparently occurring when there has been a personal library folder created during the R installation process.  
  • Improved was the help system, which includes a number of illustrative figures now.  
  • Semitransparency of plotting symbols (that can be set through function setTransparency) or fields (e.g., in spiderByGroupFields).Use preferably PDF export to preserve it.
  • New possibility of assigning colours according to values of a variable (assignColVar). 
  • Table of molecular weights from the CIAAW official web site (http://www.ciaaw.org) has replaced the existing one.  
  • New diagrams:
    • New geotectonic diagrams of Müller et al. (1992) for potassic igneous rocks
    • New Nb/Yb–Th/Yb and Nb/Yb–TiO2 /Yb plots of Pearce (2008) 
  • New plugin:
    • Rutile saturation algorithms of Ryerson & Watson (1987) and Hayden & Watson (2007)
  • File input/output:
    • improved import from GeoRoc, references in the end saved into file, references.txt and shown in a separate window upon load,
    • reading ROC, PEG, CSV files even on 64bit systems,
    • improved merging of files,
    • fixed problems with comments in data files.
  •  Legends:
    • improved appearance of legends, esp. for single colour and/or single plotting symbol,
    • corrected were problems with legends in spider.contour and spiderByGroupFields,
    • fixed were legends in figMulti, in addition their backgrounds became semitransparent.
  •  Calculations:
    • addResults replaces any already existing variables of the given name,
    • printSamples got a new parameter, print=FALSE, that allows to use the function just for calculations, i.e. skipping the printing,
    • millications can be newly calculated from any matrix/vector ,
    • the function groupsByLabel assigns a value (Undefined) to analyses for which the grouping information is missing,
    • calcCore did not work correctly for fractions. For instance, Nb/Ta ratios were Inf for Ta contents that were not determined. This affected scaling of plots etc.,
    • summaryRangesByGroup and strip work correctly even for subsets.
 
  •  Plotting:
    • new function plateLabelSlots to annotate individual slots by letters, numbers or Roman numerals,
    • binary and plotWithLimits allow linear fits also when some (or both) of the axes is/are logarithmic.
    • contourGroups is more robust now - and works better on datasets with missing values.

 Enjoy!
Vojtech

3 comments:

  1. Hi!
    How do I prepare the excel sheet for Sr-Nd Isotopes diagrams? Is there any excel sheet sample for use in the GCDkit?

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    Replies
    1. Hi,
      data format for Sr-Nd data is just the same as for other data types, e.g. samples in rows and compositions in columns, with sample names in the first column and chemical labels in the first row. Columns with isotopic data should be labeled '87Sr/86Sr' and '143Nd/144Nd'. For initial calculations you also need columns with Sr, Rb, Sm and Nd concentrations. Age can be stated in column 'Age' or entered during data loading procedure if identical for all samples.
      Examples can be found in directory '\R-3.2.1\library\GCDkit\Test_data', which is probably sitting in your 'Program Files' dir.
      More info is in the GCDkit help (type '?loadData' into GCDkit console) or in the (freely available) 'Back Matter' of the GCDkit book (http://link.springer.com/book/10.1007/978-3-662-46792-3/page/2)
      Cheers,
      Vojta E

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    2. Dear Vojta Erban,
      Thank you so much for helpful information. I solved my problem with your information. I found example data file in cbp_iso.data in Test_data folder. Lastly, I would like to thanks to you and your team for creating this program. Because it is an absolutely wonderful program. And also thanks for free download at the gcdkit.org.

      Best wishes,
      M. Ali GUCER

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