selectNorm {GCDkit} | R Documentation |
Displays available normalization schemes and lets the user to choose one interactively.
selectNorm(ref=NULL,elems = "Rb,Sr,Ba,Cr,Ni,La,Ce,Y,Zr",REE.only=FALSE,multiple=FALSE)
ref |
character: a specification of the normalizing model. |
elems |
character: a default list of elements. |
REE.only |
logical: should be only listed normalization schemes for REE? |
multiple |
logical: is a result with several normalizing schemes allowed? |
There are two ways of using this function. Firstly, a search pattern can be specified for a query of the available normalizing model names. The corresponding parameter 'ref' can contain a substring or even a regular expression. The function fails if no matches are found or the search is ambiguous.
The second possibility is to choose from the list of available normalizing schemes. The first option offers normalization by a single sample. Its name can be typed in or, after pressing the Enter key, picked from a list. Then the user is prompted to specify the list and order of elements/oxides that should appear on the plot. The easiest way is to type directly the names of the columns, separated by commas. Alternatively can be used their sequence numbers or ranges. Also built-in lists can be employed, such as 'LILE', 'REE', 'major' and 'HFSE' or their combinations with the column names. These lists are simple character vectors, and additional ones can be built by the user (see Examples). Note that currently only a single, stand-alone, user-defined list can be employed as a search criterion.
The samples to be plotted can be selected based on combination of three searching
mechanisms (by sample name/label, range or a Boolean condition) -
see selectSubset
for details.
The second option is similar but it allows to normalize by average concentrations
in a group of samples specified by one of the three searching mechanisms as
above (see selectSubset
).
The composition of various standards
available for normalization and subsequent plotting of
spider
diagrams is stored in the file
'spider.data
' in the main GCDkit directory. It is a comma delimited file
such as:
Normalization data used for spiderplots MORB (Pearce 1983) Sr,K,Rb,Ba,Th,Ta,Nb,Ce,P,Zr,Hf,Sm,Ti,Y,Yb 120,1245,2,20,.2,.18,3.5,10,534,90,2.4,3.3,8992,30,3.4 REE chondrite (Boynton 1984) La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu .31,.808,.122,.6,1,.195,.0735,.2590,.0474, .322,.0718,.21,0.0324,.209,.0322 ORG (PearceEtAl.1984) K2O,Rb,Ba,Th,Ta,Nb,Ce,Hf,Zr,Sm,Y,Yb 0.4,4,50,0.8,0.7,10,35,9,340,9,70,8.0
The first row is always skipped and can contain any comments. The following ones
have a fixed structure. For each normalization scheme, the first row contains
the title and reference. If title starts with 'REE
', the normalization is
supposed to be for REE only and special parameters, such as 'Eu/Eu*
', are
calculated. The second line gives a comma delimited list of elements in the order
they should appear on the plot. The last line is a comma delimited list of
normalization values. There are empty lines left between the normalization schemes.
As the file 'spider.data
' is read every time 'selectNorm
is called,
the user can add or delete normalization schemes on his will using a text editor.
A numeric matrix with one row, containing the normalizing values. The row name contains the name of the model and reference.
Vojtech Janousek, vojtech.janousek@geology.cz
Implemented spiderplots:
Becker H, Horan M F, Walker R J, Gao S, Lorand J-P, Rudnick R L (2006) Highly siderophile element composition of the Earth's primitive upper mantle: constraints from new data on peridotite massifs and xenoliths. Geochim Cosmochim Acta 70: 4528-4550 doi: 10.1016/j.gca.2006.06.004
Boynton W V (1984) Cosmochemistry of the rare earth elements: meteorite studies. In: Henderson P (eds) Rare Earth Element Geochemistry. Elsevier, Amsterdam, pp 63-114
Jochum K P (1996) Rhodium and other platinum-group elements in carbonaceous chondrites. Geochim Cosmochim Acta 60: 3353-3357 doi: 10.1016/0016-7037(96)00186-X
McDonough W, Sun S S (1995) The composition of the Earth. Chem Geol 120: 223-253 doi: 10.1016/0009-2541(94)00140-4
Nakamura N (1974) Determination of REE, Ba, Fe, Mg, Na and K in carbonaceous and ordinary chondrites. Geochim Cosmochim Acta 38: 757-775 doi: 10.1016/0016-7037(74)90149-5
Pearce J A (1983) Role of sub-continental lithosphere in magma genesis at active continental margins. Continental Basalts and Mantle Xenoliths. Shiva, Nantwich, pp 230-249
Pearce J A (1996) A user's guide to basalt discrimination diagrams. In: Wyman D A (eds) Trace Element Geochemistry of Volcanic Rocks: Applications for Massive Sulphide Exploration. Geological Association of Canada, Short Course Notes 12, pp 79-113
Pearce J A (2014) Immobile element fingerprinting of ophiolites. Elements 10: 101-108 doi: 10.2113/gselements.10.2.101
Pearce J A, Harris N W, Tindle A G (1984) Trace element discrimination diagrams for the tectonic interpretation of granitic rocks. J Petrology 25: 956-983 doi:10.1093/petrology/25.4.956
Sun S S, McDonough W F (1989) Chemical and isotopic systematics of oceanic basalts: implications for mantle composition and processes. In: Saunders A D, Norry M (eds) Magmatism in Ocean Basins. Geological Society of London Special Publications 42, pp 313-345
Sun S S, Bailey D K, Tarney J, Dunham K (1980) Lead isotopic study of young volcanic rocks from mid-ocean ridges, ocean islands and island arcs. Philos Trans R Soc London A297: 409-445 doi: 10.1098/rsta.1980.022410.1029/95RG00262
Taylor S R, McLennan S M (1985) The Continental Crust: Its Composition and Evolution. Blackwell, Oxford, pp 1-312
Taylor S R, McLennan S M (1995) The geochemical evolution of the continental crust. Reviews in Geophysics 33: 241-265 doi: 10.1029/95RG00262
Thompson R N (1982) British Tertiary province. Scott J Geol 18: 49-107
Weaver B L, Tarney J (1984) Empirical approach to estimating the composition of the continental crust. Nature 310: 575-577 doi: 10.1038/310575a0
Wood D A, Joron J L, Treuil M, Norry M, Tarney J (1979) Elemental and Sr isotope variations in basic lavas from Iceland and the surrounding ocean floor; the nature of mantle source inhomogeneities. Contrib Mineral Petrol 70: 319-339 doi: 10.1007/BF00375360
selectNorm() selectNorm("Boynton") # Regular expressions in action, we take the string from beginning # and then replace space and left bracket by dots selectNorm("^Primitive Mantle..McDonough 1995")