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 normalization scheme. |
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? |
A search pattern can be specified directly (in batch mode) in order to query the available normalizing model names. The corresponding parameter 'ref' can contain a substring appearing in the name of the normalizing scheme (or even a regular expression).
Alternatively, the parameter 'ref' can refer to a name of a sample to be used for normalization, or even a regular expression if average of several of them is desired.
The function fails if no matches are found or the search in names of normalizing schemes is ambiguous (returns more than a single match), unless 'multiple = TRUE'.
The second possibility is to pick an option from the list of available normalizing schemes via GUI.
The first option therein offers normalization by a single sample. Its name can be typed in or, after pressing the Enter key, picked from a list.
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
).
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 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.
Vojtěch Janoušek, vojtech.janousek@geology.cz
Implemented spiderplots:
Anders E, Grevesse N (1989) Abundances of the elements: meteoritic and solar. Geochim Cosmochim Acta 53:197-214 doi: 10.1016/0016-7037(89)90286-X
Becker H, Horan MF, Walker RJ, Gao S, Lorand J-P, Rudnick RL (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 WV (1984) Cosmochemistry of the rare earth elements: meteorite studies. In: Henderson P (eds) Rare Earth Element Geochemistry. Elsevier, Amsterdam, pp 63-114 doi: 10.1016/B978-0-444-42148-7.50008-3
Jochum KP (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 SS (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 JA (1983) Role of the sub-continental lithosphere in magma genesis at active continental margins. In: Hawkesworth CJ, Norry MJ (eds) Continental Basalts and Mantle Xenoliths. Nantwich, Shiva, pp 230-249
Pearce JA (1996) A user's guide to basalt discrimination diagrams. In: Wyman DA (eds) Trace Element Geochemistry of Volcanic Rocks: Applications for Massive Sulphide Exploration. Geological Association of Canada, Short Course Notes 12, pp 79-113
Pearce JA (2014) Immobile element fingerprinting of ophiolites. Elements 10: 101-108 doi: 10.2113/gselements.10.2.101
Pearce JA, Harris NW, Tindle AG (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 SS, McDonough WF (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 doi: 10.1144/GSL.SP.1989.042.01.19
Sun SS, Bailey DK, 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.1980.0224
Taylor SR, McLennan SM (1985) The Continental Crust: Its Composition and Evolution. Blackwell, Oxford, pp 1-312
Taylor SR, McLennan SM (1995) The geochemical evolution of the continental crust. Reviews in Geophysics 33: 241-265 doi: 10.1029/95RG00262
Thompson RN (1982) British Tertiary province. Scott J Geol 18: 49-107
Weaver BL, Tarney J (1984) Empirical approach to estimating the composition of the continental crust. Nature 310: 575-577 doi: 10.1038/310575a0
Wood DA, Joron JL, 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("Boynton") # To select from the whole list, try selectNorm() # Regular expressions in action, we take the string from beginning # and then replace space and left bracket by dots selectNorm("^Primitive Mantle..McDonough 1995") # Selecting several samples by regular expression data(sazava) accessVar("sazava") selectNorm("Po-4",elems="Cs,Rb,Ba,Nb,La,Yb") selectNorm("^Po",elems="Cs,Rb,Ba,Nb,La,Yb")