| Type: | Package |
| Title: | The Ultimate Igneous Norm |
| Version: | 0.8.6 |
| Date: | 2022-06-20 |
| Imports: | shiny,shinythemes,shinyWidgets,pracma,Ternary,grDevices,graphics,utils |
| Description: | The computer program is an efficient igneous norm algorithm and rock classification system written in R but run as shiny app. |
| URL: | https://github.com/TheRFrog/shinyNORRRM |
| BugReports: | https://github.com/TheRFrog/shinyNORRRM/issues/ |
| License: | GPL-3 |
| Depends: | R (≥ 4.2.0) |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.1.2 |
| NeedsCompilation: | no |
| Packaged: | 2022-06-23 03:21:57 UTC; linus |
| Author: | Carlos Eduardo Sánchez Torres [aut],
Kevin Samuel Cárdenas-Muñoz [aut],
Luis Alejandro Elizondo-Pacheco [aut],
Reneé González-Guzmán
 [cre] |
| Maintainer: | Reneé González-Guzmán <rguzman@geociencias.unam.mx> |
| Repository: | CRAN |
| Date/Publication: | 2022-06-23 18:10:02 UTC |
shinyNORRRM-: The Ultimate Igneous Norm
Description
The computer program is an efficient igneous norm algorithm and rock classification system written in R and running in shiny.
Details
“' install.packages("shinyNORRRM") shinyNORRRM::shinyNORRRM() “'
Author(s)
Maintainer: Reneé González-Guzmán rguzman@geociencias.unam.mx (ORCID)
See Also
Useful links:
Report bugs at https://github.com/TheRFrog/shinyNORRRM/issues
The standard atomic weights
Description
Data frame with symbols, element names, and standard atomic weights.
Usage
data(AtomWeight)Format
The format is a data frame with 92 rows and 3 columns, including the row names.
Details
This table is based on the 2011 table after the IUPAC (International Union of Pure and Applied Chemistry), Commission on Isotopic Abundances and Atomic Weights. Note that row names are the symbol of the elements.
Source
References
Wieser, M.E., and others. 2013. Pure and Applied Chemistry. International Union of Pure and Applied Chemistry (IUPAC). v. 78, no. 11, pp. 2051–2066.
See Also
Examples
data(AtomWeight)
AtomWeight['H','AWeight']
rm(AtomWeight)#cleanup
##
Data collection of igneous rocks from the Deccan region (India)
Description
Compilation of major and trace element analysis of 7019 igneous rocks from the Deccan region, India.
Usage
data(Deccan)Format
The format is a data frame with 7019 rows and 30 columns.
Details
The database is part of a global whole-rock geochemical database, sourced from various existing databases and supplemented with an extensive list of individual publications.
Source
The database is part of the compiled data in Gard et al. (2019). For full details see doi:10.5194/essd-11-1553-2019.
References
Gard, M., Hasterok, D. and Halpin, J.A., 2019. Global whole-rock geochemical database compilation. Earth System Science Data, 11(4), pp.1553-1566.
See Also
Examples
data(Deccan)
rm(Deccan)#cleanup
##
Data collection of igneous rocks from Eastern Mexican Alkaline Province
Description
Compilation of major and trace element analysis of 46 igneous rocks from San Carlos-Cruillas, Tamaulipas, Mexico.
Usage
data(EAP)Format
The format is a data frame with 46 rows and 28 columns.
Details
The origin of the Eastern Mexican Alkaline Province has been explained by landward arc migration and subsequent asthenospheric upwelling after slab roll-back of the Farallon Plate. Detailed geochemical analysis suggests the participation of two types of metasomatized mantle regions: a lithospheric source modified by past subduction processes and an asthenospheric source slightly affected by carbonatite-related metasomatism. Variations in the partial melting degrees controlled the extent of magma enrichment in the latter. Major and trace element geochemistry, together with geochronological data and field relations, evinced an older post-orogenic setting related to the arc-like rocks (Eocene) and a younger intraplate extensional environment associated with all enriched igneous rocks (Oligocene-Miocene). Bivariate diagrams of SiO2 vs. trace element ratios and multi-element patterns indicate that magmas from the SSCC complex dominantly evolved through fractional crystallization with a limited crustal contribution.
Source
The database is also available in Elizondo-Pacheco et al. (2022). For full details see https://academic.oup.com/petrology/article/63/5/egac027/6553218 .
References
Elizondo-Pacheco, L. A., Ramírez-Fernández, J. A., De Ignacio, C., González-Guzmán, R., Rodríguez-Saavedra, P., Leal-Cuellar, V. A. & Montalvo-Arrieta, J. C. (2022). Generation of Arc-Like and OIB-Like Magmas Triggered by Slab Detachment in the Eastern Mexican Alkaline Province: Petrological Evidence from the Cenozoic Sierra de San Carlos-Cruillas Complex, Tamaulipas. Journal of Petrology, 63(5), egac027.
See Also
Examples
data(EAP)
rm(EAP)#cleanup
##
Data collection of igneous rocks used in IUGSTAS software
Description
Compilation of major elements data for 37 representative samples of volcanic rocks.
Usage
data(IUGS)Format
The format is a data frame with 37 rows and 28 columns.
Details
This data is available from the Cambridge University Press, as a part of IUGSTAS software.
References
Le Maitre, R.W et al. 2002. Igneous Rocks: A Classification and Glossary of Terms: Recommendations of the International Union of Geological Sciences, Subcommission on the Systematics of Igneous Rocks. Cambridge University Press, 2002, 252 pp.
See Also
Examples
data(IUGS)
rm(IUGS)#cleanup
##
Indices
Description
The adjusted oxide data,
Usage
Indices(data, Calcite)
Arguments
data |
a whole rock major adjusted oxide chemical data. |
Calcite |
if it is TRUE, CaO will be used in the computation. |
Value
Returns a dataset with several petrological parameters.
Author(s)
Renee Gonzalez Guzman rguzman@geociencias.unam.mx
References
Elizondo-Pacheco, L. A., Ramírez-Fernández, J. A., De Ignacio, C., González-Guzmán, R., Rodríguez-Saavedra, P., Leal-Cuellar, V. A. & Montalvo-Arrieta, J. C. (2022). Generation of Arc-Like and OIB-Like Magmas Triggered by Slab Detachment in the Eastern Mexican Alkaline Province: Petrological Evidence from the Cenozoic Sierra de San Carlos-Cruillas Complex, Tamaulipas. Journal of Petrology, 63(5), egac027.
See Also
Examples
#create a dataframe with major elements indicating the appropriate parameters of rocks
#example of dataframes: EAP.csv, IUGS.csv, and TephraKam.csv
data(IUGS)
data <- adjRock(IUGS, Type= "Volcanic", Fe.adjustment = "Middlemost",
Cancrinite = FALSE, Calcite = FALSE)
Indices(data, Calcite = FALSE)
rm(IUGS,data)#cleanup
##
The oxides molecular weights of normative minerals
Description
Data frame with normative mineral names, chemical nomenclature, oxides molecular weights and theoretical density of minerals used in the Norm computations.
Usage
data(MinWeight)Format
The format is a data frame with 36 rows and 6 columns, including the row names.
Details
This table is calculated from the 2011 table values after the IUPAC (International Union of Pure and Applied Chemistry), Commission on Isotopic Abundances and Atomic Weights. Note that row names are the name of the normative minerals.
References
Wieser, M.E., and others. 2013. Pure and Applied Chemistry. International Union of Pure and Applied Chemistry (IUPAC). v. 78, no. 11, pp. 2051–2066.
See Also
Examples
data(MinWeight)
MinWeight['Quartz','ConsWeight']
##
MinWeight['Quartz','Density']
##
rm(MinWeight)#cleanup
The molecular weights
Description
Data frame with chemical nomenclature and molecular weights used in the ultimate Norm computation.
Usage
data(OxiWeight)Format
The format is a data frame with 26 rows and 3 columns, including the row names.
Details
This table is calculated from the 2011 table values after the IUPAC (International Union of Pure and Applied Chemistry), Commission on Isotopic Abundances and Atomic Weights. Note that row names are the chemical nomenclature of the oxides and the third column is the oxide weight rounded.
References
Wieser, M.E., and others. 2013. Pure and Applied Chemistry. International Union of Pure and Applied Chemistry (IUPAC). v. 78, no. 11, pp. 2051–2066.
See Also
Examples
data(OxiWeight)
OxiWeight ['SiO2','OWeight']
##
rm(OxiWeight)#cleanup
Data collection of igneous rocks from the Kamchatka volcanic arc (northwestern Pacific)
Description
Compilation of major and minor element analysis of 7596 igneous rocks from Kamchatka, Rusia.
Usage
data(TephraKam)Format
The format is a data frame with 7596 rows and 30 columns.
Details
The database contains 7596 single-shard major and minor element analyses obtained by electron microprobe. The samples characterize about 300 explosive eruptions, which occurred in Kamchatka from the Miocene up to recent times.
Source
The database is also available in Portnyagin et al. (2019). For full details see doi:10.5194/essd-12-469-2020.
References
Portnyagin, M.V., Ponomareva, V.V., Zelenin, E.A., Bazanova, L.I., Pevzner, M.M., Plechova, A.A., Rogozin, A.N. and Garbe-Schönberg, D., 2020. TephraKam: geochemical database of glass compositions in tephra and welded tuffs from the Kamchatka volcanic arc (northwestern Pacific). Earth System Science Data, 12(1), pp.469-486.
See Also
Examples
data(TephraKam)
##
rm(TephraKam)#cleanup
Recalculate the compositions of the rocks in an anhydrous basis (volatile-free; 100% adjusted)
Description
The oxide data, from SiO2 to P2O5 (or CO2) are first recalculated to 100 percent on an anhydrous basis, and then Fe oxidation ratio adjustment is done according to the recommendations of Middlemost (1989), or Le Maitre (1976), or else the measured Fe2O3/FeO ratios are maintained. Finally, the oxide data is recalculated to 100 percent on an anhydrous basis from Fe2O3/FeO ratios calculated.
Usage
adjRock(data, Type, Fe.adjustment, Cancrinite, Calcite)
Arguments
data |
a whole rock major and trace element chemical data (as percent %). It is important to note that Fe2O3 or FeO could be Fe2O3T or FeOT if any of this values are NA or 0. |
Type |
rock type, if the argument is "Volcanic" is shown the volcanic rock type after (Le Bas et al., 1986), iron oxidation ratio is calculated following the equation of Le Maitre (1976) for Volcanic rocks, if the argument is "Plutonic", then Plutonic adjusts are done. |
Fe.adjustment |
if the argument is "Middlemost", iron oxidation ratio is calculated depending on rock type at Middlemost (1989). if the argument is "Le Maitre", iron oxidation ratio is calculated depending on rock type at Le Maitre (1976). if the argument is "Fe+3/Fe+2", iron oxidation ratio is calculated depending on their own concentration). |
Cancrinite |
if the argument is TRUE, CO2 will be used in whole rock adjust. |
Calcite |
if the argument is TRUE, CO2 will be used in whole rock adjust. |
Value
Returns a dataset of adjust oxide data (.adj) on an anhydrous basis.
Author(s)
Maintainer: Reneé González-Guzmán rguzman@geociencias.unam.mx (ORCID)
References
Le Maitre, R.W. 1976. Some problems of the projection of chemical data into mineralogical classifications. Contribution Mineralogical Petrology. v. 56, pp. 181–189. Middlemost, E.A.K. 1989. Iron oxidation ratios, norms and the classification of volcanic rocks. Chemical Geology. v. 77, pp. 19–26.
See Also
Examples
#create a dataframe with major elements indicating the appropriate parameters of rocks
#example of dataframes: EAP.csv, IUGS.csv, and TephraKam.csv
data(IUGS)
adjRock(IUGS, Type= "Volcanic", Fe.adjustment = "Middlemost", Cancrinite = FALSE, Calcite = FALSE)
rm(IUGS)#cleanup
shinyNORRRM - launches the shinyNORRRM app
Description
Starts the shinyNORRRM app in the client's browser.
Usage
shinyNORRRM(host = "127.0.0.1", port = NULL, browser = NULL)
Arguments
host |
host link (defaults to the local machine "127.0.0.1") |
port |
port number (randomly chosen unless specified as a certain number) |
browser |
path to browser exe (defaults to standard browser) |
Details
shinyNORRRM is the interface of NORRRM
Value
A shiny app
Examples
## Not run:
## Launch application on localhost (127.0.0.1)
## -------------------------------------------
## By default shinyNORRRM starts the application on localhost
## and a randomly selected port (e.g. 9876), in which case you can connect
## to the running application by navigating your browser to
## http://localhost:9876.
shinyNORRRM()
## Launch application on a different host
## --------------------------------------
## You can also run the application on a different host
## by specifying a hostname and port. Just make sure to
## use an open port on your machine. Here "open" means
## that the port should not be used by another service
## and the port is opened by your firewall.
shinyNORRRM(host="your-hostname", port=8888)
## Launch application on a different browser
## ----------------------------------------
## To run the shinyNORRRM app on a different browser than your standard browser
## use the "browser" argument to set the path to the respective .exe file (e.g., Windows system)
launch_interim(browser = "C:/Program Files/Mozilla Firefox/firefox.exe")
## End(Not run)
The Igneous Norm (major and trace elements)
Description
Computed from the chemical composition, the normative mineralogy is an alternative approach for mineralogical classification and useful for set up the naming of igneous rocks (e.g., as parts of the TAS classification). The CIPW Norm (acronym from the surnames of the authors: Cross, Iddings, Pirrson and Washington, Cross et al., 1902) is the most commonly used calculation algorithm to estimate the standard mineral assemblages for igneous rocks, generated over more than a hundred years ago and thereafter modified by some authors to the passage of the years (e.g., Verma et al., 2002). It is based upon assumptions about the order of mineral formation and known phase relationships of rocks and minerals, using simplified mineral formulas.
In this option, the trace elements that can be used are Ba, Co, Cr Cs, Li, Ni, Rb, S, Sr, V and Zr. Additionally, minor element concentrations of F, S, and SO3 (expressed as wt. percent) are handled like trace elements as well. Sulfur concentration when available is reported as either SO3 or S, in which case their separate identity should be maintained.
Usage
ultimateCIPW(data, Type, Fe.adjustment, Cancrinite, Calcite)
Arguments
data |
a whole rock major and trace element chemical data. It is important to note that Fe2O3 or FeO could be Fe2O3T or FeOT if any of this values are NA or 0. On the other hands, the format of CO2 and F column must be 'CO2.' and 'F.', respectively. |
Type |
rock type, if is TRUE is shown the volcanic rock type after Middlemost in output, if it is FALSE, then Plutonic rock classification is done. |
Fe.adjustment |
if is TRUE, iron oxidation ratio is calculated depending on rock type. |
Cancrinite |
if is TRUE, CO2 will be used in whole rock adjust. If the concentration of CO2 is more than 0, and the modal cancrinite is present then Sodium carbonate is calculated. |
Calcite |
if is TRUE, CO2 will be used in whole rock adjust. If the concentration of CO2 is more than 0, and the modal calcite is present then Calcite is calculated. |
Value
Calculate the igneous Norm and others geochemical parameters.
Author(s)
Renee Gonzalez Guzman rguzman@geociencias.unam.mx
References
Cross, W., Iddings, J.P., Pirsson, L. V., Washington, Henry S. 1902, A quantitative chemico-mineralogical classification and nomenclature of igneous rocks: The Journal of Geology, v. 10, no. 6, pp. 555–690.
Verma, S.P., Torres-Alvarado, I.S., and Velasco-Tapia, F., 2003, A revised CIPW norm: Schweizerische Mineralogische und Petrographische Mitteilungen, v. 83, no. 2, pp. 197–216.
See Also
Examples
#create a dataframe with major elements indicating the appropriate parameters of rocks
#example of dataframes: EAP.csv, IUGS.csv, and TephraKam.csv
data(EAP)
ultimateCIPW(EAP, Type= "Volcanic", Fe.adjustment = "Middlemost",
Cancrinite = FALSE, Calcite = FALSE)
##
rm(EAP)#cleanup