| Title: | The Ultimate Igneous Norm |
|---|---|
| Description: | The computer program is an efficient igneous norm algorithm and rock classification system written in R but run as shiny app. |
| Authors: | Carlos Eduardo Sánchez Torres [aut],
Kevin Samuel Cárdenas-Muñoz [aut],
Luis Alejandro Elizondo-Pacheco [aut],
Reneé González-Guzmán [cre] |
| Maintainer: | Reneé González-Guzmán <[email protected]> |
| License: | GPL-3 |
| Version: | 0.8.6 |
| Built: | 2024-11-17 04:09:47 UTC |
| Source: | https://github.com/therfrog/shinynorrrm |
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.
adjRock(data, Type, Fe.adjustment, Cancrinite, Calcite)adjRock(data, Type, Fe.adjustment, Cancrinite, Calcite)
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. |
Returns a dataset of adjust oxide data (.adj) on an anhydrous basis.
Maintainer: Reneé González-Guzmán [email protected] (ORCID)
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.
#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#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
Data frame with symbols, element names, and standard atomic weights.
data(AtomWeight)data(AtomWeight)
The format is a data frame with 92 rows and 3 columns, including the row names.
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.
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.
data(AtomWeight) AtomWeight['H','AWeight'] rm(AtomWeight)#cleanup ##data(AtomWeight) AtomWeight['H','AWeight'] rm(AtomWeight)#cleanup ##
Compilation of major and trace element analysis of 7019 igneous rocks from the Deccan region, India.
data(Deccan)data(Deccan)
The format is a data frame with 7019 rows and 30 columns.
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.
The database is part of the compiled data in Gard et al. (2019). For full details see doi:10.5194/essd-11-1553-2019.
Gard, M., Hasterok, D. and Halpin, J.A., 2019. Global whole-rock geochemical database compilation. Earth System Science Data, 11(4), pp.1553-1566.
data(Deccan) rm(Deccan)#cleanup ##data(Deccan) rm(Deccan)#cleanup ##
Compilation of major and trace element analysis of 46 igneous rocks from San Carlos-Cruillas, Tamaulipas, Mexico.
data(EAP)data(EAP)
The format is a data frame with 46 rows and 28 columns.
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.
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 .
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.
data(EAP) rm(EAP)#cleanup ##data(EAP) rm(EAP)#cleanup ##
The adjusted oxide data,
Indices(data, Calcite)Indices(data, Calcite)
data |
a whole rock major adjusted oxide chemical data. |
Calcite |
if it is TRUE, CaO will be used in the computation. |
Returns a dataset with several petrological parameters.
Renee Gonzalez Guzman [email protected]
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.
#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 ###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 ##
Compilation of major elements data for 37 representative samples of volcanic rocks.
data(IUGS)data(IUGS)
The format is a data frame with 37 rows and 28 columns.
This data is available from the Cambridge University Press, as a part of IUGSTAS software.
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.
data(IUGS) rm(IUGS)#cleanup ##data(IUGS) rm(IUGS)#cleanup ##
Data frame with normative mineral names, chemical nomenclature, oxides molecular weights and theoretical density of minerals used in the Norm computations.
data(MinWeight)data(MinWeight)
The format is a data frame with 36 rows and 6 columns, including the row names.
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.
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.
data(MinWeight) MinWeight['Quartz','ConsWeight'] ## MinWeight['Quartz','Density'] ## rm(MinWeight)#cleanupdata(MinWeight) MinWeight['Quartz','ConsWeight'] ## MinWeight['Quartz','Density'] ## rm(MinWeight)#cleanup
Data frame with chemical nomenclature and molecular weights used in the ultimate Norm computation.
data(OxiWeight)data(OxiWeight)
The format is a data frame with 26 rows and 3 columns, including the row names.
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.
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.
data(OxiWeight) OxiWeight ['SiO2','OWeight'] ## rm(OxiWeight)#cleanupdata(OxiWeight) OxiWeight ['SiO2','OWeight'] ## rm(OxiWeight)#cleanup
Starts the shinyNORRRM app in the client's browser.
shinyNORRRM(host = "127.0.0.1", port = NULL, browser = NULL)shinyNORRRM(host = "127.0.0.1", port = NULL, browser = NULL)
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) |
shinyNORRRM is the interface of NORRRM
A shiny app
## 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)## 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)
Compilation of major and minor element analysis of 7596 igneous rocks from Kamchatka, Rusia.
data(TephraKam)data(TephraKam)
The format is a data frame with 7596 rows and 30 columns.
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.
The database is also available in Portnyagin et al. (2019). For full details see doi:10.5194/essd-12-469-2020.
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.
data(TephraKam) ## rm(TephraKam)#cleanupdata(TephraKam) ## rm(TephraKam)#cleanup
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.
ultimateCIPW(data, Type, Fe.adjustment, Cancrinite, Calcite)ultimateCIPW(data, Type, Fe.adjustment, Cancrinite, Calcite)
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. |
Calculate the igneous Norm and others geochemical parameters.
Renee Gonzalez Guzman [email protected]
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.
#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#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