EarthChem {GCDkit} | R Documentation |
This function serves for importing the whole-rock geochemical data from EarthChem.org online database. Since 2010, EarthChem has been part of IEDA (Integrated Earth Data Applications), the National Science Foundation (NSF)-funded data facility for solid earth geoscience data. The data are gathered from several publicly available databases such as PetDB, SedDB, NAVDAT, or are contributed, and can be accessed through the EarthChem's REST Search Service utilized by our function.
EarthChem(x,GUI=FALSE) EarthChemC(x,GUI=FALSE)
x |
a list of parameters, given below, detailed account of which is to be found at the web page with the EarthChem REST Server Documentation |
. See also Examples.
GUI |
logical; is the function called from the GUI? |
The function EarthChem
imports the specified data taking advantage of the EarthChem REST
Search Service, which accepts GET string variables that determine search criteria.
The function EarthChemC
is just EarthChem
, compiled for speed.
The results are returned using html or xml protocols, and can be then imported to the GCDkit
using the library 'XML'
.
Possible parameters are (in square brackets are GCDkit default values)
Data source specification (reference(s)) | |
author | author |
title | title of the article |
journal | journal |
doi | Digital Object Identifier (not always available) |
misnumber | minimum publication year of the citation article |
maxpubyear | maximum publicationyear (reqd with the former option) |
exactpubyear | exact year of publication |
keyword | free-text generic descriptor field |
Sample ID, location or age | |
sampleid | sample number/identifier from the original database |
polygon | geographic region, specified by geographic coordinates |
north, east, south, west | coordinates of a geographic envelope, all to be provided together |
minage | minimum age of the sample (Ma) |
maxage | maximum age of the sample (Ma) |
exactage | age of the sample (Ma) |
geologicalage | geological age |
material | either 'bulk', 'whole rock', 'glass' or 'inclusion' |
Output format | |
searchtype | type of search, only 'rowdata' (table of items matching the criteria) |
is implemented so far [rowdata]. | |
outputtype | either 'html' or 'xml' [html] |
outputlevel | either 'sample' or 'method' [sample] |
startrow | sequence number of the first output row minus 1 [0] |
endrow | sequence number of the last output row minus 1 [number_of_hits-1] |
standarditems | logical; output just the standard items? [yes] |
outputitems | comma-separated list of output items |
showcolumnnames | logical; import the names of variables? [yes] |
(Invisibly) the query string. If no hits were found, the function returns (again invisibly) the value -1.
Imports the data into the GCDkit system. Stores the imported dataset into memory
(i.e., the variable WRCube
) together with the fields source
that contains
the string "EarthChem" and date with tome of the search, EarthChem.query.var
with
the query variable (a list) and EarthChem.query.url
with URL sent to the web service.
Then, the previously active dataset becomes the current one.
XML library is required.
Function by Vojtěch Janoušek, vojtech.janousek@geology.cz (with helpful assistance from Jason Ash, jasonash@ku.edu).
Tcl/Tk GUI by Oscar Laurent, oscar.laurent@get.omp.eu
The XML package was written by Duncan Temple Lang.
For further details, see the EarthChem Resources for Developers and, in particular, EarthChem REST Server Documentation
## Not run: # Some of these examples are based on original examples # from http://portal.earthchem.org/rest_search_documentation # The whole dataset EarthChemC(list(author="ackerman",outputtype="html",showcolumnnames="yes", outputitems="sample_id,source,longitude,latitude")) plotDiagram("TAS",FALSE,TRUE) # Just 50 records EarthChemC(list(author="ackerman",outputtype="html",showcolumnnames="yes",startrow=0,endrow=50, outputitems="sample_id,source,longitude,latitude")) # Read the first 100 Cambrian samples EarthChemC(list(geologicalage="cambrian",outputtype="html",startrow=0,endrow=100, outputitems="sample_id,source,longitude,latitude")) # Different values of outputtype just invoke different parsers, the results should be identical EarthChemC(list(author="janousek",outputtype="xml", outputitems="sample_id,source,longitude,latitude")) EarthChemC(list(author="janousek",outputtype="html", outputitems="sample_id,source,longitude,latitude")) # Read a static map directly into R # Samples from the eastern United States and adjacent part of Atlantic Ocean (EarthChem REST example) query<-"http://portal.earthchem.org/restsearchservice? north=49&east=-100&south=23&west=-24&outputtype=staticmap" shell.exec(query) # opens in browser ## End(Not run)