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#irisws

Access to the Incorporated Research Institutions in Seismology (IRIS) Web Services (WS) from within R

This project is intended to serve as a tool to access Incorporated Research Institutions in Seismology (IRIS) Web Services (WS) using the R programming language. The repository is a self-consistent R-package, meaning one can do the following:

install.packages("devtools", dependencies=TRUE)
library(devtools)
install_github("abarbour/irisws", dependencies=TRUE)

and from then on

library(irisws)
# inspect documentation
?irisws
# list current webservice functions:
webservices()  
# and so on...

The latter command prints a list of the webservice access-functions currently included.

This project has limited functionality at the moment, and is evolving -- you should update often. But, once this code is of suitable completeness (and reasonably well tested), I plan to upload it to CRAN. Feel free to contact me (@abarbour) should you have questions, or wish to contribute; or, use github as it was intended and submit some pull requests! :)

Note that you will also need to do the following for all features in the package to function properly:

pkgs <- c("httr","lubridate","png","RCurl","reshape2","XML","XML2R")
install.packages(pkgs, dependencies=TRUE)

but these should've been installed at the install_github stage.

Examples

Raw-data (timeseries)

Among other types of data, seismic data is easily accessed with the timeseries webservice. For example, the following command will download an image (generated internally) of two hours of 1-Hz pore pressure data at PBO station B084, containing signals from the 2010 M7.2 El Mayor Cucapah earthquake:

require(irisws)

# download the data plotted in a png file
# (the figure itself is generated within the IRIS-WS internal framework)

w <- ws.timeseries(network="PB",    # network code
	station="B084",                 # station code
	location="--",                  # location code
	channel="LDD",                  # channel code
	starttime="2010.094T22:00:00",  # the beginning of the data
	duration=7200,                  # how many second from 'starttime' to download
	output="plot",                  # output format
	filename="myplot.png")          # the filename of the output

which, upon success, is loaded into w. Loading is an optional feature, but TRUE by default. The figure returned by the original query should resemble something like this:

alt text

The object w in this example also includes additional information besides the data returned from IRIS-WS:

str(w, nchar.max = 40)
#List of 5
# $ file     : chr "myplot.png"
# $ query    : chr "http://service.iris.edu/irisws/timeseri"| __truncated__
# $ success  : logi TRUE
# $ opts     : list()
# $ querydata: 'nativeRaster' int [1:700, 1:1000] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ...
#  ..- attr(*, "channels")= int 4

The data loaded into w -- in this case an object with class "nativeRaster" -- can be accessed with the querydata method:

qd <- querydata(w)
str(qd)
# 'nativeRaster' int [1:700, 1:1000] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ...
# - attr(*, "channels")= int 4

One could then, for example, plot the image from within R (> 2.11):

if (exists("rasterImage")) {
   plot(1:2, type='n')
   rasterImage(querydata(w), 1.2, 1.27, 1.8, 1.73, interpolate=FALSE)
}

We just demonstrated how to set the output format to a internally-generated plot ( with output="plot" ), but there are in fact a number of (more useful) formats which can be obtained -- see the documentation ( ?ws.timeseries ) for ways to specify other formats.

Basic support for Seismic Analysis Code (SAC) files

In regards to obtaining data in a different output format, the package includes a limited support framework for working with Seismic Analysis Code (SAC) files directly -- these are commonly used in seismological applications, and are usually named with the suffix .sac.

To illustrate some of the functionality, we have included a .sac (binary) file to play with, which can be read-in and plotted, for example:

require(irisws)

sacfi <- system.file("sac/elmayorB084_LDD.sac", package="irisws")

# this is a little-endian binary file, so be sure to specify it so the result
# makes sense (your system might be "big")
x <- read.sac(sacfi, is.binary=TRUE, endianness="little")

# the function 'read.sac' returns an object of class 'saclist', for which
# there is a plot method:
plot(x)

The plot.saclist method yields a figure similar to the one shown above.

Query parameters from .wadl files

I have difficulty keeping track of the the various parameters required for a given webservice (not to mention the myriad optional arguments).
Because of this, we include a mechanism to quickly inspect for parameters via the associated .wadl description; this eliminates the need to check the service's webpage, unless details of the different options are needed.

require(irisws)

#  Access the .wadl file for the timeseries application
wd <- waddler("timeseries")

#  find the parameters acceptable in a query...
print(p <- parameters(wd))

#  and ones which are required
print(subset(p, required))

Another way to solve this would be to hard-code the query-parameter names as function arguments, but this will be left for development in the distant future.