This package provides S4 classes for downloading and processing seismological
data available from Earthscope Consortium (https://www.earthscope.org) (formerly IRIS) or
other data centers offering FDSN web services.
Core classes Trace, Stream and IrisClient and their associated methods
are inspired by the functionality available in the python ObsPy package (https://obspy.org/).
The "IRISSeismic-intro" vignette gives introductory examples on using the package.
In 2023, IRIS (Incorporated Research Institutions for Seismology) and UNAVCO merged to form EarthScope Consortium. IRIS (now EarthScope) webservices are unchanged but can now be accessed at https://service.earthscope.org as well as https://service.iris.edu.
Jonathan Callahan jonathan@mazamascience.com
version 1.6.7
update maintainer contact information
update IRIS references to EarthScope
version 1.6.6
for web service calls that support the nodata=<204|404> option, use nodata=204
corrected the crossSpectrum documentation, Pxy is the cross-periodogram for ts1 and ts2
version 1.6.5
examples and vignette updated for better error handling when accessing internet resources
version 1.6.4
updated to (modified version of) libmseed-2.19.8
version 1.6.3
Stream object @ timing_quality now averages the values of the miniSEED blockette 1001 timing quality values, instead of summing the blockette 1001 values and dividing by the number of records
version 1.6.2
getDataselect, modified default time out values
fixed url in documentation
version 1.6.0
irisNetrc definition moved inside getDataselect function
restored getTimeseries function
default values for class Trace InstrumentSensitivity and SensitivityFrequency changed to NA from 1.0
added transferFunctionSpectra function
version 1.5.2
updated getDataAvailablity to use new fdsnws availability web service specification https://service.iris.edu/fdsnws/availability/1/
fixed bug in getDataAvailability when mergequality=FALSE
fixed bug in getDataAvailability affecting start/end times, introduced in version 1.5.1
fixed bug in mergeTraces when trace has gap at end, introduced in version 1.5.1
version 1.5.1
changed a subset of time format OS to OS6
fixed bug in mergeTraces when fdsnws/dataselect implementation cuts on records instead of sample
version 1.5.0
added spacing as an option to getEvalresp
modified getEvalresp to use IrisClient service_type
new getDataAvailability() to return dataframe of miniseed data extents in the IRIS archive using IRIS web service https://service.iris.edu/irisws/availability/1/
minor change to src code to pass CRAN checks
version 1.4.9
additional error handling
minor updates to the plot.Trace and plot.Stream functions
updated src/libmseed to version 2.19.6
version 1.4.8
updated src/libmseed to version 2.19.5
fix bug related to leap seconds
functions that call web services now follow redirects
some error outputs have changed slightly
rmsVariance function, na.rm=TRUE calculates data length minus NA values
rmsVariance.Stream now honors na.rm=TRUE
getGaps() error handling now checks for negative sample rates
getEvent, getEvalresp now truncates start and end input times to seconds (time format OS0 instead of OS) to fix error when user set options(digits.secs=) > 3
version 1.4.7
additional error handling for getDistaz
added input service_type to IrisClient, defaults to fdsnws
plot.Trace x-axis labels are "MM dd" instead of days of week for traces > 1 day and < 1 week
getDataselect will retry once if it encounters http code 401
additional error handling for spectralUtils
version 1.4.6
bug fix for IRISSeismic::slice
version 1.4.5
fixed bug in noiseModels for low noise model results at periods > 10000 seconds
retry if getEvent returns a service unavailable message
version 1.4.4
modified error messages for getEvalresp() and getDistaz()
version 1.4.3
changed getEvent default url from https://earthquake.usgs.gov/fdsnws/event/1/ to https://earthquake.usgs.gov/fdsnws/event/1/
version 1.4.2
updated libmseed version to 2.19
version 1.4.1
updated libmseed version to 2.18
fix for reading miniseed with out of order records
version 1.4.0
addition of repository argument to getDataselect and getSNCL, to match change in fdsnws-dataselect web service
version 1.3.9
fixes compile warning generated by clang
removes followlocation=TRUE from getDataselect RCurl options
version 1.3.8
getDataselect does not add a quality indicator to url by default. IRIS webservices itself defaults to quality="M"
getStation and getChannel do not add includerestricted indicator to url by default. IRIS webservices itself defaults to TRUE
better handling of textConnections
version 1.3.7
users can now supply instrument response information in the form of frequency, amplitude, phase
to the functions psdStatistics, psdList2NoiseMatrix, psdPlot,
in place of the getEvalresp webservice call. Function argument order for psdPlot is changed.
added showMedian option to psdPlot
version 1.3.5
added ignoreEpoch option to getDataselect
version 1.3.4 -- webservices and plotting
getEvent forwards https://service.iris.edu/fdsnws/event/1/ calls to https://earthquake.usgs.gov/fdsnws/event/1/
getDistaz changes output dataframe column name ellipsoid..attrs to ellipsoid.name
plot.Trace allows for user supplied ylab and xlab input
version 1.3.3 -- documentation
Updated documentation and corrected outdated links
version 1.3.2 -- bug fix
noiseModels(), minor correction to the New High Noise Model
version 1.3.1 -- bug fixes
psdStatistics() correctly handles NA values when calculating high and low PDF bin limits and returns pct_above and pct_below vectors of correct length
version 1.3.0 -- compatibility with IRIS webservices
getDistaz() returns new variables from output of https://services.iris.edu/irisws/distaz/1/
version 1.2.2 -- PDF bug fix
psdList2NoiseMatrix() adds 1 second to start time in getEvalresp call to work around a quirk in https://services.iris.edu/irisws/evalresp/1/ webservice that will not return a response if the start time is exactly on a metadata epoch boundary.
version 1.2.1 -- PDF
psdPlot() now compatible with changes to psdStatistics() in previous version. Adds ylo, yhi arguments to customize y-axis limits in plot.
version 1.2.0 -- PDF
psdStatistics() changes method of setting PDF bins from fixed values to bins based on the high and low PSD values and shifts bin centers by 0.5 dB. The result now matches output from https://services.iris.edu/mustang/noise-pdf.
verison 1.1.7 -- improved error handling
getDataselect(), getNetwork(), getStation(), getChannel(), getAvailability(), getEvalresp(), getTraveltime() error handling now report unexpected http status codes.
version 1.1.6 -- bug fixes
getGaps() fixes issues with multiple sample rates and setting minimum gap length.
mergeTraces.Stream() relaxes criteria for acceptable sample rate jitter.
version 1.1.5 -- trace rotation
rotate2D() changes orthogonality test tolerance from 5 degrees to 3 degrees.
version 1.1.4 -- trace rotation
rotate2D() exits if traces are not orthogonal.
version 1.1.3 -- bug fix
psdStatistics() fixes bug in calculation of pct_above and pct_below.
version 1.1.1 -- bug fixes
getGaps() minor bug fix.
mergeTraces.Stream() minor bug fix.
version 1.0.10 -- new data request argument and bug fixes
Imports seismicRoll (>= 1.1.0).
getGaps() fixes bugs in calculation of initial and final gap of Trace.
getDataselect(), getSNCL() adds "inclusiveEnd" argument, a logical that determines whether a data point that falls exactly on the requested endtime is included in the Trace.
libmseed change, when multiple sample rates exist in miniseed records use the mode of all sample rates instead of using the sample rate in the first record.
psdList() added rule for octave generation for channel codes that start with "V".
version 1.0.9 -- Trace class expansion and bug fixes
Improved error handling for getAvailability(), getChannel(), getDataselect(), getEvalresp(), miniseed2Stream().
parseMiniSEED.c, unpackdata.c updated. Fixes protection stack overflow issue.
getGaps() includes a 0.5/sampling_rate tolerance factor.
miniseed2Stream() uses endtime from parseMiniSEED instead of calculating from the sample rate.
Trace class now contains slots for optional metadata "latitude", "longitude", "elevation", "depth", "azimuth", "dip", "SensitivityFrequency".
rotate2D() uses Trace class "azimuth" slot information to identify channel orientation before rotation instead of assuming lead and lag channel from trace input order.
version 1.0.8 -- fixes required by ISPAQ
Removed 'maps' and 'mapdata' from Suggested: packages.
Changed URL syntax for FDSN web services to use "format=..." instead of "output=...".
Fixed bug in getSNCL() so that it works when the "quality" argument is missing.
version 1.0.6 -- CRAN updates required
Removed "mode" argument form Trace.as.vector() signature.
version 1.0.4 -- name change to IRISSeismic
Name change required because 'seismic' was recently taken.
Using explicit references for 'utils' and 'stats' package functions as this is now required for CRAN.
version 1.0.3 -- cleanup for submission to CRAN
Updated libmseed to version 2.16
version 0.2.8.0 -- minor tweaks to 0.2.7
Updated links to IRIS web services in the documentation.
McNamaraBins() ignores bin #0 (~= DC)
McNamaraPSD() conversion to dB occurs after binning, not before
version 0.2.7.0 -- hilbert transform
New hilbertFFT() function.
New hilbert() trace method.
version 0.2.6.0 -- cross correlation
Added surfaceDistance() function.
Added rotate2D() function.
version 0.2.5.0 -- channel orientation
Jumping to version 0.2.5 to match project milestone names.
Added getSNCL() convenience wrapper for getDataselect() method.
Added getDistaz() method of IrisClient.
Added miniseed2Stream() and readMiniseedFile() functions.
Added getRotation() method of IrisClient.
version 0.2.3.0 -- cross spectrum
Moved McNamaraPSD() from trace method to spectral utility function.
Added spectral utility functions:
crossSpectrum()
McNamaraBins()
All get~ methods that return dataframes now guarantee a default ordering of rows.
version 0.2.2.0 -- PSD and friends
Add dependency on pracma package.
Use pracma::detrend() function in DDT.Trace().
Added "increment" parameter to STALTA.Trace().
Removed STALTA.Trace() algorithm "classic_LR2".
Fixed URL generation for getEvalresp() when location="".
Added NamaraPSD.Trace() method.
Added PSD/PDF utility functions:
noiseMatrix2PdfMatrix()
noiseModels()
psdDF2NoiseMatrix()
psdList()
psdList2NoiseMatrix()
psdStatistics()
psdPlot()
version 0.2.1.1 -- Bug fix release
Removed dependcy on signal, XML packages.
version 0.2.1.0 -- FDSN web services
Conversion to FDSN web services including the following new/rewritten methods:
getNetwork, getStation, getChannel, getAvailability, getUnavailability
Updated version of getEvent to return a dataframe with columns named "latitude" and "longitude"
for consistency with all other web services
Updated documentation and Rscripts to match the API changes in the conversion to FDSN web services.
Removal of all StationXML classes in favor of storing that information in slots of the Trace class.
Updates to Trace object slots @Sensor, @InstrumentSensitivity and @InputUnits
to store information as character, numeric and character instead of StationXML classes.
The TraceHeader@quality slot now reflects the data quality returned in the miniSEED record
rather than the quality that was requested by getDataselect. (Requests with quality=B for "Best" typically return
quality=M.)
Improved STALTA.Trace() method removes experimental algorithms and now uses C++ code from package
rollSeismic to calculate rolling means.
Updated IrisClient now uses web services from https://service.iris.edu for the following methods:
getDataselect, getEvalresp, getEvent
version 0.2.0.0
Removed PSD methods of Stream and Trace. PSD algorithms are now part of the PSD metric.
Improved mergeTraces.Stream() method now accepts fillMethod="fillZero".
version 0.1.9.0
New rollSeismic package for fast rolling algorithms implemented in C++/Rcpp.
New num_spikes metric based on seismicRoll::roll_hampel outlier detection.
New correlation metric.
New scripts glitchMetrics.Rscript, correlationMetric.Rscript, pressureCorrelation.Rscript
New trace@stats@processing slot for data processing information.
New Stream methods: mergeTraces, plot
Improved getGaps.Stream() method properly handles initial and final gaps.
Improved MCR error messing.
version 0.1.8.0 -- IrisClient methods getEvent and getTraveltime, improved SNR metric
version 0.1.7.0 -- PSD
version 0.1.6.0 -- improved errors, miniSEED parser
version 0.1.5.0 -- code cleanup, improved errors, package vignette
version 0.1.4.0 -- STA/LTA, upDownTimes, basic plotting
version 0.1.3.0 -- SNR, memory profiling
version 0.1.2.0 -- ...
version 0.1.1.0 -- ...
ObsPy: https://obspy.org/
EarthScope web services: https://service.earthscope.org/
IrisClient-class,
Trace-class,
Stream-class,
# Open a connection to EarthScope webservices
iris <- new("IrisClient", debug=TRUE)
starttime <- as.POSIXct("2010-02-27 06:45:00", tz="GMT")
endtime <- as.POSIXct("2010-02-27 07:45:00", tz="GMT")
# Get the seismic data
result <- try(st <- getDataselect(iris,"IU","ANMO","00","BHZ",starttime,endtime))
if (inherits(result,"try-error")) {
message(geterrmessage())
} else {
# Extract the first trace, display the metadata and plot it
tr1 <- st@traces[[1]]
show(tr1@stats)
plot(tr1)
}
Run the code above in your browser using DataLab