R: Classes and methods for seismic data analysis

IRISSeismic-package {IRISSeismic}

R Documentation

Classes and methods for seismic data analysis

Description

This package provides S4 classes for downloading and processing seismological data available from the IRIS Data Management Center (DMC) (http://ds.iris.edu/ds/nodes/dmc/). Core classes Trace, Stream and IrisClient and their associated methods are inspired by the functionality available in the python ObsPy package (http://obspy.org/).

Introduction

The "IRISSeismic-intro" vignette gives introductory examples on using the package.

History

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 http://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 http://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 http://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 http://service.iris.edu/fdsnws/event/1/ calls to http://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 http://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 http://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 http://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 http://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 – ...

Author(s)

Jonathan Callahan jonathan@mazamascience.com

References

ObsPy: http://obspy.org/

IRIS DMC web services: https://service.iris.edu/

Examples

# Open a connection to IRIS DMC 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)
}

[Package IRISSeismic version 1.6.6 Index]