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IRISSeismic-package        package:IRISSeismic         R Documentation

_C_l_a_s_s_e_s _a_n_d _m_e_t_h_o_d_s _f_o_r _s_e_i_s_m_i_c _d_a_t_a _a_n_a_l_y_s_i_s

_D_e_s_c_r_i_p_t_i_o_n:

     This package provides S4 classes for downloading and processing
     seismological data available from the IRIS Data Management Center
     (DMC) (<URL: 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 (<URL: http://obspy.org/>).

_I_n_t_r_o_d_u_c_t_i_o_n:

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

_H_i_s_t_o_r_y:

     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 <URL:
          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 - ...

_A_u_t_h_o_r(_s):

     Jonathan Callahan <email: jonathan@mazamascience.com>

_R_e_f_e_r_e_n_c_e_s:

     ObsPy: <URL: http://obspy.org/>

     IRIS DMC web services: <URL: http://service.iris.edu/>

_S_e_e _A_l_s_o:

     'IrisClient-class', 'Trace-class', 'Stream-class',

_E_x_a_m_p_l_e_s:

     # 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
     st <- getDataselect(iris,"IU","ANMO","00","BHZ",starttime,endtime)
     
     # Extract the first trace, display the metadata and plot it
     tr1 <- st@traces[[1]]
     show(tr1@stats)
     plot(tr1)
     

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