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refactored documentation
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‎docs/api.rst

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‎docs/classes.rst

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Grid Classes
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++++++++++++
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:mod:`~plateflex` defines the following ``Grid`` classes:
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- :class:`~plateflex.classes.Grid`
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- :class:`~plateflex.classes.TopoGrid`
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- :class:`~plateflex.classes.GravGrid`
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- :class:`~plateflex.classes.BougGrid`
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- :class:`~plateflex.classes.FairGrid`
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- :class:`~plateflex.classes.RhocGrid`
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- :class:`~plateflex.classes.ZcGrid`
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These classes can be initialized with a grid of the corresponding data
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type, and contain methods for the following functionality:
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- Extracting contours at some level of the grid
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- Performing a wavelet transform using a Morlet wavelet
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- Obtaining the wavelet scalogram from the wavelet transform
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- Plotting the input grids, wavelet transform components, and scalograms
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Grid
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----
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.. autoclass:: plateflex.classes.ZcGrid
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:members:
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Project Class
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+++++++++++++
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This module further contains the class :class:`~plateflex.classes.Project`,
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which itself is a container of :class:`~plateflex.classes.Grid` objects
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(at least one each of :class:`~plateflex.classes.TopoGrid` and
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:class:`~plateflex.classes.GravGrid`). Methods are available to:
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- Add :class:`~plateflex.classes.Grid` or :class:`~plateflex.classes.Project` objects to the project
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- Iterate over :class:`~plateflex.classes.Grid` objects
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- Initialize the project
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- Perform the wavelet admittance and coherence between topography (:class:`~plateflex.classes.TopoGrid` object) and gravity anomalies (:class:`~plateflex.classes.GravGrid` object)
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- Plot the wavelet admnittance and coherence spectra
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- Estimate model parameters at single grid cell
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- Estimate model parameters at every (or decimated) grid cell
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- Plot the statistics of the estimated parameters at single grid cell
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- Plot the observed and predicted admittance and coherence functions at single grid cell
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- Plot the final grids of model parameters
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Project
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--------
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‎docs/conf.rst

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Configuration module
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++++++++++++++++++++
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.. automodule:: plateflex.conf
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:members:

‎docs/estimate.rst

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Module estimate
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---------------
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Estimate functions
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++++++++++++++++++
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.. automodule:: plateflex.estimate
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:members:

‎docs/getting_started.rst

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.. figure:: ../plateflex/examples/picture/plateflex_logo.png
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:align: center
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.. automodule:: plateflex
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:members:
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Global Variables
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----------------
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Making gridded data
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-------------------
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Packaged with this software is a set of topography, gravity and crustal structure data that
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are easily imported into the ``PlateFlex`` package. Those data sets have been produced by
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processing global grids of data from the
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`WGM2012 <http://bgi.omp.obs-mip.fr/data-products/Grids-and-models/wgm2012>`_,
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`GEBCO <https://www.gebco.net/data_and_products/gridded_bathymetry_data/>`_ and
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`CRUST1.0 <https://igppweb.ucsd.edu/~gabi/crust1.html>`_ models using
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`GMT <https://www.generic-mapping-tools.org>`_.
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The WGM2012 models are used to extract Topography, Bouguer and Free-air anomaly data
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over North America, and Free-air anomaly data over the NW Pacific.
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The GEBCO model is used for the Bathymetry over the NW Pacific.
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The CRUST1.0 models are used to extract the crustal thickness and crustal
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density (corresponding to upper crust, or layer #6) over both North America and the NW Pacific.
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Since those models are all defined using a different registration and grid sampling,
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we use GMT to manipulate the grids and produce consistent data sets to use with
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``PlateFlex``. We used GMT 5.4.1 in the following examples. These commands should be
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copied to a bash script file and executed from the terminal.
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WGM2012
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*******
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These models are defined at a resolution of 2' with a gridline registration.
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.. sourcecode:: bash
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# Set region and projection for North America. Use a transverse mercator
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# with a central meridian of -95 degrees to minimize high-latitude distortions.
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reg=-R-125/13/-28/58+r
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proj=-JT-95/3i
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# Make map of region
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ps=Bouguer_NA.ps
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gmt grdimage WGM2012_Bouguer_ponc_2min.grd $reg $proj -K -P \
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-B10WSne -CPALET_WGM_Bouguer_Global.cpt -X1.5i -Y1.25i > $ps
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gmt psscale -CPALET_WGM_Bouguer_Global.cpt -DJRM+o0.25i/0+e+mc -R -J -O >> $ps
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# Project onto Cartesian grid with sampling interval of 20 km
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gmt grdproject WGM2012_Bouguer_ponc_2min.grd -GBouguer_NA.grd $proj $reg -D20 -Fk
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# Save grid information as header for use with PlateFlex software
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gmt grdinfo -C Bouguer_NA.grd > header.txt
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sed 's/^/# /g' header.txt > Bouguer_NA.xyz
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gmt grd2xyz Bouguer_NA.grd >> Bouguer_NA.xyz
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You can repeat these commands for the corresponding Free-air anomaly and Topography data.
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GEBCO
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*****
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This model is defined on a very fine grid (15" resolution) with a gridline registration.
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We first resample the grid onto a 2' grid.
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.. sourcecode:: bash
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# Set region and projection for NW Pacific - here we use a regular
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# Mercator since it straddles the equator.
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reg=-R145/215/-15/45
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proj=-JM3i
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# Resample on a 2' grid
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gmt grdsample GEBCO_data/GEBCO_2019.nc -GGEBCO_resampled_2m.grd -I2m -Rd
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# Make map of region
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ps=Bathy_PAC.ps
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gmt grdimage GEBCO_resampled_2m.grd $reg $proj -K -P \
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-B10WSne -CPALET_WGM_ETOPO1_Global.cpt -X1.5i -Y1.25i > $ps
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gmt psscale -CPALET_WGM_ETOPO1_Global.cpt -DJRM+o0.25i/0+e+mc -R -J -O >> $ps
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# Project onto Cartesian grid
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gmt grdproject GEBCO_resampled_2m.grd -GBathy_PAC.grd $proj $reg -D10 -Fk
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# Dump grid onto ASCII file with header
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gmt grdinfo -C Bathy_PAC.grd > header.txt
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sed 's/^/# /g' header.txt > Bathy_PAC.xyz
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gmt grd2xyz Bathy_PAC.grd >> Bathy_PAC.xyz
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CRUST1.0
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********
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The CRUST1.0 model is defined on a very coarse grid (1 degree). This is not a
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problem as we only use those fields in the inversion step, and not in the
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calculation of the wavelet transform. However, we still require an identical
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grid specification, so the first step is to resample them on a fine grid
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using spline interpolation.
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.. note::
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You first need to extract the proper layer within CRUST1.0. For crustal
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thickness, the weblink contains a global grid of crustal thickness (crsthk.xyz).
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For the density layer, you will have to use the provided fortran code getCN1xyz.f
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and rename the output file xyz-ro6 to something like crustal_density.xyz
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(for example). Layer 6 corresponds to the upper crustal layer. See the weblink for details.
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.. sourcecode:: bash
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# Set region and projection for North America
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reg=-R145/215/-15/45
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proj=-JM3i
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# Create 2 .grd file from the ASCII data
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gmt xyz2grd crsthk.xyz -Gcrust_thickness_1deg.grd -Rd -I1 -T
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# Resample on a 2' grid using spline interpolation
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gmt grdsample crust_thickness_1deg.grd -Gcrust_thickness_2m.grd -nb -Rg -I2m
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# Make map of region
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ps=Crust_thick_PAC.ps
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gmt makecpt -Chaxby -T5/30/1 > crust.cpt
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gmt grdimage crust_thickness_2m.grd $reg $proj -K -P \
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-B10WSne -Ccrust.cpt -X1.5i -Y1.25i > $ps
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gmt psscale -Ccrust.cpt -DJRM+o0.25i/0+e+mc -R -J -O >> $ps
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# Project onto Cartesian grid
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gmt grdproject crust_thickness_2m.grd -Gcrust_thickness.grd $proj $reg -D10 -Fk
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# Dump grid onto ASCII file with header
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gmt grdinfo -C crust_thickness.grd > header.txt
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sed 's/^/# /g' header.txt > crustal_thickness_PAC.xyz
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gmt grd2xyz crust_thickness.grd >> crustal_thickness_PAC.xyz

‎docs/index.rst

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.. figure:: ../plateflex/examples/picture/logo_plateflex.png
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:align: center
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.. image:: https://travis-ci.com/paudetseis/PlateFlex.svg?branch=master
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:target: https://travis-ci.com/paudetseis/PlateFlex
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PlateFlex Project Documentation
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===============================
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Documentation
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=============
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The flexure of elastic plates is a central concept in the theory of plate tectonics,
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where the Earth's lithosphere (crust and uppermost mantle) reacts to applied loads
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Young's modulus with the cube of the elastic plate thickness. Estimating the *effective*
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elastic thickness (:math:`T_e`) of the lithosphere (thickness
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of an equivalent ideal elastic plate) gives important clues on the rheology of the
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lithosphere and its thermal state.
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Estimating :math:`T_e` can be done by modeling the cross-spectral properties
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(admittance and coherence) between topography and gravity anomaly data,
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which are proxies for the distribution of flexurally compensated surface and subsurface
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loads. These spectral properties can be calculated using different spectral
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estimation techniques - however, to map :math:`T_e` variations it is
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important to use analysis windows small enough for good spatial resolution, but
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large enough to capture the effect of flexure at long wavelengths. The wavelet
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transform is particularly well suited for this analysis because it avoids splitting
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the grids into small windows and can therefore produce cross-spectral functions
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at each point of the input grid.
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lithosphere and its thermal state. Estimating :math:`T_e` is typically done by
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modeling the cross-spectral properties (admittance and coherence) between
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topography and gravity anomaly data, which are proxies for the distribution of
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flexurally compensated surface and subsurface loads.
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This package contains ``python`` and ``fortran`` modules to calculate the wavelet spectral
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and cross-spectral quantities of 2D gridded data of topography and gravity anomalies.
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surface and subsurface loads (:math:`\alpha`). The software uses the analytical
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functions with uniform :math:`F` and :math:`\alpha` to fit the admittance and/or coherence functions.
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The estimation can be done using non-linear least-squares or probabilistic (i.e., bayesian)
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inference methods.
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The analysis can be done using either the Bouguer or Free air gravity anomalies, and
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inference methods. The analysis can be done using either the Bouguer or Free air gravity anomalies, and
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over land or ocean areas. Computational workflows are covered in the Jupyter
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notebooks bundled with this package. The software contains methods to make beautiful and
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insightful plots using the `seaborn` package.
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The cross-spectral quantities calculated here are the real-valued
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admittance and squared-real coherency, as discussed in the references
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.. image:: https://travis-ci.com/paudetseis/PlateFlex.svg?branch=master
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:target: https://travis-ci.com/paudetseis/PlateFlex
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.. toctree::
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:maxdepth: 1
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:maxdepth: 1
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:caption: Getting Started
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api
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getting_started
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.. toctree::
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:maxdepth: 1
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:caption: Configuration modules
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:caption: API Documentation
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conf
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.. toctree::
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:maxdepth: 1
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:caption: Classes
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classes
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.. toctree::
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:maxdepth: 1
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:caption: Modules
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estimate
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plotting
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‎docs/links.rst

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-----------------
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* `PlateFlex Git repository <https://github.com/paudetseis/PlateFlex>`_
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References
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----------
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* Audet, P. (2014). Toward mapping the effective elastic thickness of planetary lithospheres
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from a spherical wavelet analysis of gravity and topography. Physics of the Earth and
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Planetary Interiors, 226, 48-82. https://doi.org/10.1016/j.pepi.2013.09.011
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* Kalnins, L.M., and Watts, A.B. (2009). Spatial variations in effective elastic thickness
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in the Western Pacific Ocean and their implications for Mesozoic volcanism. Earth and
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Planetary Science Letters, 286, 89-100. https://doi.org/10.1016/j.epsl.2009.06.018
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* Kirby, J.F., and Swain, C.J. (2009). A reassessment of spectral Te estimation in
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continental interiors: The case of North America. Journal of Geophysical Research, 114,
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B08401. https://doi.org/10.1029/2009JB006356
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* Kirby, J.F. (2014). Estimation of the effective elastic thickness of the lithosphere
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using inverse spectral methods: The state of the art. Tectonophysics,
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631, 87-116. https://doi.org/10.1016/j.tecto.2014.04.021

‎docs/plotting.rst

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Module plotting
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Plotting functions
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.. automodule:: plateflex.plotting
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:members:

‎plateflex/__init__.py

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from the package by running:
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.. sourcecode:: python
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doc.install_doc(path='Examples')
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To run the notebooks you will have to further install ``jupyter``:
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.. sourcecode:: bash
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conda install jupyter
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.. sourcecode:: bash
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cd Examples
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jupyter notebook

‎plateflex/plotting.py

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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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"""
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This :mod:`~plateflex`` module contains the following functions for plotting:
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This :mod:`~plateflex` module contains the following functions for plotting:
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- :func:`~plateflex.plotting.plot_real_grid`
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- :func:`~plateflex.plotting.plot_bayes_stats`

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