From a923b901ffc5774ddaf6f47634fe0104134d9581 Mon Sep 17 00:00:00 2001 From: Wei Kang Date: Tue, 25 Sep 2018 21:45:39 -0700 Subject: [PATCH] preparing online docs --- .gitignore | 25 ++ doc/Makefile | 24 ++ doc/_static/images/pysal_favicon.ico | Bin 0 -> 15086 bytes doc/_static/pysal-styles.css | 73 +++++ doc/_static/references.bib | 20 ++ doc/api.rst | 41 +++ doc/conf.py | 260 ++++++++++++++++++ doc/generated/mgwr.gwr.GWR.fit.rst | 9 + doc/generated/mgwr.gwr.GWR.predict.rst | 9 + doc/generated/mgwr.gwr.GWR.rst | 12 + doc/generated/mgwr.gwr.GWRResults.rst | 17 ++ doc/generated/mgwr.gwr.GWRResultsLite.rst | 15 + doc/generated/mgwr.gwr.GWResults.ENP.rst | 9 + doc/generated/mgwr.gwr.GWResults.RSS.rst | 9 + doc/generated/mgwr.gwr.GWResults.TSS.rst | 9 + .../mgwr.gwr.GWResults.adj_alpha.rst | 9 + doc/generated/mgwr.gwr.GWResults.bse.rst | 9 + doc/generated/mgwr.gwr.GWResults.conf_int.rst | 9 + doc/generated/mgwr.gwr.GWResults.cooksD.rst | 9 + .../mgwr.gwr.GWResults.cov_params.rst | 9 + .../mgwr.gwr.GWResults.critical_tval.rst | 9 + .../mgwr.gwr.GWResults.filter_tvals.rst | 9 + doc/generated/mgwr.gwr.GWResults.influ.rst | 9 + doc/generated/mgwr.gwr.GWResults.localR2.rst | 9 + .../mgwr.gwr.GWResults.local_collinearity.rst | 9 + doc/generated/mgwr.gwr.GWResults.pDev.rst | 9 + doc/generated/mgwr.gwr.GWResults.sigma2.rst | 9 + ...mgwr.gwr.GWResults.spatial_variability.rst | 9 + doc/generated/mgwr.gwr.GWResults.std_res.rst | 9 + doc/generated/mgwr.gwr.GWResults.summary.rst | 9 + doc/generated/mgwr.gwr.GWResults.tr_S.rst | 9 + doc/generated/mgwr.gwr.GWResults.tr_STS.rst | 9 + doc/generated/mgwr.gwr.GWResults.tvalues.rst | 9 + doc/generated/mgwr.gwr.GWResults.use_t.rst | 9 + doc/generated/mgwr.gwr.GWResults.y_bar.rst | 9 + doc/generated/mgwr.gwr.MGWR.fit.rst | 9 + doc/generated/mgwr.gwr.MGWR.predict.rst | 9 + doc/generated/mgwr.gwr.MGWR.rst | 9 + .../mgwr.gwr.MGWRResults.critical_tval.rst | 9 + .../mgwr.gwr.MGWRResults.filter_tvals.rst | 9 + ...gwr.gwr.MGWRResults.local_collinearity.rst | 9 + doc/generated/mgwr.gwr.MGWRResults.rst | 15 + ...wr.gwr.MGWRResults.spatial_variability.rst | 9 + .../mgwr.gwr.MGWRResults.summary.rst | 9 + doc/make.bat | 36 +++ mgwr/gwr.py | 43 ++- mgwr/kernels.py | 8 +- 47 files changed, 876 insertions(+), 10 deletions(-) create mode 100644 doc/Makefile create mode 100644 doc/_static/images/pysal_favicon.ico create mode 100644 doc/_static/pysal-styles.css create mode 100644 doc/_static/references.bib create mode 100644 doc/api.rst create mode 100644 doc/conf.py create mode 100644 doc/generated/mgwr.gwr.GWR.fit.rst create mode 100644 doc/generated/mgwr.gwr.GWR.predict.rst create mode 100644 doc/generated/mgwr.gwr.GWR.rst create mode 100644 doc/generated/mgwr.gwr.GWRResults.rst create mode 100644 doc/generated/mgwr.gwr.GWRResultsLite.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.ENP.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.RSS.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.TSS.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.adj_alpha.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.bse.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.conf_int.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.cooksD.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.cov_params.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.critical_tval.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.filter_tvals.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.influ.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.localR2.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.local_collinearity.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.pDev.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.sigma2.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.spatial_variability.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.std_res.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.summary.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.tr_S.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.tr_STS.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.tvalues.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.use_t.rst create mode 100644 doc/generated/mgwr.gwr.GWResults.y_bar.rst create mode 100644 doc/generated/mgwr.gwr.MGWR.fit.rst create mode 100644 doc/generated/mgwr.gwr.MGWR.predict.rst create mode 100644 doc/generated/mgwr.gwr.MGWR.rst create mode 100644 doc/generated/mgwr.gwr.MGWRResults.critical_tval.rst create mode 100644 doc/generated/mgwr.gwr.MGWRResults.filter_tvals.rst create mode 100644 doc/generated/mgwr.gwr.MGWRResults.local_collinearity.rst create mode 100644 doc/generated/mgwr.gwr.MGWRResults.rst create mode 100644 doc/generated/mgwr.gwr.MGWRResults.spatial_variability.rst create mode 100644 doc/generated/mgwr.gwr.MGWRResults.summary.rst create mode 100644 doc/make.bat diff --git a/.gitignore b/.gitignore index bee8a64..bdfa089 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,26 @@ __pycache__ +*.swp +*.pyc +.rope* +.idea/ +notebooks/.ipynb_checkpoints/ +.DS_Store +.ipynb_checkpoints/ +*.bak +.eggs/ +*.egg-info/ + +# Packages +*.egg +*.egg-info +dist +build +eggs +parts +bin +var +sdist +develop-eggs +.installed.cfg +lib +lib64 \ No newline at end of file diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000..74bafd8 --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,24 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +SPHINXPROJ = mgwr +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a 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+.topnavicons { + margin-left: 10% !important; +} + +.topnavicons li { + margin-left: 0px !important; + min-width: 100px; + text-align: center; +} + +.topnavicons .thumbnail { + margin-right: 10px; + border: none; + box-shadow: none; + text-align: center; + font-size: 85%; + font-weight: bold; + line-height: 10px; + height: 100px; +} + +.topnavicons .thumbnail img { + display: block; + margin-left: auto; + margin-right: auto; +} + + +/* Table with a scrollbar */ +.bodycontainer { max-height: 600px; width: 100%; margin: 0; overflow-y: auto; } +.table-scrollable { margin: 0; padding: 0; } \ No newline at end of file diff --git a/doc/_static/references.bib b/doc/_static/references.bib new file mode 100644 index 0000000..5fd30c7 --- /dev/null +++ b/doc/_static/references.bib @@ -0,0 +1,20 @@ +%% This BibTeX bibliography file was created using BibDesk. +%% http://bibdesk.sourceforge.net/ + +%% Created for Wei Kang at 2018-08-05 16:12:26 -0700 + + +%% Saved with string encoding Unicode (UTF-8) + + + +@book{Press2007, + Address = {Cambridge}, + Author = {Press, William H and Teukolsky, Saul A and Vetterling, William T and Flannery, Brian P}, + Date-Added = {2018-06-12 22:53:57 +0000}, + Date-Modified = {2018-06-12 22:54:05 +0000}, + Edition = {3rd}, + Keywords = {rank.py}, + Publisher = {Cambridge Univ Pr}, + Title = {Numerical recipes: the art of scientific computing}, + Year = {2007}} diff --git a/doc/api.rst b/doc/api.rst new file mode 100644 index 0000000..793ecde --- /dev/null +++ b/doc/api.rst @@ -0,0 +1,41 @@ +.. _api_ref: + +.. currentmodule:: mgwr + +API reference +============= + +.. _gwr_api: + +GWR Model Estimation and Inference +---------------------------------- + +.. autosummary:: + :toctree: generated/ + + mgwr.gwr.GWR + mgwr.gwr.GWRResults + mgwr.gwr.GWRResultsLite + + +MGWR Estimation and Inference +----------------------------- + +.. autosummary:: + :toctree: generated/ + + mgwr.gwr.MGWR + mgwr.gwr.MGWRResults + + +Utility Functions +----------------- + +Kernal Specifications +~~~~~~~~~~~~~~~~~~~~~ + +.. autosummary:: + :toctree: generated/ + + mgwr.kernel.fix_gauss + mgwr.kernel. \ No newline at end of file diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 0000000..295096e --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,260 @@ +# -*- coding: utf-8 -*- +# +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import sys, os +import sphinx_bootstrap_theme + + +sys.path.insert(0, os.path.abspath('../../')) + +#import your package to obtain the version info to display on the docs website +import mgwr + + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# +# needs_sphinx = '1.0' +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [#'sphinx_gallery.gen_gallery', + 'sphinx.ext.autodoc', + 'sphinx.ext.autosummary', + 'sphinx.ext.viewcode', + 'sphinxcontrib.bibtex', + 'sphinx.ext.mathjax', + 'sphinx.ext.doctest', + 'sphinx.ext.intersphinx', + 'numpydoc', + 'matplotlib.sphinxext.plot_directive'] + + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = "mgwr" # string of your project name, for example, 'giddy' +copyright = '2018, pysal developers' +author = 'pysal developers' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The full version. +version = mgwr.__version__ #should replace it with your PACKAGE_NAME +release = mgwr.__version__ #should replace it with your PACKAGE_NAME + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = None + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This patterns also effect to html_static_path and html_extra_path +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'tests/*'] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +# html_theme = 'alabaster' +html_theme = 'bootstrap' +html_theme_path = sphinx_bootstrap_theme.get_html_theme_path() +html_title = "%s v%s Manual" % (project, version) + +# (Optional) Logo of your package. Should be small enough to fit the navbar (ideally 24x24). +# Path should be relative to the ``_static`` files directory. +#html_logo = "_static/images/package_logo.jpg" + +# (Optional) PySAL favicon +html_favicon = "_static/images/pysal_favicon.ico" + + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# +html_theme_options = { + + # Navigation bar title. (Default: ``project`` value) + 'navbar_title': "mgwr", # string of your project name, for example, 'giddy' + + # Render the next and previous page links in navbar. (Default: true) + 'navbar_sidebarrel': False, + + # Render the current pages TOC in the navbar. (Default: true) + #'navbar_pagenav': True, + #'navbar_pagenav': False, + + # No sidebar + 'nosidebar': True, + + # Tab name for the current pages TOC. (Default: "Page") + #'navbar_pagenav_name': "Page", + + # Global TOC depth for "site" navbar tab. (Default: 1) + # Switching to -1 shows all levels. + 'globaltoc_depth': 2, + + # Include hidden TOCs in Site navbar? + # + # Note: If this is "false", you cannot have mixed ``:hidden:`` and + # non-hidden ``toctree`` directives in the same page, or else the build + # will break. + # + # Values: "true" (default) or "false" + 'globaltoc_includehidden': "true", + + # HTML navbar class (Default: "navbar") to attach to
element. + # For black navbar, do "navbar navbar-inverse" + #'navbar_class': "navbar navbar-inverse", + + # Fix navigation bar to top of page? + # Values: "true" (default) or "false" + 'navbar_fixed_top': "true", + + + # Location of link to source. + # Options are "nav" (default), "footer" or anything else to exclude. + 'source_link_position': 'footer', + + # Bootswatch (http://bootswatch.com/) theme. + # + # Options are nothing (default) or the name of a valid theme + # such as "amelia" or "cosmo", "yeti", "flatly". + 'bootswatch_theme': "yeti", + + # Choose Bootstrap version. + # Values: "3" (default) or "2" (in quotes) + 'bootstrap_version': "3", + + # Navigation bar menu + 'navbar_links': [ + ("Installation", "installation"), + ("API", "api"), + ("References", "references"), + ], + +} + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} +# html_sidebars = {'sidebar': ['localtoc.html', 'sourcelink.html', 'searchbox.html']} + +# -- Options for HTMLHelp output ------------------------------------------ + +# Output file base name for HTML help builder. +htmlhelp_basename = 'mgwr'+'doc' + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # + # 'papersize': 'letterpaper', + + # The font size ('10pt', '11pt' or '12pt'). + # + # 'pointsize': '10pt', + + # Additional stuff for the LaTeX preamble. + # + # 'preamble': '', + + # Latex figure (float) alignment + # + # 'figure_align': 'htbp', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + (master_doc, 'mgwr.tex', u'mgwr Documentation', + u'pysal developers', 'manual'), +] + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + (master_doc, 'mgwr', u'mgwr Documentation', + [author], 1) +] + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + (master_doc, 'mgwr', u'mgwr Documentation', + author, 'mgwr', 'multiscale gwr', + 'Miscellaneous'), +] + + +# ----------------------------------------------------------------------------- +# Autosummary +# ----------------------------------------------------------------------------- + +# Generate the API documentation when building +autosummary_generate = True +numpydoc_show_class_members = True +class_members_toctree = True +numpydoc_show_inherited_class_members = True +numpydoc_use_plots = True + +# display the source code for Plot directive +plot_include_source = True + +def setup(app): + app.add_stylesheet("pysal-styles.css") + +# Example configuration for intersphinx: refer to the Python standard library. +intersphinx_mapping = {'https://docs.python.org/3.6/': None} + diff --git a/doc/generated/mgwr.gwr.GWR.fit.rst b/doc/generated/mgwr.gwr.GWR.fit.rst new file mode 100644 index 0000000..9874aa2 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWR.fit.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWR +============ + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWR.fit + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWR.predict.rst b/doc/generated/mgwr.gwr.GWR.predict.rst new file mode 100644 index 0000000..b3067d4 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWR.predict.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWR +============ + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWR.predict + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWR.rst b/doc/generated/mgwr.gwr.GWR.rst new file mode 100644 index 0000000..31037c1 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWR.rst @@ -0,0 +1,12 @@ +mgwr.gwr.GWR +============ + +.. currentmodule:: mgwr.gwr + +.. autoclass:: GWR + + + .. automethod:: __init__ + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWRResults.rst b/doc/generated/mgwr.gwr.GWRResults.rst new file mode 100644 index 0000000..c481a6b --- /dev/null +++ b/doc/generated/mgwr.gwr.GWRResults.rst @@ -0,0 +1,17 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. autoclass:: GWRResults + + + .. automethod:: __init__ + + + + + + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWRResultsLite.rst b/doc/generated/mgwr.gwr.GWRResultsLite.rst new file mode 100644 index 0000000..4ac3138 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWRResultsLite.rst @@ -0,0 +1,15 @@ +mgwr.gwr.GWRResultsLite +======================= + +.. currentmodule:: mgwr.gwr + +.. autoclass:: GWRResultsLite + + + .. automethod:: __init__ + + + + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.ENP.rst b/doc/generated/mgwr.gwr.GWResults.ENP.rst new file mode 100644 index 0000000..267531b --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.ENP.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.ENP + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.RSS.rst b/doc/generated/mgwr.gwr.GWResults.RSS.rst new file mode 100644 index 0000000..9b7b274 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.RSS.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.RSS + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.TSS.rst b/doc/generated/mgwr.gwr.GWResults.TSS.rst new file mode 100644 index 0000000..42c7a43 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.TSS.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.TSS + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.adj_alpha.rst b/doc/generated/mgwr.gwr.GWResults.adj_alpha.rst new file mode 100644 index 0000000..eeb12a6 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.adj_alpha.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.adj_alpha + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.bse.rst b/doc/generated/mgwr.gwr.GWResults.bse.rst new file mode 100644 index 0000000..bb21a94 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.bse.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.bse + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.conf_int.rst b/doc/generated/mgwr.gwr.GWResults.conf_int.rst new file mode 100644 index 0000000..969154a --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.conf_int.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.conf_int + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.cooksD.rst b/doc/generated/mgwr.gwr.GWResults.cooksD.rst new file mode 100644 index 0000000..75eb0eb --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.cooksD.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.cooksD + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.cov_params.rst b/doc/generated/mgwr.gwr.GWResults.cov_params.rst new file mode 100644 index 0000000..2439774 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.cov_params.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.cov_params + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.critical_tval.rst b/doc/generated/mgwr.gwr.GWResults.critical_tval.rst new file mode 100644 index 0000000..4b40590 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.critical_tval.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.critical_tval + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.filter_tvals.rst b/doc/generated/mgwr.gwr.GWResults.filter_tvals.rst new file mode 100644 index 0000000..12b1013 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.filter_tvals.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.filter_tvals + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.influ.rst b/doc/generated/mgwr.gwr.GWResults.influ.rst new file mode 100644 index 0000000..e69b2d9 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.influ.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.influ + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.localR2.rst b/doc/generated/mgwr.gwr.GWResults.localR2.rst new file mode 100644 index 0000000..fc172e3 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.localR2.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.localR2 + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.local_collinearity.rst b/doc/generated/mgwr.gwr.GWResults.local_collinearity.rst new file mode 100644 index 0000000..eeaf2ae --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.local_collinearity.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.local_collinearity + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.pDev.rst b/doc/generated/mgwr.gwr.GWResults.pDev.rst new file mode 100644 index 0000000..fc62efc --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.pDev.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.pDev + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.sigma2.rst b/doc/generated/mgwr.gwr.GWResults.sigma2.rst new file mode 100644 index 0000000..10caa48 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.sigma2.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.sigma2 + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.spatial_variability.rst b/doc/generated/mgwr.gwr.GWResults.spatial_variability.rst new file mode 100644 index 0000000..08653c5 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.spatial_variability.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.spatial_variability + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.std_res.rst b/doc/generated/mgwr.gwr.GWResults.std_res.rst new file mode 100644 index 0000000..eeb6afe --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.std_res.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.std_res + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.summary.rst b/doc/generated/mgwr.gwr.GWResults.summary.rst new file mode 100644 index 0000000..52e976a --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.summary.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.summary + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.tr_S.rst b/doc/generated/mgwr.gwr.GWResults.tr_S.rst new file mode 100644 index 0000000..11066fc --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.tr_S.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.tr_S + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.tr_STS.rst b/doc/generated/mgwr.gwr.GWResults.tr_STS.rst new file mode 100644 index 0000000..fb34c2c --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.tr_STS.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.tr_STS + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.tvalues.rst b/doc/generated/mgwr.gwr.GWResults.tvalues.rst new file mode 100644 index 0000000..f935804 --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.tvalues.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.tvalues + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.use_t.rst b/doc/generated/mgwr.gwr.GWResults.use_t.rst new file mode 100644 index 0000000..6ddaa4f --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.use_t.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.use_t + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.GWResults.y_bar.rst b/doc/generated/mgwr.gwr.GWResults.y_bar.rst new file mode 100644 index 0000000..bc3736d --- /dev/null +++ b/doc/generated/mgwr.gwr.GWResults.y_bar.rst @@ -0,0 +1,9 @@ +mgwr.gwr.GWRResults +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: GWRResults.y_bar + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.MGWR.fit.rst b/doc/generated/mgwr.gwr.MGWR.fit.rst new file mode 100644 index 0000000..de304df --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWR.fit.rst @@ -0,0 +1,9 @@ +mgwr.gwr.MGWR +=================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: MGWR.fit + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.MGWR.predict.rst b/doc/generated/mgwr.gwr.MGWR.predict.rst new file mode 100644 index 0000000..012a6bb --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWR.predict.rst @@ -0,0 +1,9 @@ +mgwr.gwr.MGWR +============== + +.. currentmodule:: mgwr.gwr + +.. automethod:: MGWR.predict + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.MGWR.rst b/doc/generated/mgwr.gwr.MGWR.rst new file mode 100644 index 0000000..bab27e7 --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWR.rst @@ -0,0 +1,9 @@ +mgwr.gwr.MGWR +============= + +.. currentmodule:: mgwr.gwr + +.. autoclass:: MGWR + + + .. automethod:: __init__ diff --git a/doc/generated/mgwr.gwr.MGWRResults.critical_tval.rst b/doc/generated/mgwr.gwr.MGWRResults.critical_tval.rst new file mode 100644 index 0000000..b4df35d --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWRResults.critical_tval.rst @@ -0,0 +1,9 @@ +mgwr.gwr.MGWRResults +==================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: MGWRResults.critical_tval + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.MGWRResults.filter_tvals.rst b/doc/generated/mgwr.gwr.MGWRResults.filter_tvals.rst new file mode 100644 index 0000000..5fac216 --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWRResults.filter_tvals.rst @@ -0,0 +1,9 @@ +mgwr.gwr.MGWRResults +==================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: MGWRResults.filter_tvals + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.MGWRResults.local_collinearity.rst b/doc/generated/mgwr.gwr.MGWRResults.local_collinearity.rst new file mode 100644 index 0000000..5640433 --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWRResults.local_collinearity.rst @@ -0,0 +1,9 @@ +mgwr.gwr.MGWRResults +==================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: MGWRResults.local_collinearity + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.MGWRResults.rst b/doc/generated/mgwr.gwr.MGWRResults.rst new file mode 100644 index 0000000..1d5ea11 --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWRResults.rst @@ -0,0 +1,15 @@ +mgwr.gwr.MGWRResults +==================== + +.. currentmodule:: mgwr.gwr + +.. autoclass:: MGWRResults + + + .. automethod:: __init__ + + + + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.MGWRResults.spatial_variability.rst b/doc/generated/mgwr.gwr.MGWRResults.spatial_variability.rst new file mode 100644 index 0000000..63c5ee1 --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWRResults.spatial_variability.rst @@ -0,0 +1,9 @@ +mgwr.gwr.MGWRResults +==================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: MGWRResults.spatial_variability + + + \ No newline at end of file diff --git a/doc/generated/mgwr.gwr.MGWRResults.summary.rst b/doc/generated/mgwr.gwr.MGWRResults.summary.rst new file mode 100644 index 0000000..089d83f --- /dev/null +++ b/doc/generated/mgwr.gwr.MGWRResults.summary.rst @@ -0,0 +1,9 @@ +mgwr.gwr.MGWRResults +==================== + +.. currentmodule:: mgwr.gwr + +.. automethod:: MGWRResults.summary + + + \ No newline at end of file diff --git a/doc/make.bat b/doc/make.bat new file mode 100644 index 0000000..b7ad327 --- /dev/null +++ b/doc/make.bat @@ -0,0 +1,36 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=python -msphinx +) +set SOURCEDIR=. +set BUILDDIR=_build +set SPHINXPROJ=mgwr + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The Sphinx module was not found. Make sure you have Sphinx installed, + echo.then set the SPHINXBUILD environment variable to point to the full + echo.path of the 'sphinx-build' executable. Alternatively you may add the + echo.Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% + +:end +popd diff --git a/mgwr/gwr.py b/mgwr/gwr.py index a1d6457..7192318 100755 --- a/mgwr/gwr.py +++ b/mgwr/gwr.py @@ -282,18 +282,34 @@ def fit(self, ini_params=None, tol=1.0e-5, max_iter=20, Parameters ---------- - ini_betas : array + ini_betas : array, optional k*1, initial coefficient values, including constant. Default is None, which calculates initial values during - estimation - tol: float - Tolerence for estimation convergence - max_iter : integer + estimation. + tol: float, optional + Tolerence for estimation convergence. + Default is 1.0e-5. + max_iter : integer, optional Maximum number of iterations if convergence not - achieved - solve : string + achieved. Default is 20. + solve : string, optional Technique to solve MLE equations. - 'iwls' = iteratively (re)weighted least squares (default) + Default is 'iwls', meaning iteratively ( + re)weighted least squares. + searching : bool, optional + Whether to estimate a lightweight GWR that + computes the minimum diagnostics needed for + bandwidth selection (could speed up + bandwidth selection for GWR) or to estimate + a full GWR. Default is False. + + Returns + ------- + : + If searching=True, return a GWRResult + instance; otherwise, return a GWRResultLite + instance. + """ self.fit_params['ini_params'] = ini_params self.fit_params['tol'] = tol @@ -619,6 +635,7 @@ def scale(self, scale=None): def cov_params(self, cov, exog_scale=None): """ Returns scaled covariance parameters + Parameters ---------- cov : array @@ -1251,6 +1268,8 @@ def resid_ss(self): class MGWR(GWR): """ + Multiscale GWR estimation and inference. + Parameters ---------- coords : array-like @@ -1310,6 +1329,7 @@ class MGWR(GWR): spherical : boolean True for shperical coordinates (long-lat), False for projected coordinates (defalut). + Attributes ---------- coords : array-like @@ -1400,7 +1420,9 @@ class MGWR(GWR): Examples -------- + #basic model calibration + >>> import libpysal as ps >>> from mgwr.gwr import MGWR >>> from mgwr.sel_bw import Sel_BW @@ -1486,11 +1508,16 @@ def fit(self): return MGWRResults(self, params, predy, S, CCT, R, w) def predict(self): + ''' + Not implemented. + ''' raise NotImplementedError('N/A') class MGWRResults(GWRResults): """ + Class including common properties for a MGWR model. + Parameters ---------- model : MGWR object diff --git a/mgwr/kernels.py b/mgwr/kernels.py index 566d8bc..65946c3 100644 --- a/mgwr/kernels.py +++ b/mgwr/kernels.py @@ -12,6 +12,9 @@ #implementation. That is, pysal counts self neighbors with knn automatically. def fix_gauss(coords, bw, points=None, dmat=None,sorted_dmat=None,spherical=False): + """ + Fixed Gaussian + """ w = _Kernel(coords, function='gwr_gaussian', bandwidth=bw, truncate=False, points=points, dmat=dmat,sorted_dmat=sorted_dmat,spherical=spherical) return w.kernel @@ -43,8 +46,8 @@ def adapt_exp(coords, nn, points=None, dmat=None,sorted_dmat=None,spherical=Fals #Customized Kernel class user for GWR because the default PySAL kernel class #favors memory optimization over speed optimizations and GWR often needs the -#speed optimization since it is not always assume points far awar are truncated -#to zero +#speed optimization since it is not always assume points far awary +# are truncated #to zero def cdist(coords1,coords2,spherical): def _haversine(lon1, lat1, lon2, lat2): @@ -71,6 +74,7 @@ def _haversine(lon1, lat1, lon2, lat2): class _Kernel(object): """ + GWR kernel function specifications. """ def __init__(self, data, bandwidth=None, fixed=True, k=None,