From 833dd95643a589d2a573ef7cb1b4118d8f470dc2 Mon Sep 17 00:00:00 2001 From: Feng Zhu Date: Mon, 8 Jul 2024 14:12:13 -0600 Subject: [PATCH] Update installation guide for macOS --- docs/_sources/ug-installation.rst | 2 +- docs/searchindex.js | 2 +- docs/ug-installation.html | 2 +- docsrc/ug-installation.rst | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/_sources/ug-installation.rst b/docs/_sources/ug-installation.rst index f50b3b4..b2a892b 100644 --- a/docs/_sources/ug-installation.rst +++ b/docs/_sources/ug-installation.rst @@ -70,7 +70,7 @@ Then install some dependencies via :code:`conda`: .. code-block:: bash - conda install jupyter notebook cartopy statsmodels pykdtree + conda install jupyter notebook cartopy statsmodels pykdtree netcdf4 Once the above dependencies have been installed, simply diff --git a/docs/searchindex.js b/docs/searchindex.js index 8acb39e..9e52fd9 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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22], "interact": 15, "ppe": [16, 17], "paleoclim": 17, "ta": 17, "pr": 17, "setup": 17, "differ": 17, "mont": 17, "carlo": 17, "iter": 17, "analysi": 18, "network": [18, 22], "proxyrecord": [18, 21, 22, 23, 24, 25, 26, 27, 28, 29], "proxydatabas": [18, 19, 20, 21, 22], "composit": 19, "archiv": 19, "With": 19, "The": 19, "core": [19, 26], "multipl": 19, "handl": 20, "duplic": 20, "find": 20, "panda": 21, "datafram": 21, "index": 22, "add": 22, "sever": 22, "togeth": 22, "form": 22, "list": 22, "substract": 22, "from": 22, "bivari": 23, "linear": [23, 28], "regress": [23, 28], "sr": 24, "ca": 24, "varv": 27, "thick": 27, "univari": 28, "v": 29, "lite": 29, "api": 30, "refer": 30, "enst": 30, "instal": 33, "conda": 33, "download": 33, "script": 33, "miniconda3": 33, "maco": 33, "intel": 33, "appl": 33, "silicon": 33, "linux": 33, "3": 33}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "nbsphinx": 4, "sphinx": 60}, "alltitles": {"Overview": [[0, "overview"]], "Bug reports and enhancement requests": [[0, "bug-reports-and-enhancement-requests"]], "Updating the Documentation": [[1, "updating-the-documentation"]], "About the cfr documentation": [[1, "about-the-cfr-documentation"]], "Updating docstrings": [[1, "updating-docstrings"]], "Updating tutorial notebooks": [[1, "updating-tutorial-notebooks"]], "Building the cfr documentation": [[1, "building-the-cfr-documentation"]], "Previewing the cfr documentation": [[1, "previewing-the-cfr-documentation"]], "Pushing your changes": [[1, "pushing-your-changes"], [2, "pushing-your-changes"]], "Working with the Codebase": [[2, "working-with-the-codebase"]], "Version control, Git, and GitHub": [[2, "version-control-git-and-github"]], "Forking": [[2, "forking"]], "Creating a development environment": [[2, "creating-a-development-environment"]], "Creating a branch": [[2, "creating-a-branch"]], "Contributing new or updating existing functionalities": [[2, "contributing-new-or-updating-existing-functionalities"]], "Stylistic considerations": [[2, "stylistic-considerations"]], "Conventions": [[2, "conventions"]], "Committing your code": [[2, "committing-your-code"]], "Filing a Pull Request": [[2, "filing-a-pull-request"]], "Updating your pull request": [[2, "updating-your-pull-request"]], "Delete your merged branch (optional)": [[2, "delete-your-merged-branch-optional"]], "Tips for a successful pull request": [[2, "tips-for-a-successful-pull-request"]], "cfr: a Python package for Climate Field Reconstruction": [[3, "cfr-a-python-package-for-climate-field-reconstruction"]], "Input/Output": [[4, "Input/Output"], [21, "Input/Output"]], "a netCDF file => cfr.ClimateField": [[4, "a-netCDF-file-=>-cfr.ClimateField"]], "cfr.ClimateField => a netCDF file": [[4, "cfr.ClimateField-=>-a-netCDF-file"]], "xarray.DataArray => cfr.ClimateField": [[4, "xarray.DataArray-=>-cfr.ClimateField"]], "cfr.ClimateField => xarray.DataArray": [[4, "cfr.ClimateField-=>-xarray.DataArray"]], "numpy.ndarray => cfr.ClimateField": [[4, "numpy.ndarray-=>-cfr.ClimateField"]], "cfr.ClimateField => numpy.ndarray": [[4, "cfr.ClimateField-=>-numpy.ndarray"]], "Remote loading gridded climate data": [[4, "Remote-loading-gridded-climate-data"]], "Remote loading iCESM simulations": [[4, "Remote-loading-iCESM-simulations"]], "Basic Operations": [[5, "Basic-Operations"], [22, "Basic-Operations"]], "Load the test netCDF file as a ClimateField": [[5, "Load-the-test-netCDF-file-as-a-ClimateField"]], "Time slicing": [[5, "Time-slicing"]], "Rename the variable": [[5, "Rename-the-variable"]], "Plot a field map at a time point": [[5, "Plot-a-field-map-at-a-time-point"]], "Get the anomaly field": [[5, "Get-the-anomaly-field"]], "Center the field": [[5, "Center-the-field"]], "Annualize/Seasonalize a ClimateField": [[5, "Annualize/Seasonalize-a-ClimateField"]], "Regrid a ClimateField": [[5, "Regrid-a-ClimateField"]], "Crop a cfr.ClimateField": [[5, "Crop-a-cfr.ClimateField"]], "Calculate the weighted mean of a sptial area": [[5, "Calculate-the-weighted-mean-of-a-sptial-area"]], "Validate a field against another": [[5, "Validate-a-field-against-another"]], "Running GraphEM with the Command Line Interface (CLI)": [[6, "Running-GraphEM-with-the-Command-Line-Interface-(CLI)"]], "Generating the configs.yml file": [[6, "Generating-the-configs.yml-file"], [10, "Generating-the-configs.yml-file"]], "Testing running the reconstruction job based on the generated configs.yml file": [[6, "Testing-running-the-reconstruction-job-based-on-the-generated-configs.yml-file"], [10, "Testing-running-the-reconstruction-job-based-on-the-generated-configs.yml-file"]], "Leveraging the CLI": [[6, "Leveraging-the-CLI"], [10, "Leveraging-the-CLI"]], "Validation": [[6, "Validation"], [9, "Validation"]], "A primer on GraphEM": [[7, "A-primer-on-GraphEM"]], "Data Preparation": [[7, "Data-Preparation"]], "Graph estimation": [[7, "Graph-estimation"]], "1a) Cross-validation": [[7, "1a)-Cross-validation"]], "1b Reconstruction": [[7, "1b-Reconstruction"]], "running GraphEM": [[7, "running-GraphEM"]], "1.c Validation": [[7, "1.c-Validation"]], "Spatially-averaged Statistics": [[7, "Spatially-averaged-Statistics"], [7, "id1"]], "Map of CE": [[7, "Map-of-CE"], [7, "id2"]], "Timeseries comparison": [[7, "Timeseries-comparison"], [7, "id3"]], "2. Graphical Lasso": [[7, "2.-Graphical-Lasso"]], "2a. Greedy Search": [[7, "2a.-Greedy-Search"]], "2b. Cross-Validation": [[7, "2b.-Cross-Validation"]], "2c. Reconstruction": [[7, "2c.-Reconstruction"]], "Reconstructing the tropical Pacific SST with PAGES2k and GraphEM": [[8, "Reconstructing-the-tropical-Pacific-SST-with-PAGES2k-and-GraphEM"]], "GraphEM steps": [[8, "GraphEM-steps"], [16, "GraphEM-steps"]], "Create a reconstruction job object cfr.ReconJob and load the pseudoPAGES2k database": [[8, "Create-a-reconstruction-job-object-cfr.ReconJob-and-load-the-pseudoPAGES2k-database"], [16, "Create-a-reconstruction-job-object-cfr.ReconJob-and-load-the-pseudoPAGES2k-database"], [17, "Create-a-reconstruction-job-object-cfr.ReconJob-and-load-the-pseudoPAGES2k-database"]], "Annualize each proxy record": [[8, "Annualize-each-proxy-record"], [16, "Annualize-each-proxy-record"]], "Load the instrumental observations": [[8, "Load-the-instrumental-observations"], [11, "Load-the-instrumental-observations"], [12, "Load-the-instrumental-observations"], [16, "Load-the-instrumental-observations"], [17, "Load-the-instrumental-observations"]], "Annualize the observation fields": [[8, "Annualize-the-observation-fields"], [16, "Annualize-the-observation-fields"]], "Regrid the observation fields": [[8, "Regrid-the-observation-fields"], [16, "Regrid-the-observation-fields"]], "Crop the observations fields to make the problem size smaller": [[8, "Crop-the-observations-fields-to-make-the-problem-size-smaller"], [16, "Crop-the-observations-fields-to-make-the-problem-size-smaller"]], "(Optional) Save the job object for later reload": [[8, "(Optional)-Save-the-job-object-for-later-reload"], [16, "(Optional)-Save-the-job-object-for-later-reload"], [17, "(Optional)-Save-the-job-object-for-later-reload"]], "Prepare the GraphEM solver": [[8, "Prepare-the-GraphEM-solver"], [16, "Prepare-the-GraphEM-solver"]], "Run the GraphEM solver": [[8, "Run-the-GraphEM-solver"], [16, "Run-the-GraphEM-solver"]], "Validation steps": [[8, "Validation-steps"], [16, "Validation-steps"], [17, "Validation-steps"]], "Create the reconstruction result object cfr.ReconRes.": [[8, "Create-the-reconstruction-result-object-cfr.ReconRes."], [16, "Create-the-reconstruction-result-object-cfr.ReconRes."], [17, "Create-the-reconstruction-result-object-cfr.ReconRes."]], "Load the reconstructed variables": [[8, "Load-the-reconstructed-variables"], [16, "Load-the-reconstructed-variables"], [17, "Load-the-reconstructed-variables"]], "Validate the reconstructed NINO3.4": [[8, "Validate-the-reconstructed-NINO3.4"], [16, "Validate-the-reconstructed-NINO3.4"], [17, "Validate-the-reconstructed-NINO3.4"]], "Validate the reconstructed fields": [[8, "Validate-the-reconstructed-fields"], [16, "Validate-the-reconstructed-fields"], [17, "Validate-the-reconstructed-fields"]], "Comparison to the LMR/PDA based reconstruction": [[8, "Comparison-to-the-LMR/PDA-based-reconstruction"]], "Assimilating records whose PSMs cannot be calibrated": [[9, "Assimilating-records-whose-PSMs-cannot-be-calibrated"]], "Create a reconstruction job object": [[9, "Create-a-reconstruction-job-object"]], "Load a proxy database": [[9, "Load-a-proxy-database"]], "Filter the proxy database": [[9, "Filter-the-proxy-database"]], "Annualize/seasonalize the proxy database": [[9, "Annualize/seasonalize-the-proxy-database"]], "Load climate model priors": [[9, "Load-climate-model-priors"]], "Forward modeling without calling the PSMs": [[9, "Forward-modeling-without-calling-the-PSMs"]], "Annualize/seasonalize the climate model prior": [[9, "Annualize/seasonalize-the-climate-model-prior"]], "Regrid the prior field": [[9, "Regrid-the-prior-field"]], "Crop the prior field": [[9, "Crop-the-prior-field"]], "Data assimilation": [[9, "Data-assimilation"]], "Running DA with the Command Line Interface (CLI)": [[10, "Running-DA-with-the-Command-Line-Interface-(CLI)"]], "Reconstructing the tropical Pacific SST with PAGES2k": [[11, "Reconstructing-the-tropical-Pacific-SST-with-PAGES2k"]], "Load the PAGES2k database": [[11, "Load-the-PAGES2k-database"], [12, "Load-the-PAGES2k-database"]], "Filter the database": [[11, "Filter-the-database"]], "Annualize the database": [[11, "Annualize-the-database"]], "Load the gridded climate data": [[11, "Load-the-gridded-climate-data"], [12, "Load-the-gridded-climate-data"]], "Load the model prior": [[11, "Load-the-model-prior"], [12, "Load-the-model-prior"]], "Proxy system modeling": [[11, "Proxy-system-modeling"], [12, "Proxy-system-modeling"]], "Calibrating the proxy system models": [[11, "Calibrating-the-proxy-system-models"], [12, "Calibrating-the-proxy-system-models"]], "Forwarding the proxy system models": [[11, "Forwarding-the-proxy-system-models"], [12, "Forwarding-the-proxy-system-models"]], "Annualizing, regridding, and cropping the prior field": [[11, "Annualizing,-regridding,-and-cropping-the-prior-field"], [12, "Annualizing,-regridding,-and-cropping-the-prior-field"]], "Run the DA solver": [[11, "Run-the-DA-solver"], [12, "Run-the-DA-solver"]], "Validate the reconstruction": [[11, "Validate-the-reconstruction"], [12, "Validate-the-reconstruction"]], "Load the validation target": [[11, "Load-the-validation-target"], [12, "Load-the-validation-target"]], "Field validation": [[11, "Field-validation"], [12, "Field-validation"]], "Timeseries validation": [[11, "Timeseries-validation"]], "Reconstructing precipitation": [[12, "Reconstructing-precipitation"]], "Validation Dashboards": [[13, "Validation-Dashboards"]], "Load the real and pseudo PAEGS2k datasets": [[13, "Load-the-real-and-pseudo-PAEGS2k-datasets"]], "Dashboard for a tree.TRW record": [[13, "Dashboard-for-a-tree.TRW-record"]], "Dashboard for a tree.MXD record": [[13, "Dashboard-for-a-tree.MXD-record"]], "Dashboard for a coral.d18O record": [[13, "Dashboard-for-a-coral.d18O-record"]], "Dashboard for a coral.SrCa record": [[13, "Dashboard-for-a-coral.SrCa-record"]], "Dashboard for a ice.d18O record": [[13, "Dashboard-for-a-ice.d18O-record"]], "Dashboard for a lake.varve_thickness record": [[13, "Dashboard-for-a-lake.varve_thickness-record"]], "Database Filtering": [[14, "Database-Filtering"]], "Load the pseudoPAEGS2k dataset": [[14, "Load-the-pseudoPAEGS2k-dataset"]], "Filter the pseudoPAGES2k dataset": [[14, "Filter-the-pseudoPAGES2k-dataset"]], "By proxy types": [[14, "By-proxy-types"]], "By proxy IDs": [[14, "By-proxy-IDs"]], "By a latitude range": [[14, "By-a-latitude-range"]], "By a longitude range": [[14, "By-a-longitude-range"]], "By a square (latitude + longitude ranges)": [[14, "By-a-square-(latitude-+-longitude-ranges)"]], "By a circle (center + distance)": [[14, "By-a-circle-(center-+-distance)"]], "Loading and Visualization": [[15, "Loading-and-Visualization"]], "Load the pseudoPAGES2k dataset with xarray": [[15, "Load-the-pseudoPAGES2k-dataset-with-xarray"]], "Load the pseudoPAEGS2k dataset with cfr": [[15, "Load-the-pseudoPAEGS2k-dataset-with-cfr"]], "Visualize the pseudoPAGES2k dataset": [[15, "Visualize-the-pseudoPAGES2k-dataset"]], "Access and visualize a specific record": [[15, "Access-and-visualize-a-specific-record"]], "Check the proxy IDs on an interactive map": [[15, "Check-the-proxy-IDs-on-an-interactive-map"]], "PPE: A GraphEM-based Reconstruction": [[16, "PPE:-A-GraphEM-based-Reconstruction"]], "Center each proxy record": [[16, "Center-each-proxy-record"]], "PPE: A PDA-based Reconstruction": [[17, "PPE:-A-PDA-based-Reconstruction"]], "Paleoclimate data assimilation (PDA) steps": [[17, "Paleoclimate-data-assimilation-(PDA)-steps"]], "Load the model prior (iCESM simulated tas & pr fields)": [[17, "Load-the-model-prior-(iCESM-simulated-tas-&-pr-fields)"]], "Setup the proxy system models (PSMs) for different proxy types": [[17, "Setup-the-proxy-system-models-(PSMs)-for-different-proxy-types"]], "Calibrate the PSMs": [[17, "Calibrate-the-PSMs"]], "Run the PSMs": [[17, "Run-the-PSMs"]], "Annualize the model prior fields": [[17, "Annualize-the-model-prior-fields"]], "Regrid the model prior fields": [[17, "Regrid-the-model-prior-fields"]], "Run the DA solver with Monte-Carlo iterations": [[17, "Run-the-DA-solver-with-Monte-Carlo-iterations"]], "Analysis": [[18, "Analysis"]], "Load the PAGES2k network and access a ProxyRecord": [[18, "Load-the-PAGES2k-network-and-access-a-ProxyRecord"]], "Annualize a ProxyRecord": [[18, "Annualize-a-ProxyRecord"]], "Annualize a ProxyDatabase": [[18, "Annualize-a-ProxyDatabase"]], "Composites": [[19, "Composites"]], "Load a ProxyDatabase": [[19, "Load-a-ProxyDatabase"]], "Create composites for each archive type": [[19, "Create-composites-for-each-archive-type"]], "Without calibration to an instrumental target": [[19, "Without-calibration-to-an-instrumental-target"]], "With calibration to an instrumental target": [[19, "With-calibration-to-an-instrumental-target"]], "The composite of ice core records": [[19, "The-composite-of-ice-core-records"]], "Make a composite of multiple archives": [[19, "Make-a-composite-of-multiple-archives"]], "Handling duplicate proxies in a ProxyDatabase": [[20, "Handling-duplicate-proxies-in-a-ProxyDatabase"]], "Load a database with duplicated proxies": [[20, "Load-a-database-with-duplicated-proxies"]], "Find the duplicates": [[20, "Find-the-duplicates"]], "Remote loading databases": [[21, "Remote-loading-databases"]], "Remote loading PAGES2k": [[21, "Remote-loading-PAGES2k"]], "Remote loading pseudoPAGES2k": [[21, "Remote-loading-pseudoPAGES2k"]], "cfr.ProxyDatabase => pandas.DataFrame": [[21, "cfr.ProxyDatabase-=>-pandas.DataFrame"]], "pandas.DataFrame => cfr.ProxyDatabase": [[21, "pandas.DataFrame-=>-cfr.ProxyDatabase"]], "cfr.ProxyDatabase => a netCDF file": [[21, "cfr.ProxyDatabase-=>-a-netCDF-file"]], "a netCDF file => cfr.ProxyDatabase": [[21, "a-netCDF-file-=>-cfr.ProxyDatabase"]], "cfr.ProxyRecord => a netCDF file": [[21, "cfr.ProxyRecord-=>-a-netCDF-file"]], "a netCDF file => cfr.ProxyRecord": [[21, "a-netCDF-file-=>-cfr.ProxyRecord"]], "Load the PAGES2k network": [[22, "Load-the-PAGES2k-network"]], "Slice a ProxyDatabase by index": [[22, "Slice-a-ProxyDatabase-by-index"]], "Slice a ProxyRecord": [[22, "Slice-a-ProxyRecord"]], "Add several ProxyRecords together to form a ProxyDatabase": [[22, "Add-several-ProxyRecords-together-to-form-a-ProxyDatabase"]], "Add a list of ProxyRecords into an existing ProxyDatabase": [[22, "Add-a-list-of-ProxyRecords-into-an-existing-ProxyDatabase"]], "Merge several ProxyDatabases": [[22, "Merge-several-ProxyDatabases"]], "Substract a list of ProxyRecords from a ProxyDatabase": [[22, "Substract-a-list-of-ProxyRecords-from-a-ProxyDatabase"]], "Substract a ProxyDatabase from another": [[22, "Substract-a-ProxyDatabase-from-another"]], "Filter a ProxyDatabase": [[22, "Filter-a-ProxyDatabase"]], "Bivariate linear regression": [[23, "Bivariate-linear-regression"]], "Data preparation": [[23, "Data-preparation"], [24, "Data-preparation"], [25, "Data-preparation"], [26, "Data-preparation"], [27, "Data-preparation"], [28, "Data-preparation"], [29, "Data-preparation"]], "Proxy": [[23, "Proxy"], [24, "Proxy"], [25, "Proxy"], [26, "Proxy"], [27, "Proxy"], [28, "Proxy"], [29, "Proxy"], [30, "proxy"], [36, "proxy"]], "Model": [[23, "Model"], [24, "Model"], [25, "Model"], [26, "Model"], [27, "Model"], [28, "Model"], [29, "Model"]], "Instrumental observations": [[23, "Instrumental-observations"], [28, "Instrumental-observations"]], "Get climate data for a specific ProxyRecord": [[23, "Get-climate-data-for-a-specific-ProxyRecord"], [24, "Get-climate-data-for-a-specific-ProxyRecord"], [25, "Get-climate-data-for-a-specific-ProxyRecord"], [26, "Get-climate-data-for-a-specific-ProxyRecord"], [27, "Get-climate-data-for-a-specific-ProxyRecord"], [28, "Get-climate-data-for-a-specific-ProxyRecord"], [29, "Get-climate-data-for-a-specific-ProxyRecord"]], "Create a PSM object": [[23, "Create-a-PSM-object"], [24, "Create-a-PSM-object"], [25, "Create-a-PSM-object"], [26, "Create-a-PSM-object"], [27, "Create-a-PSM-object"], [28, "Create-a-PSM-object"], [29, "Create-a-PSM-object"]], "PSM for coral 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observation fields": [[8, "Annualize-the-observation-fields"], [16, "Annualize-the-observation-fields"]], "Regrid the observation fields": [[8, "Regrid-the-observation-fields"], [16, "Regrid-the-observation-fields"]], "Crop the observations fields to make the problem size smaller": [[8, "Crop-the-observations-fields-to-make-the-problem-size-smaller"], [16, "Crop-the-observations-fields-to-make-the-problem-size-smaller"]], "(Optional) Save the job object for later reload": [[8, "(Optional)-Save-the-job-object-for-later-reload"], [16, "(Optional)-Save-the-job-object-for-later-reload"], [17, "(Optional)-Save-the-job-object-for-later-reload"]], "Prepare the GraphEM solver": [[8, "Prepare-the-GraphEM-solver"], [16, "Prepare-the-GraphEM-solver"]], "Run the GraphEM solver": [[8, "Run-the-GraphEM-solver"], [16, "Run-the-GraphEM-solver"]], "Validation steps": [[8, "Validation-steps"], [16, "Validation-steps"], [17, "Validation-steps"]], "Create the reconstruction result object cfr.ReconRes.": [[8, "Create-the-reconstruction-result-object-cfr.ReconRes."], [16, "Create-the-reconstruction-result-object-cfr.ReconRes."], [17, "Create-the-reconstruction-result-object-cfr.ReconRes."]], "Load the reconstructed variables": [[8, "Load-the-reconstructed-variables"], [16, "Load-the-reconstructed-variables"], [17, "Load-the-reconstructed-variables"]], "Validate the reconstructed NINO3.4": [[8, "Validate-the-reconstructed-NINO3.4"], [16, "Validate-the-reconstructed-NINO3.4"], [17, "Validate-the-reconstructed-NINO3.4"]], "Validate the reconstructed fields": [[8, "Validate-the-reconstructed-fields"], [16, "Validate-the-reconstructed-fields"], [17, "Validate-the-reconstructed-fields"]], "Comparison to the LMR/PDA based reconstruction": [[8, "Comparison-to-the-LMR/PDA-based-reconstruction"]], "Assimilating records whose PSMs cannot be calibrated": [[9, "Assimilating-records-whose-PSMs-cannot-be-calibrated"]], "Create a reconstruction job object": [[9, "Create-a-reconstruction-job-object"]], "Load a proxy database": [[9, "Load-a-proxy-database"]], "Filter the proxy database": [[9, "Filter-the-proxy-database"]], "Annualize/seasonalize the proxy database": [[9, "Annualize/seasonalize-the-proxy-database"]], "Load climate model priors": [[9, "Load-climate-model-priors"]], "Forward modeling without calling the PSMs": [[9, "Forward-modeling-without-calling-the-PSMs"]], "Annualize/seasonalize the climate model prior": [[9, "Annualize/seasonalize-the-climate-model-prior"]], "Regrid the prior field": [[9, "Regrid-the-prior-field"]], "Crop the prior field": [[9, "Crop-the-prior-field"]], "Data assimilation": [[9, "Data-assimilation"]], "Running DA with the Command Line Interface (CLI)": [[10, "Running-DA-with-the-Command-Line-Interface-(CLI)"]], "Reconstructing the tropical Pacific SST with PAGES2k": [[11, "Reconstructing-the-tropical-Pacific-SST-with-PAGES2k"]], "Load the PAGES2k database": [[11, "Load-the-PAGES2k-database"], [12, "Load-the-PAGES2k-database"]], "Filter the database": [[11, "Filter-the-database"]], "Annualize the database": [[11, "Annualize-the-database"]], "Load the gridded climate data": [[11, "Load-the-gridded-climate-data"], [12, "Load-the-gridded-climate-data"]], "Load the model prior": [[11, "Load-the-model-prior"], [12, "Load-the-model-prior"]], "Proxy system modeling": [[11, "Proxy-system-modeling"], [12, "Proxy-system-modeling"]], "Calibrating the proxy system models": [[11, "Calibrating-the-proxy-system-models"], [12, "Calibrating-the-proxy-system-models"]], "Forwarding the proxy system models": [[11, "Forwarding-the-proxy-system-models"], [12, "Forwarding-the-proxy-system-models"]], "Annualizing, regridding, and cropping the prior field": [[11, "Annualizing,-regridding,-and-cropping-the-prior-field"], [12, "Annualizing,-regridding,-and-cropping-the-prior-field"]], "Run the DA solver": [[11, "Run-the-DA-solver"], [12, "Run-the-DA-solver"]], "Validate the reconstruction": [[11, "Validate-the-reconstruction"], [12, "Validate-the-reconstruction"]], "Load the validation target": [[11, "Load-the-validation-target"], [12, "Load-the-validation-target"]], "Field validation": [[11, "Field-validation"], [12, "Field-validation"]], "Timeseries validation": [[11, "Timeseries-validation"]], "Reconstructing precipitation": [[12, "Reconstructing-precipitation"]], "Validation Dashboards": [[13, "Validation-Dashboards"]], "Load the real and pseudo PAEGS2k datasets": [[13, "Load-the-real-and-pseudo-PAEGS2k-datasets"]], "Dashboard for a tree.TRW record": [[13, "Dashboard-for-a-tree.TRW-record"]], "Dashboard for a tree.MXD record": [[13, "Dashboard-for-a-tree.MXD-record"]], "Dashboard for a coral.d18O record": [[13, "Dashboard-for-a-coral.d18O-record"]], "Dashboard for a coral.SrCa record": [[13, "Dashboard-for-a-coral.SrCa-record"]], "Dashboard for a ice.d18O record": [[13, "Dashboard-for-a-ice.d18O-record"]], "Dashboard for a lake.varve_thickness record": [[13, "Dashboard-for-a-lake.varve_thickness-record"]], "Database Filtering": [[14, "Database-Filtering"]], "Load the pseudoPAEGS2k dataset": [[14, "Load-the-pseudoPAEGS2k-dataset"]], "Filter the pseudoPAGES2k dataset": [[14, "Filter-the-pseudoPAGES2k-dataset"]], "By proxy types": [[14, "By-proxy-types"]], "By proxy IDs": [[14, "By-proxy-IDs"]], "By a latitude range": [[14, "By-a-latitude-range"]], "By a longitude range": [[14, "By-a-longitude-range"]], "By a square (latitude + longitude ranges)": [[14, "By-a-square-(latitude-+-longitude-ranges)"]], "By a circle (center + distance)": [[14, "By-a-circle-(center-+-distance)"]], "Loading and Visualization": [[15, "Loading-and-Visualization"]], "Load the pseudoPAGES2k dataset with xarray": [[15, "Load-the-pseudoPAGES2k-dataset-with-xarray"]], "Load the pseudoPAEGS2k dataset with cfr": [[15, "Load-the-pseudoPAEGS2k-dataset-with-cfr"]], "Visualize the pseudoPAGES2k dataset": [[15, "Visualize-the-pseudoPAGES2k-dataset"]], "Access and visualize a specific record": [[15, "Access-and-visualize-a-specific-record"]], "Check the proxy IDs on an interactive map": [[15, "Check-the-proxy-IDs-on-an-interactive-map"]], "PPE: A GraphEM-based Reconstruction": [[16, "PPE:-A-GraphEM-based-Reconstruction"]], "Center each proxy record": [[16, "Center-each-proxy-record"]], "PPE: A PDA-based Reconstruction": [[17, "PPE:-A-PDA-based-Reconstruction"]], "Paleoclimate data assimilation (PDA) steps": [[17, "Paleoclimate-data-assimilation-(PDA)-steps"]], "Load the model prior (iCESM simulated tas & pr fields)": [[17, "Load-the-model-prior-(iCESM-simulated-tas-&-pr-fields)"]], "Setup the proxy system models (PSMs) for different proxy types": [[17, "Setup-the-proxy-system-models-(PSMs)-for-different-proxy-types"]], "Calibrate the PSMs": [[17, "Calibrate-the-PSMs"]], "Run the PSMs": [[17, "Run-the-PSMs"]], "Annualize the model prior fields": [[17, "Annualize-the-model-prior-fields"]], "Regrid the model prior fields": [[17, "Regrid-the-model-prior-fields"]], "Run the DA solver with Monte-Carlo iterations": [[17, "Run-the-DA-solver-with-Monte-Carlo-iterations"]], "Analysis": [[18, "Analysis"]], "Load the PAGES2k network and access a ProxyRecord": [[18, "Load-the-PAGES2k-network-and-access-a-ProxyRecord"]], "Annualize a ProxyRecord": [[18, "Annualize-a-ProxyRecord"]], "Annualize a ProxyDatabase": [[18, "Annualize-a-ProxyDatabase"]], "Composites": [[19, "Composites"]], "Load a ProxyDatabase": [[19, "Load-a-ProxyDatabase"]], "Create composites for each archive type": [[19, "Create-composites-for-each-archive-type"]], "Without calibration to an instrumental target": [[19, "Without-calibration-to-an-instrumental-target"]], "With calibration to an instrumental target": [[19, "With-calibration-to-an-instrumental-target"]], "The composite of ice core records": [[19, "The-composite-of-ice-core-records"]], "Make a composite of multiple archives": [[19, "Make-a-composite-of-multiple-archives"]], "Handling duplicate proxies in a ProxyDatabase": [[20, "Handling-duplicate-proxies-in-a-ProxyDatabase"]], "Load a database with duplicated proxies": [[20, "Load-a-database-with-duplicated-proxies"]], "Find the duplicates": [[20, "Find-the-duplicates"]], "Remote loading databases": [[21, "Remote-loading-databases"]], "Remote loading PAGES2k": [[21, "Remote-loading-PAGES2k"]], "Remote loading pseudoPAGES2k": [[21, "Remote-loading-pseudoPAGES2k"]], "cfr.ProxyDatabase => pandas.DataFrame": [[21, "cfr.ProxyDatabase-=>-pandas.DataFrame"]], "pandas.DataFrame => cfr.ProxyDatabase": [[21, "pandas.DataFrame-=>-cfr.ProxyDatabase"]], "cfr.ProxyDatabase => a netCDF file": [[21, "cfr.ProxyDatabase-=>-a-netCDF-file"]], "a netCDF file => cfr.ProxyDatabase": [[21, "a-netCDF-file-=>-cfr.ProxyDatabase"]], "cfr.ProxyRecord => a netCDF file": [[21, "cfr.ProxyRecord-=>-a-netCDF-file"]], "a netCDF file => cfr.ProxyRecord": [[21, "a-netCDF-file-=>-cfr.ProxyRecord"]], "Load the PAGES2k network": [[22, "Load-the-PAGES2k-network"]], "Slice a ProxyDatabase by index": [[22, "Slice-a-ProxyDatabase-by-index"]], "Slice a ProxyRecord": [[22, "Slice-a-ProxyRecord"]], "Add several ProxyRecords together to form a ProxyDatabase": [[22, "Add-several-ProxyRecords-together-to-form-a-ProxyDatabase"]], "Add a list of ProxyRecords into an existing ProxyDatabase": [[22, "Add-a-list-of-ProxyRecords-into-an-existing-ProxyDatabase"]], "Merge several ProxyDatabases": [[22, "Merge-several-ProxyDatabases"]], "Substract a list of ProxyRecords from a ProxyDatabase": [[22, "Substract-a-list-of-ProxyRecords-from-a-ProxyDatabase"]], "Substract a ProxyDatabase from another": [[22, "Substract-a-ProxyDatabase-from-another"]], "Filter a ProxyDatabase": [[22, "Filter-a-ProxyDatabase"]], "Bivariate linear regression": [[23, "Bivariate-linear-regression"]], "Data preparation": [[23, "Data-preparation"], [24, "Data-preparation"], [25, "Data-preparation"], [26, "Data-preparation"], [27, "Data-preparation"], [28, "Data-preparation"], [29, "Data-preparation"]], "Proxy": [[23, "Proxy"], [24, "Proxy"], [25, "Proxy"], [26, "Proxy"], [27, "Proxy"], [28, "Proxy"], [29, "Proxy"], [30, "proxy"], [36, "proxy"]], "Model": [[23, "Model"], [24, "Model"], [25, "Model"], [26, "Model"], [27, "Model"], [28, "Model"], [29, "Model"]], "Instrumental observations": [[23, "Instrumental-observations"], [28, "Instrumental-observations"]], "Get climate data for a specific ProxyRecord": [[23, "Get-climate-data-for-a-specific-ProxyRecord"], [24, "Get-climate-data-for-a-specific-ProxyRecord"], [25, "Get-climate-data-for-a-specific-ProxyRecord"], [26, "Get-climate-data-for-a-specific-ProxyRecord"], [27, "Get-climate-data-for-a-specific-ProxyRecord"], [28, "Get-climate-data-for-a-specific-ProxyRecord"], [29, "Get-climate-data-for-a-specific-ProxyRecord"]], "Create a PSM object": [[23, "Create-a-PSM-object"], [24, "Create-a-PSM-object"], [25, "Create-a-PSM-object"], [26, "Create-a-PSM-object"], [27, "Create-a-PSM-object"], [28, "Create-a-PSM-object"], [29, "Create-a-PSM-object"]], "PSM for coral Sr/Ca": [[24, "PSM-for-coral-Sr/Ca"]], "PSM for coral d18O": [[25, "PSM-for-coral-d18O"]], "PSM for ice core d18O": [[26, "PSM-for-ice-core-d18O"]], "PSM for lake varve thickness": [[27, "PSM-for-lake-varve-thickness"]], "Univariate linear regression": [[28, "Univariate-linear-regression"]], "PSM for tree TRW (VS-Lite)": [[29, "PSM-for-tree-TRW-(VS-Lite)"]], "Instrumental observation": [[29, "Instrumental-observation"]], "API Reference": [[30, "api-reference"]], "Climate": [[30, "climate"], [31, "climate"]], "PSM": [[30, "psm"], [37, "psm"]], "DA": [[30, "da"]], "ReconJob": [[30, "reconjob"]], "ReconRes": [[30, "reconres"]], "EnsTS": [[30, "ensts"]], "GraphEM": [[32, "graphem"]], "Installation": [[33, "installation"]], "Install the Conda environment": [[33, "install-the-conda-environment"]], "Step 1: Download the installation script for miniconda3": [[33, "step-1-download-the-installation-script-for-miniconda3"]], "macOS (Intel)": [[33, "macos-intel"]], "macOS (Apple Silicon)": [[33, "macos-apple-silicon"]], "Linux": [[33, "linux"]], "Step 2: Install Miniconda3": [[33, "step-2-install-miniconda3"]], "Step 3: Test your Installation": [[33, "step-3-test-your-installation"]], "Install cfr": [[33, "install-cfr"]], "LMR": [[34, "lmr"]], "pseudoPAGES2k": [[35, "pseudopages2k"]]}, "indexentries": {"bilinear (class in cfr.psm)": [[30, "cfr.psm.Bilinear"]], "climatefield (class in cfr.climate)": [[30, "cfr.climate.ClimateField"]], "coral_srca (class in cfr.psm)": [[30, "cfr.psm.Coral_SrCa"]], "coral_d18o (class in cfr.psm)": [[30, "cfr.psm.Coral_d18O"]], "enkf (class in cfr.da)": [[30, "cfr.da.EnKF"]], "ensts (class in cfr.ts)": [[30, "cfr.ts.EnsTS"]], "ice_d18o (class in cfr.psm)": [[30, "cfr.psm.Ice_d18O"]], "lake_varvethickness (class in cfr.psm)": [[30, "cfr.psm.Lake_VarveThickness"]], "linear (class in cfr.psm)": [[30, "cfr.psm.Linear"]], "proxydatabase (class in cfr.proxy)": [[30, "cfr.proxy.ProxyDatabase"]], "proxyrecord (class in cfr.proxy)": [[30, "cfr.proxy.ProxyRecord"]], "reconjob (class in cfr.reconjob)": [[30, "cfr.reconjob.ReconJob"]], "reconres (class in cfr.reconres)": [[30, "cfr.reconres.ReconRes"]], "vslite (class in cfr.psm)": [[30, "cfr.psm.VSLite"]], "annualize() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.annualize"]], "annualize() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.annualize"]], "annualize() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.annualize"]], "annualize_clim() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.annualize_clim"]], "annualize_proxydb() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.annualize_proxydb"]], "calib_psms() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.calib_psms"]], "center() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.center"]], "center() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.center"]], "center() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.center"]], "center_proxydb() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.center_proxydb"]], "clear_proxydb_tags() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.clear_proxydb_tags"]], "compare() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.compare"]], "compare() (cfr.ts.ensts method)": [[30, "cfr.ts.EnsTS.compare"]], "concat() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.concat"]], "copy() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.copy"]], "copy() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.copy"]], "copy() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.copy"]], "copy() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.copy"]], "copy() (cfr.ts.ensts method)": [[30, "cfr.ts.EnsTS.copy"]], "correct_elev_tas() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.correct_elev_tas"]], "correct_elev_tas() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.correct_elev_tas"]], "count_availability() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.count_availability"]], "crop() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.crop"]], "crop_clim() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.crop_clim"]], "dashboard() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.dashboard"]], "dashboard_clim() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.dashboard_clim"]], "del_clim() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.del_clim"]], "del_clim() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.del_clim"]], "del_pseudo() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.del_pseudo"]], "erase_cfg() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.erase_cfg"]], "fetch() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.fetch"]], "fetch() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.fetch"]], "fetch() (cfr.ts.ensts method)": [[30, "cfr.ts.EnsTS.fetch"]], "filter() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.filter"]], "filter_proxydb() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.filter_proxydb"]], "find_duplicates() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.find_duplicates"]], "forward() (cfr.psm.coral_srca method)": [[30, "cfr.psm.Coral_SrCa.forward"]], "forward() (cfr.psm.ice_d18o method)": [[30, "cfr.psm.Ice_d18O.forward"]], "forward_psms() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.forward_psms"]], "from_da() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.from_da"]], "from_df() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.from_df"]], "from_df() (cfr.ts.ensts method)": [[30, "cfr.ts.EnsTS.from_df"]], "from_ds() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.from_ds"]], "from_np() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.from_np"]], "geo_mean() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.geo_mean"]], "get_anom() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.get_anom"]], "get_clim() (cfr.proxy.proxydatabase method)": [[30, "cfr.proxy.ProxyDatabase.get_clim"]], "get_clim() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.get_clim"]], "get_eof() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.get_eof"]], "get_pseudo() (cfr.proxy.proxyrecord method)": [[30, "cfr.proxy.ProxyRecord.get_pseudo"]], "graphem_kcv() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.graphem_kcv"]], "index() (cfr.climate.climatefield method)": [[30, "cfr.climate.ClimateField.index"]], "io_cfg() (cfr.reconjob.reconjob method)": [[30, "cfr.reconjob.ReconJob.io_cfg"]], "line_density() (cfr.ts.ensts method)": [[30, 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Install cfrconda:

-
conda install jupyter notebook cartopy statsmodels pykdtree
+
conda install jupyter notebook cartopy statsmodels pykdtree netcdf4
 

 

 
Once the above dependencies have been installed, simply

diff --git a/docsrc/ug-installation.rst b/docsrc/ug-installation.rst
index f50b3b4..b2a892b 100644
--- a/docsrc/ug-installation.rst
+++ b/docsrc/ug-installation.rst
@@ -70,7 +70,7 @@ Then install some dependencies via :code:`conda`:
 
 .. code-block:: bash
 
-    conda install jupyter notebook cartopy statsmodels pykdtree
+    conda install jupyter notebook cartopy statsmodels pykdtree netcdf4
 
 Once the above dependencies have been installed, simply