Adding functions and scripts for downloading, extracting, and processing observations, initial conditions, land cover types, ERA5 drivers for anchor sites within NA.#3278

Merged

mdietze merged 84 commits intoPecanProject:developfrom DongchenZ:develop

May 21, 2024

+1,266-90

Commits on Mar 12, 2024

Add shapefiles of level 1 and 2 NA eco-region.
Dongchen Zhang
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Add a script for processing anchor site data preparations.
Dongchen Zhang
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Automatic updated namespace.
Dongchen Zhang
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Update codes for grabbing site info from a multi-settings object.
Dongchen Zhang
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Add a function for extracting ISCN SOC initial conditions.
Dongchen Zhang
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Add a function for downloading soil moisture from the CDS server.
Dongchen Zhang
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Add a function for extracting downloaded soil moisture netcdf files.
Dongchen Zhang
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Add rdata file for the ISCN SOC records along with the corresponding ecoregion codes (L1 and L2).
Dongchen Zhang
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Add a script for processing initial conditions for the anchor site.
Dongchen Zhang
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Tweak ecoregion finder function to adjust the NA area.
Dongchen Zhang
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Automatic updated namespace.
Dongchen Zhang
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Update MODIS_LAI_prep function.
Dongchen Zhang
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Add a function to download, extract and filter MODIS LC data.
Dongchen Zhang
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Add a function for extracting AGB initial conditions from GeoTIFF files.
Dongchen Zhang
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Merge branch 'develop' of https://github.com/PecanProject/pecan into develop
Dongchen Zhang
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Commits on Mar 17, 2024

Updated previous documentation.
Dongchen Zhang
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Commits on Apr 25, 2024

Update progress bar for the qsub_parallel function.
Dongchen Zhang
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Correct the unit for using the soil moisture initial condition in SDA.
Dongchen Zhang
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Correct the indexing for block based analysis function.
Dongchen Zhang
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Correct logic for the analysis run.
Dongchen Zhang
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Add arguments in the plotting function to control plot size.
Dongchen Zhang
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Update create a multi-site script to include the NA anchor sites.
Dongchen Zhang
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Fix the bug where we write ERA5 paths into the settings.xml file.
Dongchen Zhang
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Update the script to download North America ERA5 data.
Dongchen Zhang
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Provide another option for downloading SoilGrids data if the parallel download is problematic.
Dongchen Zhang
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Add argument to decide if we want to skip the high sd observations for MODIS LAI extraction.
Dongchen Zhang
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Update function for reading geotiff file of AGB initial conditions.
Dongchen Zhang
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Update the filtering scheme upon the QC band.
Dongchen Zhang
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Remove shapefiles of NA ecoregion maps from the repo.
Dongchen Zhang
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Remove R script and replace it with the RMD file.
Dongchen Zhang
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Update the usage of ecoregion maps when searching for ecoregion code.
Dongchen Zhang
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Rename the current ERA5 USA download script to NA.
Dongchen Zhang
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Replace the previous R script with a more informative Rmd file.
Dongchen Zhang
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Reverted dependency to dplyr
Dongchen Zhang
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Update documentation.
Dongchen Zhang
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Update ecoregion paths argument.
Dongchen Zhang
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Add introduction on how to build python CDS API.
Dongchen Zhang
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Update documentation
Dongchen Zhang
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Update the documentation.
Dongchen Zhang
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Merge branch 'PecanProject:develop' into develop
DongchenZ
authored
Merge branch 'develop' of https://github.com/DongchenZ/pecan into develop
Dongchen Zhang
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Bug fix
Dongchen Zhang
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Commits on Apr 26, 2024

Create interface for user to create their own credentials.
Dongchen Zhang
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Commits on Apr 27, 2024

Bug fix.
Dongchen Zhang
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Update ISCN extract function based on new Rdata file.
Dongchen Zhang
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update data.
Dongchen Zhang
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Update documentation.
Dongchen Zhang
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Update the way of automatically create the credential file.
Dongchen Zhang
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Update documentation.
Dongchen Zhang
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document iscn_soc rdata.
Dongchen Zhang
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Update dependencies.
Dongchen Zhang
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Bug fix.
Dongchen Zhang
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Fix documentation.
Dongchen Zhang
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Fix typo in roxygen.
Dongchen Zhang
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Revert back to the magrittr dependency.
Dongchen Zhang
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add namespace.
Dongchen Zhang
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Commits on May 16, 2024

Put the instruction in the roxygen structure.
Dongchen Zhang
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Updated documentation.
Dongchen Zhang
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Update logger info.
Dongchen Zhang
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Update the usage for filtering high sd data and documentation.
Dongchen Zhang
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Update the usage for exporting the csv file.
Dongchen Zhang
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Update the qc.filter usage.
Dongchen Zhang
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Rename the function to be more product specific.
Dongchen Zhang
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Update documentation.
Dongchen Zhang
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Update documentation.
Dongchen Zhang
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Move file to the correct folder.
Dongchen Zhang
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Update documentations.
Dongchen Zhang
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Update documentation.
Dongchen Zhang
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Merge branch 'PecanProject:develop' into develop
DongchenZ
authored
Merge branch 'develop' of https://github.com/DongchenZ/pecan into develop
Dongchen Zhang
committed
Update documentation.
Dongchen Zhang
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Update change log file.
Dongchen Zhang
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Bug fixes.
Dongchen Zhang
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Commits on May 21, 2024

Merge branch 'PecanProject:develop' into develop
DongchenZ
authored
Update book source.
Dongchen Zhang
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Update IC prep script
Dongchen Zhang
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Update documentation.
Dongchen Zhang
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Merge branch 'develop' of https://github.com/DongchenZ/pecan into develop
Dongchen Zhang
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Update documentation
Dongchen Zhang
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Fix ifelse.
Dongchen Zhang
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Remove the level 1 ecoregion map.
Dongchen Zhang
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Remove ecoregion map from assimsequential package.
Dongchen Zhang
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Change the package name.
Dongchen Zhang
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Update documentation.
Dongchen Zhang
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