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Adding SDA restart capability #3036

Merged
merged 113 commits into from
Oct 25, 2022
Merged

Adding SDA restart capability #3036

merged 113 commits into from
Oct 25, 2022

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helge22a
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Description

Condensing sda.enfk_MultiSite function with new functions metSplit, sda_matchparam, and build_X, added more comments to hopefully make this easier to work with. Now can run SDA at any time step (not only annual). Added new nimble model for running one site at a time through assimilation.

Motivation and Context

All changes necessary for scaling up SDA to continental scale/adding more data streams for NASA CMS project with @DongchenZ @serbinsh @mdietze @Qianyuxuan

Review Time Estimate

  • Immediately
  • Within one week
  • When possible

Types of changes

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

  • My change requires a change to the documentation.
  • My name is in the list of CITATION.cff
  • I have updated the CHANGELOG.md.
  • I have updated the documentation accordingly.
  • I have read the CONTRIBUTING document.
  • I have added tests to cover my changes.
  • All new and existing tests passed.

Alexis Helgeson and others added 30 commits August 13, 2021 09:37
edits to christina's PR
9c7db83
Removed @export from Roxygen
d401acb
Added namespace call before GEFS functions
17433e8
"Added csv with args for metprocess"
2a7a5ff
".Rd and DESCRIPTION updated by make document"
2868bab
"added @export to download noaa and process noaa functions, also adde…
bd53273 
…d defintion for object "curr"
".Rd and DESCRIPTION updated by make document"
74646c6
"added @export back to write noaa function"
6dc8566
"added call for herbaceous dataset"
931dd10
"ran make document"
28742c9
"added species info for herb data"
325722a
"changed imports line 12 from 31 to 33"
f6aa7a2
"added a check if plot species data is available or not"
9a2a998
"changes to param for extract_NEON_veg"
cdfe30b
"changes made to how dates are passed to fcns, added plot area info"
0540f27
"make updated .Rd files un-do commit"
4b5a019
"fixed evaportranspiration to Qle conversion"
3d5d3d8
"fixed units for rh calculation in downscaliing fncs"
b762667
"GEFS_export merge commits"
9680b15 
Merge branch 'GEFS_export' into sipnet_debug

# Conflicts:
#	base/qaqc/DESCRIPTION
#	base/visualization/DESCRIPTION
#	modules/data.land/man/get_veg_module.Rd
#	modules/data.land/man/put_veg_module.Rd
"ran make"
d928e17
"fixed unit conversion timing so correct units are passed to met2model"
d612960
"fixed downscale Na's issue"
07c4ed0
"deleted hard coded start and end dates"
bd14330
"changes made to better integrate herbeceous data"
81a899b
"generalized functions and removed litter C calculation"
62db058
"added function input for herb dryMass"
179168a
"removed namespace calls to data.atmosphere"
73ca5e6
"generalize downscale fcns & fixed leap year issue with solar zenith …
d0acd56 
…angle fcn"
"debugging SW flux downscaling"
a601959
"fixed SW flux calculation so both half hourly ts are estimated from …
3f5c7c0 
…hourly data"
Alexis Helgeson and others added 17 commits October 7, 2022 09:56
"added global binding variable for day and hour for Shortwave fcn"
6b6c132
@infotroph
Update modules/assim.sequential/R/sda.enkf_MultiSite.R
add2fe5 
Co-authored-by: Chris Black <chris@ckblack.org>
"add global binding variable"
1e82e43
"add comment to keep depreciated code for future PR"
8e950d6
Merge branch 'ICsdaSIPNET' of https://github.com/helge22a/pecan into …
4298ae3 
…ICsdaSIPNET
"remove commented out source call"
9b65041
"resolved unresolved merge conflicts"
0126fdd
remove library call and use namespace instead
f0dc679
"fixed examples"
7228f86
"fixed character limit"
ffadf72
"fixed examples spacing"
80b326e
"remove readr dependency for data.land"
09fe064
"remove depricated arg call"
8e98fbd
"moving vswc fcn to inst for future PR"
4249c92
"delete Rd vswc file"
371b2a4
"changed veg_info to dat"
e10fe87
Merge branch 'develop' into ICsdaSIPNET
fb06068
@serbinsh
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Wow @helge22a this is a LOT of work and a really nice PR! lots of great contributions here! I did my best to review but not sure i can dig deeper without a better understanding of running it all

@mdietze mdietze merged commit c5f4e03 into PecanProject:develop Oct 25, 2022
@helge22a helge22a mentioned this pull request Oct 28, 2022
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@infotroph infotroph infotroph left review comments

@serbinsh serbinsh serbinsh left review comments

@mdietze mdietze mdietze approved these changes

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4 participants
@helge22a @serbinsh @infotroph @mdietze