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0aa071f
first draft of data prep steps for downscaling workflow
dlebauer Jan 29, 2025
e46420b
first drafts of data prep and clustering workflows
dlebauer Feb 3, 2025
d4a7753
major revisions to prepare and clustering workflows
dlebauer Feb 3, 2025
4369a2f
very rough draft for design point simulations
dlebauer Feb 3, 2025
5b20512
Updated data preparation and clustering workflows so that they now co…
dlebauer Feb 5, 2025
4778094
Created new SIPNETWOPET model as a surrogate for design point runs in…
dlebauer Feb 5, 2025
6ca6d6d
update readme and fix SIPNETWOPET
dlebauer Feb 7, 2025
8cde4b9
move sipnetwopet to standalone script
dlebauer Feb 7, 2025
191c895
converted qmd to R script
dlebauer Feb 7, 2025
d3bb8f4
rename 00-prepare.qmd --> 00-prepare.R
dlebauer Feb 7, 2025
dc71719
Merge branch 'main' of github.com:ccmmf/workflows into 1b
dlebauer Feb 7, 2025
2c8ddbf
convert 01 and 02 qmd to R
dlebauer Feb 7, 2025
543264f
Add downscaling and aggregation workflow for woody crop SOC stocks, p…
dlebauer Feb 7, 2025
c4cd51d
Refactor SIPNETWOPET workflow: streamline data processing and still f…
dlebauer Feb 12, 2025
bf672b0
Initial draft w/ targets package
dlebauer Feb 19, 2025
968f153
Initial draft w/ targets package
dlebauer Feb 19, 2025
eff17bb
Merge branch '1b' of github.com:ccmmf/workflows into 1b
dlebauer Feb 20, 2025
6b64c7a
add first version of script to extract sipnet output
dlebauer Mar 13, 2025
7c461ff
create EFI standard tables and arrays
dlebauer Mar 14, 2025
22c3625
correct netcdf format
dlebauer Mar 14, 2025
1e7b09c
convert sipnetwopet simulated data as arrays
dlebauer Mar 18, 2025
f4aacfb
save objects as RDS instead of RData
dlebauer Mar 18, 2025
46a61d5
first draft of county aggregated SOC and AGB
dlebauer Mar 18, 2025
72c5d7a
added anchor sites table
dlebauer Mar 18, 2025
0d1801d
lots of clean up; too much to document, sorry
dlebauer Mar 21, 2025
3880a26
Merge branch 'main' of github.com:ccmmf/workflows into 1b
dlebauer Mar 21, 2025
d468ea4
added first draft of documentation
dlebauer Mar 21, 2025
19eec45
updated draft of downscaling workflow
dlebauer Mar 22, 2025
273f861
update qmd docs to generate self-contained html
dlebauer Mar 22, 2025
a5259d1
Revert README changes; remove _02_design_point_simulations, sipnetwop…
dlebauer Mar 22, 2025
65cd54b
changed from local install_git to remote install_github
dlebauer Mar 22, 2025
72256b4
fix wording
dlebauer Apr 5, 2025
99ac120
Update downscale/04_downscaling_documentation_results.qmd
dlebauer Apr 7, 2025
5dcb76d
Add partial dependence plots
dlebauer Apr 8, 2025
b109387
Merge branch '1b' of github.com:ccmmf/workflows into 1b
dlebauer Apr 8, 2025
292a5c7
Update downscale/02_extract_sipnet_output.R
dlebauer Apr 8, 2025
e2f9301
fixed typos
dlebauer Apr 9, 2025
cd973d3
reverting name change so I don't loose comments
dlebauer Apr 9, 2025
fa0a860
Update downscale/00-prepare.R
dlebauer Apr 10, 2025
2c43668
addressing PR review feedback
dlebauer Apr 10, 2025
9482450
Update downscale/00-prepare.R
dlebauer Apr 10, 2025
5d111e8
merge
dlebauer Apr 10, 2025
6dceea5
Address PR reviews - lots of changes in one commit
dlebauer Apr 11, 2025
0958654
round lat,lon in anchor_sites_ids.csv
dlebauer Apr 11, 2025
b71741e
Update downscale/00-prepare.R
dlebauer Apr 11, 2025
3c054d6
Update downscale/00-prepare.R
dlebauer Apr 11, 2025
84c135c
Update downscale/02_extract_sipnet_output.R
dlebauer Apr 11, 2025
48d79d4
Update downscale/02_extract_sipnet_output.R
dlebauer Apr 11, 2025
5377545
Refactor output file names for consistency and clarity in downscaling…
dlebauer Apr 11, 2025
fb6aeb3
Merge branch '1b' of github.com:ccmmf/workflows into 1b
dlebauer Apr 11, 2025
42a4f3e
Update downscale/02_extract_sipnet_output.R
dlebauer Apr 15, 2025
96c604c
Update downscale/02_extract_sipnet_output.R
dlebauer Apr 15, 2025
77fe472
fixing plots, including fixing units and removing partial dependency …
dlebauer Apr 15, 2025
367f983
Merge branch '1b' of github.com:ccmmf/workflows into 1b
dlebauer Apr 15, 2025
4c38cb1
Update downscale/01_cluster_and_select_design_points.R
dlebauer Apr 16, 2025
2271d7d
moved .future.R and fixed spelling in 03_ **aggregate**
dlebauer Apr 16, 2025
90deb6e
Merge branch '1b' of github.com:ccmmf/workflows into 1b
dlebauer Apr 16, 2025
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26 changes: 26 additions & 0 deletions data/anchor_sites_ids.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
id,lat,lon,location,site_name,distance,geometry
2e11530b93cd492f,36.177799888824005,-120.2041070387766,US-ASH,San Joaquin Valley Almond High Salinity,0,"c(-18200.4533456107, -204351.896427268)"
3747151a269036b7,36.94728213363369,-120.10533383829694,US-ASL,San Joaquin Valley Almond Low Salinity,0,"c(-9106.72692414989, -118913.170740419)"
2e11530b93cd492f,36.177799888824005,-120.2041070387766,US-ASM,San Joaquin Valley Almond Medium Salinity,0,"c(-18200.4533456107, -204351.896427268)"
e07417e56c78efbc,36.82778534752612,-120.13964104692187,US-PSH,San Joaquin Valley Pistachio High Salinity,0,"c(-12443.4766403388, -132135.913488504)"
e07417e56c78efbc,36.82778534752612,-120.13964104692187,US-PSL,San Joaquin Valley Pistachio Low Salinity,0,"c(-12443.4766403388, -132135.913488504)"
278cc612aa84983a,38.099349553216186,-121.5015478519803,US-Bi1,Bouldin Island Alfalfa,0,"c(-131305.841205359, 10246.5206530676)"
dce435941adb4679,38.109586695737626,-121.53611176665588,US-Bi2,Bouldin Island Corn,0,"c(-134423.030434314, 11397.1114464211)"
3cea434df9ea5a61,32.81280501889075,-115.44206224718269,US-Dea,UC Desert REC Alfalfa,0,"c(427219.032719703, -567399.727086836)"
aec9f214083b8f69,38.131541484694665,-121.55191049337776,US-DS1,Staten Corn 1,0,"c(-134720.473528729, 14114.7427923167)"
713f08eb3322d4df,38.134598947289916,-121.51170668226486,US-DS2,Staten Corn 2,0,"c(-132525.126666226, 14524.1023560269)"
175358d15d27e2f2,38.12345747466536,-121.54982768148254,US-DS3,Staten Rice 1,0,"c(-135613.932821504, 13017.4923524545)"
bfee4301f7c99060,36.35733308587667,-119.09282519975774,US-Lin,Lindcove Orchard,0,"c(81360.1815020208, -184101.87965719)"
86e23fd30a7c0360,39.577102324150175,-121.86224204465502,US-RGB,Butte County Rice Farm,0,"c(-159486.330544182, 175158.013580008)"
e34fd28a6e4fabee,37.69947277766893,-121.1391060770639,US-RGF,Stanislaus Forage Farm,0,"c(-100102.043437352, -34624.8600835721)"
62b121132228b0f8,39.59613673857021,-122.02261183095081,US-RGG,Glenn County Rice Farm,0,"c(-173815.733795438, 177251.993701875)"
7a561525ca4933d3,39.678693479807265,-122.00275036599245,US-RGO,Glenn County Organic Rice,1.48947665615348,"c(-171665.812216293, 186775.251166129)"
528fcb9581143cf5,38.167462870628164,-121.50580831669866,US-Si1,Staten Island Fallow,0,"c(-131645.501113361, 18645.981438884)"
38f1738eb5750e06,38.16651300978058,-121.52120421290903,US-Si2,Staten Island Flooded,0,"c(-132693.326336371, 18784.9819894633)"
5628e37756df9d41,38.10355405637426,-121.6381351773307,US-Tw2,Twitchell Corn,0,"c(-143324.768603639, 10189.6513305134)"
66de78917c6222b0,38.1157201973455,-121.64507432545884,US-Tw3,Twitchell Alfalfa,0,"c(-144200.168244178, 12239.4602416055)"
0fb8904477a3d0ce,38.10812386794265,-121.65528241872406,US-Twt,Twitchell Island,0,"c(-144755.572864808, 11526.4416088737)"
93d63eb396c4fcf9,38.54295166338029,-121.87235457852974,russell-ranch,Russell Ranch,0.20145926374138,"c(-163142.459970614, 60154.8849130729)"
106ced48ab2599e0,36.34077318361296,-120.10544017924985,west-side,West Side Research Center,55.7382484621095,"c(-9681.32377587362, -186108.326980472)"
04681ffea182d977,38.50242041442077,-121.97641993262302,wolfskill,Wolfskill Experimental Orchards,0,"c(-172200.763852519, 55891.621553943)"
9c562bb603f3b156,33.96726803332844,-117.34048733581272,ucr-citrus,UC Riverside Citrus Research,0,"c(245813.938552732, -446378.780685794)"
101 changes: 101 additions & 0 deletions data/design_points.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,101 @@
id,lat,lon
84389254458b3a58,39.15317154882152,-120.95862855945161
9e3b1749179a4a68,37.99925059252099,-121.20417111702339
729a6ef989c5a277,35.96903914573576,-118.98552352403604
8c23aa17d5b211ed,37.23624485456503,-120.325416895509
57ea98e608333b76,36.9069695937337,-121.68079166613182
6c1e7a1eb4c36ea5,36.376933120111964,-119.45050526430943
5b18c5e0bebe449b,34.472437079253254,-119.22014978387774
058d96dea56318e8,39.845445833262076,-121.99765987838188
df703141000c59c9,33.90118525984266,-117.4062351725988
b8b2dd94a7c44662,33.353055572072144,-117.19182032970713
dbb2c95a5cb30b5d,35.05617905596573,-119.27349643104922
32b66a2605ee700d,36.62790357625534,-119.55109778115332
4c3498f22c47aa3f,36.473246624392274,-119.58999372486372
6def26440f10476c,36.55241300729422,-119.45881344136238
59d94ec22335aba5,40.112945252187885,-122.12625218266525
04268ba7e72d7bfb,36.04216376334651,-119.36168176985615
f0c5457e0db29788,36.18711363649504,-118.99794513559745
69151056c07813d8,36.01650482108036,-119.12213181961096
096c9eebd28d0280,34.91295471748269,-120.40345170635351
ebb783e86d2ac6fb,33.5784705873275,-116.03157176577903
cf0be21778f4dfa5,36.64072986620738,-119.42861772753282
b68880e61d448b93,36.628935713055334,-119.6304967981404
1cb62b1edd188368,37.62449120008097,-120.54849914677672
92e5e100e1a3a472,39.685053412615225,-122.3378033660457
148e91e1a4352adb,39.883929087235735,-122.17230280623504
e664ce5ac2fb2b6f,39.91336805758695,-122.11623004432802
b33f7db23b64a377,37.95408699615648,-121.21347717890643
268a52869b01fe54,36.703002551108156,-120.23482871624192
bd841534f8883a00,36.79087105078594,-120.42721632875711
60f846ca525da31e,36.557282635126995,-119.2223647492762
e5d633da3758c491,38.698241380798265,-122.82083682384803
ce81d5b03685a33e,36.48936289567316,-119.44392501284031
ae81f35c7ed7c3f1,37.58450083241338,-121.28798414625811
01609970faa3c5b9,38.247486225652,-122.1132785251325
08da82da7c956979,38.10501623512874,-121.2107110261319
d1dd970659a71943,34.37258472945189,-119.03318351437721
39b7dba5debef188,36.643806231195825,-119.28748125011076
8b27eb5fc60d506c,36.25395494422166,-119.26318761718049
29baab2f12e2fd80,36.62869595451381,-119.55927338546941
7f1efab0660af0a9,38.29195260046744,-121.54984763089621
9c19b1bcbd391e00,36.665696469841485,-120.07237592351424
462a123c3840df4e,36.88372637787987,-119.96643408398732
2bd084fb5a916420,37.52907547714805,-121.1363874822378
a05ea26a797f4bad,36.74201351767665,-119.66029084888854
6fe9d9756f962d11,38.999929717176904,-122.85197002568268
8c37c59148a2b480,36.950873550214546,-121.79638001291717
cf9c2d9309d78058,35.656293805156665,-119.9791657782526
765ad4a2cb597b04,37.61727674898043,-120.85985117950787
d69343ed38ea49c7,35.93301364948056,-119.0188799294081
c8ca707e38904560,37.430698407931075,-120.825633670933
984a04e7d14a80a3,37.378490673407306,-120.70411638617661
cf1c223d4e408116,37.07745477447745,-120.44392158740519
11aa82e47c15b8df,34.38595949634103,-118.81445533388944
f5cde95be18bb83d,39.61336729923421,-121.84504941875572
2c9f5faf24bff9fd,36.139246198074844,-119.10524906004886
30d7e9a739591579,38.694890771466596,-122.04115169522713
889d6cb7440babd8,39.14835505068194,-121.78504578064799
7afa2a6c097c1f5b,36.362595802193916,-119.10984333853257
7b2e85c30ecfcbe8,36.036952558710894,-118.96561932450625
ecc585936d3203a5,36.63049097515202,-119.58155869596567
a860cdc63cfc7cd1,35.98506301531852,-119.01458795848025
17b056351d1484f8,36.738759687243714,-120.03573971347572
e968e9c8f8574cb2,36.383833240819285,-119.65554268083451
000f186bcf4b2be5,37.29108282118807,-121.04882363442482
54d2ebadd8e4e8e2,37.491197984797665,-121.0085531562697
6616b64433b71c3c,35.772843204255615,-119.09087891682833
1114b0b499d4854c,36.51520247850828,-119.42062406057501
4032fbd64a0b5147,36.76356458613677,-119.50957323217338
6328b22167f31aad,33.86884047977172,-117.40837842690881
9a28cf783448dc03,34.29707712580956,-119.06013978221256
25d92d00fe5f31ea,35.99612889983196,-119.13104338547221
254f091dee798a22,39.867933961656206,-122.16830730681002
f87888e9df3fab14,39.70189739031584,-121.79205467074456
05ce4008f973ff67,36.49534520970872,-119.5917993311476
132df615713a9102,36.96032567057031,-121.37833422008488
64cf20b7075f16bd,36.28704555525085,-119.12755106080951
8c469dfef3eac688,39.73425797216054,-122.13900242983709
d4aa2f4b173e52d9,39.894655731543544,-122.218282577988
7a8855e8f27579dd,36.82200408868894,-120.01066959023188
02ed5f046523985e,37.66867911623095,-121.71245595264062
3bde8bc179b8fcae,36.90691122790127,-119.67871974793037
5e21d98f69f14285,35.49646210616489,-119.7232326291538
5aabe8a4b61ac4b1,37.70219947002282,-120.98628447816145
ba5921d796f688e5,39.54046659749015,-122.22839029392931
bf27f77fb0ee40e0,39.14372601708733,-121.57068428157207
4c49ef413147e623,38.50692937324865,-121.97470253705194
427606829eff9a98,36.60051373911106,-119.25963820359836
24766015396f3dde,36.63384726465495,-119.49151662644384
95af7876982dad47,39.667825249028695,-122.25810998713746
e3daa31507eccfd0,39.16472984057072,-121.76550564744215
b609ae97085420fb,37.87291873963135,-121.30336862647805
1e113c95a1054df5,38.01749742979522,-121.19637437982693
d6ce58a349148d32,36.20587304779096,-120.25336201321787
2e11530b93cd492f,36.177799888824005,-120.2041070387766
3747151a269036b7,36.94728213363369,-120.10533383829694
2e11530b93cd492f,36.177799888824005,-120.2041070387766
e07417e56c78efbc,36.82778534752612,-120.13964104692187
e07417e56c78efbc,36.82778534752612,-120.13964104692187
bfee4301f7c99060,36.35733308587667,-119.09282519975774
9c562bb603f3b156,33.96726803332844,-117.34048733581272
26 changes: 26 additions & 0 deletions data_raw/anchor_sites.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
external_site_id,site_name,lat,lon,crops,pft
US-ASH,San Joaquin Valley Almond High Salinity,36.1697,-120.201,Almond,woody perennial crop
US-ASL,San Joaquin Valley Almond Low Salinity,36.9466,-120.1024,Almond,woody perennial crop
US-ASM,San Joaquin Valley Almond Medium Salinity,36.1777,-120.2026,Almond,woody perennial crop
US-PSH,San Joaquin Valley Pistachio High Salinity,36.2347,-119.9247,Pistachio,woody perennial crop
US-PSL,San Joaquin Valley Pistachio Low Salinity,36.8276,-120.1397,Pistachio,woody perennial crop
US-Bi1,Bouldin Island Alfalfa,38.0992,-121.4993,Alfalfa,hay and haylage crops
US-Bi2,Bouldin Island Corn,38.1091,-121.5351,Corn,row crops
US-Dea,UC Desert REC Alfalfa,32.8136,-115.4423,Alfalfa,hay and haylage crops
US-DS1,Staten Corn 1,38.1335,-121.539,Corn,row crops
US-DS2,Staten Corn 2,38.1375,-121.514,Corn,row crops
US-DS3,Staten Rice 1,38.1235,-121.549,Rice,row crops
US-Lin,Lindcove Orchard,36.3566,-119.0922,Oranges,woody perennial crop
US-RGB,Butte County Rice Farm,39.5782,-121.8579,Rice,row crops
US-RGF,Stanislaus Forage Farm,37.6995,-121.1369,Forage crops,hay and haylage crops
US-RGG,Glenn County Rice Farm,39.5944,-122.0253,Rice,row crops
US-RGO,Glenn County Organic Rice,39.6805,-122.0026,Organic rice,row crops
US-Si1,Staten Island Fallow,38.1747,-121.5047,Fallow,NA
US-Si2,Staten Island Flooded,38.1758,-121.5167,Rice,row crops
US-Tw2,Twitchell Corn,38.0969,-121.6365,Corn,row crops
US-Tw3,Twitchell Alfalfa,38.1152,-121.6469,Alfalfa,herbaceous perennial
US-Twt,Twitchell Island,38.1087,-121.6531,NA,NA
russell-ranch,Russell Ranch,38.543,-121.874,"tomato, corn, wheat",row crops
west-side,West Side Research Center,36.342,-120.108,Row crops including cotton,row crops
wolfskill,Wolfskill Experimental Orchards,38.503,-121.977,Fruit and nut breeding,woody perennial crop
ucr-citrus,UC Riverside Citrus Research,33.967,-117.34,Citrus variety collection,woody perennial crop
10 changes: 10 additions & 0 deletions downscale/.future.R
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
# This file will load any time the future package is loaded.
# see ?future::plan for more details

# Auto-detect cores and leave one free
no_cores <- max(future::availableCores( ) - 1, 1)
future::plan(future::multicore, workers = no_cores)

PEcAn.logger::logger.info(paste("Using", no_cores, "cores for parallel processing"))

PEcAn.logger::logger.warn(paste("Using", no_cores, "cores for parallel processing"))
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