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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

Commits on Aug 13, 2021

  1. edits to christina's PR

    Alexis Helgeson committed Aug 13, 2021
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  2. Removed @export from Roxygen

    Alexis Helgeson committed Aug 13, 2021
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  3. Added namespace call before GEFS functions

    Alexis Helgeson committed Aug 13, 2021
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Commits on Aug 18, 2021

  1. "Added csv with args for metprocess"

    Alexis Helgeson committed Aug 18, 2021
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Commits on Aug 30, 2021

  1. ".Rd and DESCRIPTION updated by make document"

    Alexis Helgeson committed Aug 30, 2021
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  2. "added @export to download noaa and process noaa functions, also adde… 

    …d defintion for object "curr"
    Alexis Helgeson committed Aug 30, 2021
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  3. ".Rd and DESCRIPTION updated by make document"

    Alexis Helgeson committed Aug 30, 2021
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Commits on Sep 7, 2021

  1. "added @export back to write noaa function"

    Alexis Helgeson committed Sep 7, 2021
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Commits on Sep 14, 2021

  1. "added call for herbaceous dataset"

    Alexis Helgeson committed Sep 14, 2021
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Commits on Sep 15, 2021

  1. "ran make document"

    Alexis Helgeson committed Sep 15, 2021
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Commits on Sep 21, 2021

  1. "added species info for herb data"

    Alexis Helgeson committed Sep 21, 2021
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  2. "changed imports line 12 from 31 to 33"

    Alexis Helgeson committed Sep 21, 2021
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Commits on Sep 23, 2021

  1. "added a check if plot species data is available or not"

    Alexis Helgeson committed Sep 23, 2021
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Commits on Oct 4, 2021

  1. "changes to param for extract_NEON_veg"

    Alexis Helgeson committed Oct 4, 2021
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Commits on Oct 7, 2021

  1. "changes made to how dates are passed to fcns, added plot area info"

    Alexis Helgeson committed Oct 7, 2021
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Commits on Oct 27, 2021

  1. "make updated .Rd files un-do commit"

    Alexis Helgeson committed Oct 27, 2021
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Commits on Oct 30, 2021

  1. "fixed evaportranspiration to Qle conversion"

    Alexis Helgeson committed Oct 30, 2021
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Commits on Nov 3, 2021

  1. "fixed units for rh calculation in downscaliing fncs"

    Alexis Helgeson committed Nov 3, 2021
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  2. "GEFS_export merge commits" 

    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
    Alexis Helgeson committed Nov 3, 2021
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Commits on Nov 4, 2021

  1. "ran make"

    Alexis Helgeson committed Nov 4, 2021
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Commits on Nov 16, 2021

  1. "fixed unit conversion timing so correct units are passed to met2model"

    Alexis Helgeson committed Nov 16, 2021
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Commits on Nov 17, 2021

  1. "fixed downscale Na's issue"

    Alexis Helgeson committed Nov 17, 2021
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  2. "deleted hard coded start and end dates"

    Alexis Helgeson committed Nov 17, 2021
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Commits on Nov 19, 2021

  1. "changes made to better integrate herbeceous data"

    Alexis Helgeson committed Nov 19, 2021
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Commits on Feb 2, 2022

  1. "generalized functions and removed litter C calculation"

    Alexis Helgeson committed Feb 2, 2022
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  2. "added function input for herb dryMass"

    Alexis Helgeson committed Feb 2, 2022
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Commits on Feb 4, 2022

  1. "removed namespace calls to data.atmosphere"

    Alexis Helgeson committed Feb 4, 2022
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Commits on Feb 7, 2022

  1. "generalize downscale fcns & fixed leap year issue with solar zenith … 

    …angle fcn"
    Alexis Helgeson committed Feb 7, 2022
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Commits on Feb 9, 2022

  1. "debugging SW flux downscaling"

    Alexis Helgeson committed Feb 9, 2022
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Commits on Feb 10, 2022

  1. "fixed SW flux calculation so both half hourly ts are estimated from … 

    …hourly data"
    Alexis Helgeson committed Feb 10, 2022
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Commits on Feb 18, 2022

  1. "SW flux debugging"

    Alexis Helgeson committed Feb 18, 2022
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Commits on Feb 21, 2022

  1. "skip match pft for now"

    Alexis Helgeson committed Feb 21, 2022
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Commits on Mar 11, 2022

  1. "edited write.configs to loop over IC ens"

    Alexis Helgeson committed Mar 11, 2022
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Commits on Mar 26, 2022

  1. "changes to ic funcs"

    Alexis Helgeson committed Mar 26, 2022
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Commits on Apr 29, 2022

  1. "re-ran make"

    Alexis Helgeson committed Apr 29, 2022
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  2. "re-ran make"

    Alexis Helgeson committed Apr 29, 2022
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Commits on May 16, 2022

  1. merge commits from sipnet_debug 

    Merge branch 'sipnet_debug' into ICsdaSIPNET

# Conflicts:
#	base/logger/DESCRIPTION
#	base/qaqc/DESCRIPTION
#	base/visualization/DESCRIPTION
#	models/sipnet/R/write.configs.SIPNET.R
#	modules/data.land/R/cohort2pool.R
#	modules/data.land/R/extract_NEON_veg.R
#	modules/data.land/man/extract_NEON_veg.Rd
    Alexis Helgeson committed May 16, 2022
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Commits on May 26, 2022

  1. "updates to SDA fcns"

    Alexis Helgeson committed May 26, 2022
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Commits on Jun 1, 2022

  1. "HF LAI SDA"

    Alexis Helgeson committed Jun 1, 2022
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  2. "merge with develop" 

    Merge branch 'develop' of https://github.com/helge22a/pecan into ICsdaSIPNET

# Conflicts:
#	base/all/DESCRIPTION
#	base/logger/DESCRIPTION
#	base/visualization/DESCRIPTION
#	models/sipnet/R/met2model.SIPNET.R
#	models/sipnet/R/write.configs.SIPNET.R
#	modules/assim.sequential/R/sda.enkf_MultiSite.R
#	modules/data.land/R/cohort2pool.R
#	modules/data.land/R/extract_NEON_veg.R
#	modules/data.land/R/extract_veg.R
#	modules/data.land/R/ic_process.R
#	modules/data.land/R/write_ic.R
#	modules/data.land/man/cohort2pool.Rd
#	modules/data.land/man/extract_NEON_veg.Rd
    Alexis Helgeson committed Jun 1, 2022
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Commits on Jun 3, 2022

  1. "new multisite xml for HF and corrected make conflicts in data.land"

    Alexis Helgeson committed Jun 3, 2022
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  2. Merge branch 'develop' of https://github.com/helge22a/pecan into ICsd… 

    …aSIPNET

updating branch
    Alexis Helgeson committed Jun 3, 2022
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Commits on Jun 10, 2022

  1. "getting t=1 restart SDA working"

    Alexis Helgeson committed Jun 10, 2022
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  2. Merge https://github.com/helge22a/pecan into ICsdaSIPNET 

    merge with develop.
    Alexis Helgeson committed Jun 10, 2022
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Commits on Jun 24, 2022

  1. "added for loop for IC filepath check in check.inputs"

    Alexis Helgeson committed Jun 24, 2022
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  2. "added build_X and sda_matchparam fcns, changed restart to list objec… 

    …t for SDA"
    Alexis Helgeson committed Jun 24, 2022
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  3. "match_param working build_X not"

    Alexis Helgeson committed Jun 24, 2022
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Commits on Jun 27, 2022

  1. Merge https://github.com/helge22a/pecan into ICsdaSIPNET 

    merge with main
    Alexis Helgeson committed Jun 27, 2022
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Commits on Jul 1, 2022

  1. "cleaner version of SDA_workflow only for LAI"

    Alexis Helgeson committed Jul 1, 2022
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Commits on Jul 6, 2022

  1. "working on build_X fcn, minor edits to workflow"

    Alexis Helgeson committed Jul 6, 2022
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  2. "unexpected else flagged by make"

    Alexis Helgeson committed Jul 6, 2022
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  3. "missing }"

    Alexis Helgeson committed Jul 6, 2022
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  4. "updated .Rd files for new fcns"

    Alexis Helgeson committed Jul 6, 2022
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  5. Merge branch 'develop' of https://github.com/helge22a/pecan into ICsd… 

    …aSIPNET

merge with develop up to date w Project PEcAn
    Alexis Helgeson committed Jul 6, 2022
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Commits on Jul 7, 2022

  1. "restart changes working up to call for analysis"

    Alexis Helgeson committed Jul 7, 2022
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  2. "soilmoist xml for Cam"

    Alexis Helgeson committed Jul 7, 2022
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Commits on Jul 11, 2022

  1. "changed build X fcn to return reads for params.list and X"

    Alexis Helgeson committed Jul 11, 2022
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  2. "set Q to NULL to match default"

    Alexis Helgeson committed Jul 11, 2022
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Commits on Jul 13, 2022

  1. "added new single ob nimble model to Analysis code"

    Alexis Helgeson committed Jul 13, 2022
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Commits on Jul 14, 2022

  1. "added args to build_X, added soil pft to xml, changed dates in workf… 

    …low"
    Alexis Helgeson committed Jul 14, 2022
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  2. "changed outdir for X_build within loop to point to outdir"

    Alexis Helgeson committed Jul 14, 2022
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  3. "revert commit PecanProject#2927, periods in package name causes nimb… 

    …le to fail compilation"
    Alexis Helgeson committed Jul 14, 2022
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  4. "removed previous edits skipping toggle"

    Alexis Helgeson committed Jul 14, 2022
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  5. "library call change, removal of soil pft from SDA xml"

    Alexis Helgeson committed Jul 14, 2022
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Commits on Jul 16, 2022

  1. "runids stored in different objects depending on what t is"

    Alexis Helgeson committed Jul 16, 2022
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  2. "fixed filepath error"

    Alexis Helgeson committed Jul 16, 2022
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  3. "forecast met needs to be split by met.start, met.end"

    Alexis Helgeson committed Jul 16, 2022
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  4. "changes to workflow to work for multiple sda.start and include NAs"

    Alexis Helgeson committed Jul 16, 2022
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Commits on Jul 20, 2022

  1. "getting iterarive SDA working, now skipping days with NA"

    Alexis Helgeson committed Jul 20, 2022
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Commits on Aug 27, 2022

  1. "fixed restart so correct params are written"

    Alexis Helgeson committed Aug 27, 2022
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Commits on Aug 29, 2022

  1. "added check for ensemble member folder to write.ensemble"

    Alexis Helgeson committed Aug 29, 2022
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Commits on Aug 30, 2022

  1. "updating next.olddir with runs"

    Alexis Helgeson committed Aug 30, 2022
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Commits on Aug 31, 2022

  1. "updated run dates"

    Alexis Helgeson committed Aug 31, 2022
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Commits on Sep 13, 2022

  1. "merge with main" 

    Merge branch 'develop' of https://github.com/PecanProject/pecan into ICsdaSIPNET

# Conflicts:
#	modules/assim.sequential/R/sda_plotting.R
#	modules/assim.sequential/inst/WillowCreek/SDA_Workflow.R
#	modules/data.land/R/cohort2pool.R
#	modules/data.land/R/extract_NEON_veg.R
#	modules/data.land/R/extract_veg.R
#	modules/data.land/R/get_veg_module.R
#	modules/data.land/R/sample_ic.R
#	modules/data.land/R/write_ic.R
#	modules/data.land/man/extract_NEON_veg.Rd
    Alexis Helgeson committed Sep 13, 2022
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Commits on Sep 14, 2022

  1. "PR clean up, added new fcn for metSplit, created new folder"

    Alexis Helgeson committed Sep 14, 2022
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  2. Merge branch 'develop' of https://github.com/PecanProject/pecan into … 

    …ICsdaSIPNET

merge with main
    Alexis Helgeson committed Sep 14, 2022
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Commits on Sep 15, 2022

  1. "fix no global binding variable error"

    Alexis Helgeson committed Sep 15, 2022
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  2. "fixed global vairable binding in downscale_ShortWave_to_half_hrly"

    Alexis Helgeson committed Sep 15, 2022
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Commits on Oct 3, 2022

  1. "fix PAR, update IC fcns with main"

    Alexis Helgeson committed Oct 3, 2022
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Commits on Oct 6, 2022

  1. "no idea how this ended up in the scripts folder but it was never sup… 

    …posed to be there"
    Alexis Helgeson committed Oct 6, 2022
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  2. "remove lazydata T"

    Alexis Helgeson committed Oct 6, 2022
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  3. Update base/settings/R/check.all.settings.R 

    Co-authored-by: Chris Black <[email protected]>
    @infotroph
    ahelgeso and infotroph authored Oct 6, 2022
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  4. Update base/settings/R/check.all.settings.R 

    Co-authored-by: Chris Black <[email protected]>
    @infotroph
    ahelgeso and infotroph authored Oct 6, 2022
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  5. "added changelog entry for SIPNET LE fix"

    Alexis Helgeson committed Oct 6, 2022
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  6. "delete commented out line"

    Alexis Helgeson committed Oct 6, 2022
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  7. "removed extra indent"

    Alexis Helgeson committed Oct 6, 2022
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  8. "remove Rcurl library call"

    Alexis Helgeson committed Oct 6, 2022
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  9. Update modules/assim.sequential/inst/restart_SDAworkflow_scripts/SDA_… 

    …Workflow_LAI.R

Co-authored-by: Chris Black <[email protected]>
    @infotroph
    ahelgeso and infotroph authored Oct 6, 2022
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  10. "added back .data rlang import"

    Alexis Helgeson committed Oct 6, 2022
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  11. "changed startdate back to start_date"

    Alexis Helgeson committed Oct 6, 2022
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  12. "add .data import to extract_NEON"

    Alexis Helgeson committed Oct 6, 2022
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  13. "merge with main" 

    Merge branch 'develop' of https://github.com/PecanProject/pecan into ICsdaSIPNET

# Conflicts:
#	CHANGELOG.md
#	modules/data.land/R/get_veg_module.R
#	modules/data.land/R/sample_ic.R
    Alexis Helgeson committed Oct 6, 2022
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  14. Merge branch 'ICsdaSIPNET' of https://github.com/helge22a/pecan into … 

    …ICsdaSIPNET
    Alexis Helgeson committed Oct 6, 2022
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Commits on Oct 7, 2022

  1. "added global binding variable for day and hour for Shortwave fcn"

    Alexis Helgeson committed Oct 7, 2022
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  2. Update modules/assim.sequential/R/sda.enkf_MultiSite.R 

    Co-authored-by: Chris Black <[email protected]>
    @infotroph
    ahelgeso and infotroph authored Oct 7, 2022
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  3. "add global binding variable"

    Alexis Helgeson committed Oct 7, 2022
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  4. "add comment to keep depreciated code for future PR"

    Alexis Helgeson committed Oct 7, 2022
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  5. Merge branch 'ICsdaSIPNET' of https://github.com/helge22a/pecan into … 

    …ICsdaSIPNET
    Alexis Helgeson committed Oct 7, 2022
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  6. "remove commented out source call"

    Alexis Helgeson committed Oct 7, 2022
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  7. "resolved unresolved merge conflicts"

    Alexis Helgeson committed Oct 7, 2022
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Commits on Oct 18, 2022

  1. remove library call and use namespace instead

    Alexis Helgeson committed Oct 18, 2022
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  2. "fixed examples"

    Alexis Helgeson committed Oct 18, 2022
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  3. "fixed character limit"

    Alexis Helgeson committed Oct 18, 2022
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Commits on Oct 20, 2022

  1. "fixed examples spacing"

    Alexis Helgeson committed Oct 20, 2022
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  2. "remove readr dependency for data.land"

    Alexis Helgeson committed Oct 20, 2022
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  3. "remove depricated arg call"

    Alexis Helgeson committed Oct 20, 2022
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  4. "moving vswc fcn to inst for future PR"

    Alexis Helgeson committed Oct 20, 2022
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  5. "delete Rd vswc file"

    Alexis Helgeson committed Oct 20, 2022
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  6. "changed veg_info to dat"

    Alexis Helgeson committed Oct 20, 2022
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Commits on Oct 21, 2022

  1. Merge branch 'develop' into ICsdaSIPNET

    ahelgeso authored Oct 21, 2022
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Commits on Oct 25, 2022

  1. Merge branch 'develop' into ICsdaSIPNET

    ahelgeso authored Oct 25, 2022
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  2. "removed comment from debugging PAR"

    Alexis Helgeson committed Oct 25, 2022
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  3. Merge branch 'ICsdaSIPNET' of https://github.com/helge22a/pecan into … 

    …ICsdaSIPNET
    Alexis Helgeson committed Oct 25, 2022
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