Add the down_scale function to pecan.

PecanProject / pecan

The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox.

www.pecanproject.org

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Add the down_scale function to pecan. #3211

Closed JoshuaPloshay closed 6 months ago

JoshuaPloshay commented 1 year ago

Description

Motivation and Context

Review Time Estimate

[ ] Immediately
[ ] Within one week
[x] When possible

Types of changes

[ ] Bug fix (non-breaking change which fixes an issue)
[x] 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.

mdietze commented 1 year ago

Build is failing because of the following:

R check of modules/assim.sequential reports the following new problems. Please fix these and resubmit:
  checking dependencies in R code ... WARNING
  '::' or ':::' imports not declared from:
    ‘randomForest’ ‘readr’ ‘terra’

I think you should modify the code to eliminate the readr dependency and then add randomForest and terra under "Suggests" in the assim.sequential description file. You will probably also need to run scripts/generate_dependencies.R and commit the updated docker/depends/pecan.depends.R

mdietze commented 1 year ago

@JoshuaPloshay just wanted to re-ping you on this before your semester gets busy

sambhavnoobcoder commented 4 months ago

hi @JoshuaPloshay , I was looking into this pr and was wondering if you could share where and how the data and cords variables are being generated or fetched from ? I wanted to run the downscale_function.R but can't understand the source of the variables and parameters used in the function .

mdietze commented 4 months ago

@sambhavnoobcoder as we discussed, the covariates come from the covariates.R file, which is in the open PR https://github.com/PecanProject/pecan/pull/3272 What I'd asked you to do wasn't to post a vague comment here, but to go to the open PR and comment on the specific lines in covariates.R that are unclear. A number of the covariates are already well documented there and it's not fair to ask open ended questions here without first reading that code. We've also discussed from the very start of the project discussion that the initial test data should be the output from the Dokoohaki et al 2022 paper, which are posted on OSF: https://osf.io/efcv5/