Make it easier to run meta-analysis standalone #3728
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mdietze
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Dec 23, 2025
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I introduced at least one bug in here, caught by the CI. So hold off on merging this. I'll get that fixed and make sure the tests pass. |
infotroph
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Dec 25, 2025
ashiklom
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Dec 25, 2025
...without the file or database logic, but with some of the meta-analysis conveniences like pre-processing data, checking priors/posteriors, and calculating summary statistics. Takes inputs as lists; returns outputs as lists. Keeps file IO to a minimum (except as performed by functions this calls). See discussion in PecanProject#3718.
It's only ever used in `PEcAn.MA::jagify`. Moving it here is a step towards making `PEcAn.DB` at most a "Suggests" of `PEcAn.MA`.
...and other fixes from: PecanProject#3718 (comment)
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We should really use `saveRDS` / `readRDS`!
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Description
The
PEcAn.MA::run.meta.analysis.pftfunction has a lot of file I/O and some database interactions that make it difficult to run without the full PEcAn infrastructure. At the same time,PEcAn.MA::pecan.mais missing some useful pre- and post- checking and data processing. This introduces an intermediate function ---meta_analysis_standalone--- that includes the logic ofrun.meta.analysis.pftbut without the extra I/O and database interactions.run.meta.analysis.pfthas been refactored to be a thin wrapper aroundmeta_analysis_standalonealong with some file I/O. A minor breaking change is that all file writing now happens aftermeta_analysis_standaloneruns (e.g., before,jagged.datawas written to disk right after being created but before the meta-analysis was executed; now it's saved after the entire meta-analysis runs).I also added a short new vignette that shows how this function can be used. The Quarto notebook in #3707 can be a more complete version of this.
Motivation and Context
See discussion in #3718. Also related to open PR #3707.
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