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This homogenizes the output formats across the levels of cell and land units.
The user is expected to do this manually and provide 'run_biomee_f_bysite()' with properly formatted 'init_lu' and 'luc_forcing', the argument 'luh2' is now removed to simplify the interfaces.
…for daily and yearly
…ual totC) - added: daily tile NPP (since we have NPP in the annual output structures), - added: annual cell totC (since we had totN) - but did not add: annual cohort seedN/leafN/rootN/sapwoodN/heartwoodN even though we have these pools reported for C
LULUC implementation
This should help prevent failure on CRAN which prohibits parallel code.
…d replace with new cost_likelihood_pmodel1 => cost_likelihood_pmodel_legacy cost_likelihood_pmodel2 => cost_likelihood_pmodel
library(styler); styler::style_pkg(style = styler::tidyverse_style, strict=FALSE)
…ings_runMCMC This should help to make code clearer and easier to distinguish between these two settings. And this also add renames `sampler` to `sampler_runMCMC` for consistency. This is fully backwards compatible because of partial name matching for argument names (settings_calibrate) and for list element names (settings_runMCMC, sampler_runMCMC). Nevertheless, for settings_calibrate we still included a warning about deprecated use.
n_chains_independent => nrChains n_parallel_independent => n_parallel_nrChains
This reverts commit 448e0e6.
- Replacing of p-model example data (adding additional sites and bigD13C and LE (ET) ) - Including gmd paper vignette - Features: - Rewritten `calib_sofun()` to parallelize MCMC chains and added new possibilities for priors `createMixedPrior()` - Rewritten `cost_likelihood_pmodel()` - Changed format of example data
usethis::use_pkgdown_github_pages() and then kept the specific configurations for release and development versions.
Our current GECO template (https://github.com/geco-bern/GECO_documentation_template) gets broken by the update of bootstrap5. Note, at some point in the future it might be necessary to update to v5, see: https://tidyverse.org/blog/2021/12/pkgdown-2-0-0/
This brings it to default behavior. Where also pull_requests trigger the workflow in general, but skip the last step 'Deploy to GitHub pages' since this last step is conditional.
…2025. It's equivalent. All good.
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Needed to get calibration routine, etc.
This is to be merged prior to project start by visiting researcher (July 2026).