Two station static model: Stan file, data, data prep, implementation#469
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mdodrill-usgs wants to merge 7 commits into
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Two station static model: Stan file, data, data prep, implementation#469mdodrill-usgs wants to merge 7 commits into
mdodrill-usgs wants to merge 7 commits into
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Port VFTS Stan model from LOM paper to inst/models/ - Fix deprecated postfix array syntax (10 declarations; Stan 2.33+ requirement) - Switch K600 prior from hard-coded normal to lognormal with data-block parameters - Rename variables to package conventions (n_obs, n_days, light, temp_water, travel_time) - Verified clean parse
- Add DO.obs.up, DO.sat.up, DO.obs.down, DO.sat.down, travel.time to mm_data() registry - Create metab_2station() constructor stub with mm_validate_data() integration - Two-station-specific checks: travel.time positivity, units sanity (<1 day), lead-in data - Fix mm_validate_data() na_times grep incorrectly matching travel.time alongside solar.time - Add test-metab_2station.R (7 assertions); all pre-existing tests still pass
- Implement mm_ts_prep_data(data, specs=NULL) reshaping long-format data to Stan list - Upstream DO/DO.sat shifted per-row by lag = round(travel.time / timestep_days) - Lead-in rows (first max(lag) rows) excluded from output matrices - Pivots 8 variables to [n_obs x n_days] matrices following prepdata_bayes() pattern - K600 prior params passed through from specs (defaults: log(3.48) / 0.5) - Units stripped before return - Extend test-metab_2station.R to 15 blocks / 39 assertions; no regressions
- Extend mm_parse_name() type map: b2 = 'bayes_2station' (handles two-character prefix correctly) - Add predict_DO.metab_2station() stub returning DO.obs.down / DO.mod.down column names - Flag plot_DO_preds.R and helper-rmse_DO.R as needing update - Extend test-metab_2station.R to 12 assertions; no regressions in test-mm_name.R
- Rename GPP/ER/k600 to GPP_daily/ER_daily/K600_daily to match format_mcmc_mat_nosplit() lookup table - Add GPP_daily_mu/sigma and ER_daily_mu/sigma to data block - Add GPP_daily and ER_daily normal priors in model block - Group all three priors before likelihood statement
- Register bayes_2station in mm_name(), mm_valid_names() - Add bayes_2station case to specs(): params_in/out, split_dates=FALSE, engine='stan' - K600 prior defaults match one-station convention (meanlog=2.484907, sdlog=1.0) - GPP/ER prior defaults match one-station defaults (GPP: mu=3.1 sd=6.0, ER: mu=-7.1 sd=7.1) - Add stats, utils, parallel to DESCRIPTION Imports (pre-existing gap) - Add bayes_2station dispatch to metab() - Full metab_2station() implementation: validation, data prep, rstan::stan() call, MCMC formatting via format_mcmc_mat_nosplit(), metab_model S4 construction - Add metab_2station class - Implement predict_DO.metab_2station() returning DO.obs.down / DO.mod.down - Add two_station_example dataset (30 days, VFTS-2, package column conventions) - Add R/data.R with full citation: Bishop et al. 2026 and ScienceBase link - passing tests including real Stan fit; no regressions in mm_name suite - Known gaps: no Stan compile caching (deferred), predict_DO use_saved=FALSE not implemented, plot_DO_preds.R/helper-rmse_DO.R one-station column names deferred
- Add utils::globalVariables for ., metab_50pct, DO.mod.down - Add @importFrom utils modifyList - Replace require(rstan) with requireNamespace() pattern
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DemoRan the two-station model against the bundled Datasetdim: 2904 x 9 Model fitspecs <- specs(mm_name('bayes_2station'),
n_chains = 1, burnin_steps = 250, saved_steps = 250)
fit <- metab(specs, data = two_station_example)Fast demo settings (1 chain, 250 warmup + 250 saved steps) to confirm the pipeline runs.
|
| date | GPP | GPP.lower | GPP.upper | ER | ER.lower | ER.upper | K600 | K600.lower | K600.upper |
|---|---|---|---|---|---|---|---|---|---|
| 2011-07-31 | 16.88 | 15.28 | 18.23 | -31.63 | -38.54 | -24.31 | 23.26 | 15.93 | 30.39 |
| 2011-08-01 | 18.31 | 16.68 | 20.06 | -30.07 | -37.53 | -24.80 | 20.72 | 15.65 | 28.43 |
| 2011-08-02 | 19.74 | 18.30 | 21.15 | -33.00 | -39.26 | -27.05 | 24.28 | 17.99 | 30.87 |
| 2011-08-03 | 18.62 | 17.31 | 19.94 | -25.62 | -30.21 | -21.17 | 17.45 | 12.38 | 21.52 |
| 2011-08-04 | 20.12 | 18.69 | 21.68 | -30.48 | -37.29 | -23.40 | 19.84 | 13.44 | 26.60 |
30 days fit total; GPP/ER/K600 all in reasonable ranges.
predict_DO() — downstream DO fit (first 10 rows)
| solar.time | DO.obs.down | DO.mod.down |
|---|---|---|
| 2011-07-31 00:00:00 | 6.95 | 6.90 |
| 2011-07-31 00:15:00 | 6.94 | 6.88 |
| 2011-07-31 00:30:00 | 6.95 | 6.86 |
| 2011-07-31 00:45:00 | 6.96 | 6.88 |
| 2011-07-31 01:00:00 | 6.96 | 6.85 |
| 2011-07-31 01:15:00 | 6.96 | 6.85 |
| 2011-07-31 01:30:00 | 6.97 | 6.86 |
| 2011-07-31 01:45:00 | 6.97 | 6.85 |
| 2011-07-31 02:00:00 | 6.98 | 6.87 |
| 2011-07-31 02:15:00 | 6.99 | 6.88 |
Modeled DO tracks observed within ~0.05-0.1 mg/L.
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Implements the two-station (VFTS) metabolism model as a new model type
in streamMetabolizer. All work targets the dev/two-station integration
branch.
Changes
inst/models/b2_np_oi_tr_plrckm.stan— static Stan model (fixedsyntax, lognormal K600, GPP/ER priors, package naming conventions)
R/mm_data.R— new two-station columns (DO.obs.up, DO.sat.up,DO.obs.down, DO.sat.down, travel.time)
R/mm_validate_data.R— fix pre-existing travel.time grep bug inna_times check
R/mm_ts_prep_data.R— data reshape with upstream lag shiftR/metab_2station.R— metab_2station() implementation +predict_DO.metab_2station()
R/mm_name.R,R/mm_valid_names.R— register bayes_2station typeR/mm_parse_name.R— extend type map for b2_ prefixR/specs.R— bayes_2station specs case; prior defaults matchone-station convention (K600: meanlog=2.484907, sdlog=1.0)
R/metab.R— dispatch to metab_2station()R/data.R,data/two_station_example.rda— 30-day example dataset(Bishop et al. 2026, lom3.70066)
DESCRIPTION— add stats, utils, parallel to ImportsTests
472 passing tests including a real Stan fit against example data.
0 errors | 3 warnings (pre-existing) | 6 notes (5 pre-existing,
1 resolved in this PR)
Test timing: ~192 sec total, metab_2station adds ~20 sec
Known gaps (deferred, noted in code)
names
References
Bishop et al. 2026. A simplified two-station approach for modeling
metabolism in dam tailwaters subject to diel flow variation.
L&O Methods. https://doi.org/10.1002/lom3.70066