DOI-USGS/streamMetabolizer

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streamMetabolizer uses inverse modeling to estimate aquatic metabolism (photosynthesis and respiration) from time series data on dissolved oxygen, water temperature, depth, and light.

Stars: 47
Forks: 25
Open beginner issues: 0
Indexed issues: 93

Dominant language: Stan
License: No license data
Last GitHub push: Aug 3, 2026
Latest indexed: Sep 15, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Open All

93 open issues indexed

manage units within metab_mle() Open

enhancement

DOI-USGS/streamMetabolizer#29 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
units for convert_SW_to_PAR Open

enhancement

DOI-USGS/streamMetabolizer#38 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
allow K600 to be specified as instantaneous values Open

enhancement

DOI-USGS/streamMetabolizer#64 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Include NA rows when there are missing data Open

enhancement

DOI-USGS/streamMetabolizer#74 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
data interpolation functions Open

enhancement

DOI-USGS/streamMetabolizer#80 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
filter DO better for nighttime regression Open

enhancement

DOI-USGS/streamMetabolizer#109 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
connect approaches to code in metab_Kmodel help file Open

docs & usability

DOI-USGS/streamMetabolizer#167 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
engine_args Open

DOI-USGS/streamMetabolizer#168 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
vignette on data preparation Open

docs & usability

DOI-USGS/streamMetabolizer#172 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
vignette on fitting hierarchical K Open

docs & usability

DOI-USGS/streamMetabolizer#173 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
flattened call to metab()? Open

DOI-USGS/streamMetabolizer#174 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
add prior explorer - tiny shiny app? Open

enhancement

DOI-USGS/streamMetabolizer#178 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
plot_DO_preds could plot wrong-sign values differently Open

docs & usability

DOI-USGS/streamMetabolizer#192 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
plot_data, plot_data_daily, and/or plot_data_and_data_daily Open

enhancement

DOI-USGS/streamMetabolizer#193 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
revisit Kmodel structural options Open

enhancement

DOI-USGS/streamMetabolizer#208 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
optimize MLE Open

enhancement

DOI-USGS/streamMetabolizer#220 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
predict_metab could offer instantaneous preds Open

enhancement

DOI-USGS/streamMetabolizer#222 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
possible deSolve issue Open

DOI-USGS/streamMetabolizer#225 · 4 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
store data outside of calc_dDOdt Open

DOI-USGS/streamMetabolizer#226 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
rename attach.units to attach_units Open

DOI-USGS/streamMetabolizer#227 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
store predictions in a @preds slot Open

DOI-USGS/streamMetabolizer#228 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
store daily fits as fit$daily for all models Open

DOI-USGS/streamMetabolizer#229 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
decompose main bayes_metab function Open

DOI-USGS/streamMetabolizer#236 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
consider removing the option to split dates in bayes Open

DOI-USGS/streamMetabolizer#237 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
expand get_params to allow non-daily for hierarchical models Open

DOI-USGS/streamMetabolizer#239 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
propagate error from params to GPP, ER in non-bayes models Open

enhancement

DOI-USGS/streamMetabolizer#240 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
streamline metab_model slots Open

DOI-USGS/streamMetabolizer#247 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
address all R CMD check notes Open

wontfix

DOI-USGS/streamMetabolizer#248 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
fix log file organization Open

DOI-USGS/streamMetabolizer#254 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
encourage users to choose all priors explicitly Open

DOI-USGS/streamMetabolizer#255 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
report Rhats in bayes model printouts Open

DOI-USGS/streamMetabolizer#256 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
helpers for setting priors? Open

DOI-USGS/streamMetabolizer#257 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
get unitted to CRAN Open

wontfix

DOI-USGS/streamMetabolizer#267 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
two-station methods Open

enhancement

DOI-USGS/streamMetabolizer#270 · 0 comments · 6 reactions · 0 assignees · Indexed Sep 15, 2026
primer on metabolism modeling Open

DOI-USGS/streamMetabolizer#281 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
vignette on best practices Open

DOI-USGS/streamMetabolizer#286 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
plots for hierarchical K fits Open

DOI-USGS/streamMetabolizer#289 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
improve plot_DO_preds for pi, oipi, and sim models Open

DOI-USGS/streamMetabolizer#294 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
use native CIs for Kmodel Open

DOI-USGS/streamMetabolizer#314 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
document results units in ?metab, ?get_params, etc Open

DOI-USGS/streamMetabolizer#322 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
can GPP be NA rather than 0 for metab_night? Open

DOI-USGS/streamMetabolizer#327 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
message about both GPP=0 and prediction time period for metab_night >24hr day Open

DOI-USGS/streamMetabolizer#328 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
improve predict_DO output for pi, oipi, and sim models Open

DOI-USGS/streamMetabolizer#330 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
plot_daily Open

DOI-USGS/streamMetabolizer#334 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
label daily preds unc as SE, not SD Open

DOI-USGS/streamMetabolizer#335 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Setting priors for K Open

DOI-USGS/streamMetabolizer#373 · 10 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
adjustments for gpp process error Open

DOI-USGS/streamMetabolizer#377 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Problems estimating GPP and ER in artifical, non-mixing containers Open

DOI-USGS/streamMetabolizer#378 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
predict_metab omits MLE errors Open

DOI-USGS/streamMetabolizer#380 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
How to fill missing input data Open

DOI-USGS/streamMetabolizer#388 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

DOI-USGS/streamMetabolizer

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