Package: EBASE 1.1.0

Marcus Beck

EBASE: Estuarine Bayesian Single-Station Estimation Method for Ecosystem Metabolism

Estimate ecosystem metabolism in a Bayesian framework for individual water quality monitoring stations with continuous dissolved oxygen time series. A mass balance equation is used that provides estimates of parameters for gross primary production, respiration, and gas exchange. Methods adapted from Grace et al. (2015) <doi:10.1002/lom3.10011> and Wanninkhof (2014) <doi:10.4319/lom.2014.12.351>. Details in Beck et al. (2024) <doi:10.1002/lom3.10620>.

Authors:Marcus Beck [aut, cre], Maria Herrmann [aut], Jill Arriola [aut], Raymond Najjar [aut]

EBASE_1.1.0.tar.gz
EBASE_1.1.0.tar.gz(r-4.5-noble)EBASE_1.1.0.tar.gz(r-4.4-noble)
EBASE_1.1.0.tgz(r-4.4-emscripten)EBASE_1.1.0.tgz(r-4.3-emscripten)
EBASE.pdf |EBASE.html✨
EBASE/json (API)
NEWS

# Install 'EBASE' in R:

install.packages('EBASE', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fawda123/ebase/issues

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

Datasets:

exdat - Sample data from Apalachicola NERRS
exres - Example results for four days from Apalachicola NERRS

3.56 score 18 scripts 350 downloads 14 exports 50 dependencies

Last updated 1 months agofrom:c1323c61c0. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 26 2024
R-4.5-linux	OK	Oct 26 2024

Exports:credible_plot credible_prep ebase ebase_eqboxy ebase_form ebase_plot ebase_prep ebase_rho ebase_schmidt ebase_years fit_plot interp_plot metab_update prior_plot

Dependencies:abind boot cli coda codetools colorspace cpp11 doParallel dplyr fansi farver foreach generics ggplot2 glue gtable isoband iterators labeling lattice lifecycle lubridate magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig purrr R2jags R2WinBUGS R6 RColorBrewer rjags rlang scales stringi stringr tibble tidyr tidyselect timechange truncnorm utf8 vctrs viridisLite withr zoo

EBASE overview

Rendered fromEBASE.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-09-25
Started: 2024-03-09

Citation

Readme and manuals

Help Manual

Help page	Topics
Plot credible intervals for a, R, and b	credible_plot
Get credible intervals for a, R, b	credible_prep
Estuarine Bayesian Single-station Estimation method for ecosystem metabolism	ebase
Oxygen saturation	ebase_eqboxy
Format ebase output	ebase_form
Plot results from EBASE	ebase_plot
Prepare data for ebase	ebase_prep
Seawater density calculation	ebase_rho
Schmidt number calculation	ebase_schmidt
Estuarine Bayesian Single-station Estimation method for ecosystem metabolism for long time series	ebase_years
Sample data from Apalachicola NERRS	exdat
Example results for four days from Apalachicola NERRS	exres
Plot observed and modeled dissolved oxygen	fit_plot
Create a diagnostic plot showing interpolated values prior to metabolism estimates	interp_plot
Update metabolism jags fit	metab_update
Plot prior distributions for a, R, and b	prior_plot