This package is considered a duplicate. The official version of this package is found at:https://fawda123.r-universe.dev/EBASE

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/issues0 issues

Pkgdown site:https://fawda123.github.io

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

On CRAN:

jags cpp

3.00 score 202 downloads 14 exports 50 dependencies

Last updated 6 months agofrom:c1323c61c0. Checks:2 OK, 1 NOTE. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 26 2025
R-4.5-linux	NOTE	Mar 26 2025
R-4.4-linux	OK	Mar 26 2025

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 Mar 26 2025.

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

Citation

To cite package ‘EBASE’ in publications use:

Beck M, Herrmann M, Arriola J, Najjar R (2024). EBASE: Estuarine Bayesian Single-Station Estimation Method for Ecosystem Metabolism. R package version 1.1.0, https://CRAN.R-project.org/package=EBASE.

Corresponding BibTeX entry:

  @Manual{,
    title = {EBASE: Estuarine Bayesian Single-Station Estimation Method
      for Ecosystem Metabolism},
    author = {Marcus Beck and Maria Herrmann and Jill Arriola and
      Raymond Najjar},
    year = {2024},
    note = {R package version 1.1.0},
    url = {https://CRAN.R-project.org/package=EBASE},
  }

Readme and manuals

EBASE

R package for Estuarine BAyesian Single-station Estimation (EBASE) method for ecosystem metabolism.

Installation

Install the package as follows:

# Install EBASE in R:
install.packages('EBASE', repos = c('https://fawda123.r-universe.dev', 'https://cloud.r-project.org'))

The JAGS software must also be installed to use this package. Follow the instructions in the link to download and install the version appropriate for your operating system.

Minimal example

library(dplyr)
library(lubridate)
library(doParallel)

# get four days of data
dat <- exdat %>%
  filter(month(DateTimeStamp) == 6 & day(DateTimeStamp) %in% 1:4)

##
# run ebase with defaults

# setup parallel backend
cl <- makeCluster(2)
registerDoParallel(cl)

res <- ebase(dat, interval = 900, Z = 1.85)

stopCluster(cl)

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