README

Modification of materials for running BASEmetab. All content derived from the original repository here.

Comparison of metabolism results from Fwoxy, Odum, BASEmetab, and EBASE using Fwoxy estimated DO here.

Comparison of BASEmetab, EBASE, and Odum metabolism results with 2012 Apalachicola generated using the scripts 1-6 here.

Comparison of EBASE and Odum metabolism results with 2012 Apalachicola data, observed dissolved oxygen, here.

Comparison of model optimization length for EBASE with 2012 Apalachicola data, observed dissolved oxygen, here.

Comparison of EBASE output to Fwoxy-estimated output from Apalachicola using multiple priors, here

Comparison of EBASE using 2021 Cat Point data to evaluate optimization period and depth as fixed or constant, here

R scripts

• script1.R Run stripped down BASEmetab code with 2012 Appalachicola data

• script2.R Run BASEmetab using the original package with 2012 Appalachicola data

• script3.R Run stripped down BASEmetab code with instantaneous K with 2012 Appalachicola data

• script4.R Run stripped down BASEmetab code with instantaneous K and metabolic day with 2012 Appalachicola data

• script5.R Run stripped down BASEmetab code with instantaneous K, metabolic day, p and theta estimated with 2012 Appalachicola data

• script6.R Run EBASE with with 2012 Appalachicola data

• fwoxy_basemetab.R Use Fwoxy estimated DO to estimate metabolism flux rates with BASEmetab, as in script5.R

• fwoxy_ebase.R Use Fwoxy estimated DO to estimate metabolism flux rates with EBASE, as in script6.R

• method_comp.R Comparisons of Odum and BASEmetab methods for the different attempts

• apacmp.R Comparison of observed and detided DO metabolic estimates using BASEmetab, EBASE, and Odum for 2012 Apalachicola data

• fwoxyapacmp.R Comparison of EBASE results with multiple priors for synthetic Apalachicola data

• varzfixz.R Create EBASE results with 2021 Cat Point data to evaluate optimization period and depth as fixed or constant

• dat_proc.R Data prep for interoperability between packages

• funcs.R Misc. helper functions