README.md

In hoehler-labgroup/Methanogen_Package: Methanogenesis Model

methanogenlab

About

Note: This model is still work in progress, so some functions may become depreciated as new updates are released.

Installation

You can install methanogenlab from github with the devtools package.

# install.packages("devtools")
devtools::install_github("hoehler-labgroup/methanogenlab")

Usage

There are currently two available models within methanogenlab, methanogenesis.time and methanogenesis.DIC. The underlying computations for each model are quite similar and will produce similar results; the main distinction is whether the model steps in time or through DIC consumed. For the latter, each step consumes a constant amount DIC (and hydrogen) leading to the production of methane, changing the overall chemistry of the closed system and the amount of biomass generated. For methanogenesis.time, however, Monod kinetics dictate the number of new cells generated at each step and can be translated to an amount of DIC necessary for that growth (i.e. a DIC step that will vary as the reaction progresses).

Below is an example using methanogenesis.time with an initial concentrations [CH4], [H2], and [DIC] at 1 μM, 500 μM, and 3.2 mM, respectively.

library(methanogenlab)
library(CHNOSZ) #some parts of CHNOSZ are not imported with methanogenlab, causing certain parts of the model to break. 
                #This will hopefully be corrected for in future updates. You can install CHNOSZ from CRAN.

model <- methanogensis.time(
CH4.initial= 1e-6,
H2.initial= 5e-4,
is.H2.limiting=FALSE,
Ks.H2=10e-6,
DIC.initial= 3.2e-3,
pH.initial= 7.5,
is.CO2.limiting=TRUE,
Ks.CO2=20e-6,
umax=0.6,
temperature= 313.15,
VolumeSolution = 80e-3,
VolumeHeadspace = 20e-3,
time.step=0.1,
total.time=30,
inoculum.cell.number = 1e6,
biomass.yield=2.4,
carbon.fraction=0.44,
cell.weight=30e-15)
)

Documentation for all functions within methanogenlab can be found in the manual

Interactive plot

You can access an online application for methanogenlab here (CURRENTLY DEPRECIATED, NOT UPDATED TO v0.1.2). The repository is located in hoehler-labgroup/shinyApps

hoehler-labgroup/Methanogen_Package documentation built on April 25, 2022, 11:40 a.m.