make_logpost: Set up the function that will calculate the log posterior.

In kdorheim/MENDplus: The microbial-enzyme-mediated decomposition model (MEND) with flexible kinetic and environmental conditions

Description

make_logpost Define the function that will calculate the log posterior. The function returned by make_logpost will be used in the metrop to conduct the mcmc. TODO figure out a better way to document the inputs/

Usage

make_logpost(
  comp,
  params,
  t = seq(0, 1000, 1),
  state = c(P = 10, M = 5, Q = 0.1, B = 2, D = 1, EP = 1e-05, EM = 1e-05, IC = 0, Tot =
    18.10002),
  carbon_pools_func = MENDplus::MEND2013_pools,
  flux_func = MENDplus::MEND2013_fluxes,
  ptable = MENDplus::MEND2013_params,
  verbose = FALSE
)

Arguments

comp	the comparison data frame it must comain at least two columns, time model time IC inorganic carbon, is the the co2 flux from microbial respiration.
params	a named vector of the inital guess of the parameters that will be calibrated in the mcmc.
t	time vector that will be used to run the model.
state	the inital state variables
carbon_pools_func	the function that governs the relationship between the different carbon pools, by default it is set to MEND2013_pools.
flux_func	the function that governs fluxes, by default is it set to MEND2013_fluxes.
ptable	A table of MEND parameter calues, by default is it set to MEND2013_params. While a different table may be used it must contain the following columns. parameter String character of the default MEND parameters. description String character describing the parameter. units String character of the parameter units. value Numeric values taken from the table 2 of the Wang et al. 2013
verbose	a TRUE/FALSE indicator to run the function in verbose mode where messages are printed out, by default set to FALSE.

Value

a function that will return the log posterior.

kdorheim/MENDplus documentation built on Sept. 18, 2020, 6:18 p.m.