create_calc_NLL: Create a function to compute the negative log likelihood of a...

In USGS-R/streamMetabolizer: Models for Estimating Aquatic Photosynthesis and Respiration

Create a function to compute the negative log likelihood of a set of metabolism parameter values

Description

Produces a function that can be given to nlm(). K600.daily may be passed to that function within the p vector (for fitting K600.daily) or as an additional argument (for fixing it).

Usage

create_calc_NLL(
  calc_DO,
  par.names = environment(environment(calc_DO)$calc_dDOdt)$metab.needs,
  err_obs_iid = FALSE,
  err_proc_iid = FALSE
)

Arguments

calc_DO	a function as from create_calc_DO
par.names	vector of names of parameters that can be expected in calls to the function created by this one (the calc_NLL function)
err_obs_iid	logical. Should IID observation error be included? If not, the model will be fit to the differences in successive DO measurements, rather than to the DO measurements themselves.
err_proc_iid	logical. Should IID process error be included?

Value

a function that will return a negative log likelihood of the data given a set of metab.pars. metab.pars is the first argument of the returned function; its names are defined in par.names.

Examples

data <- data_metab('1','30')[seq(1,48,by=2),]
dDOdt <- create_calc_dDOdt(data, ode_method='trapezoid', GPP_fun='linlight',
  ER_fun='constant', deficit_src='DO_mod')
DO <- create_calc_DO(dDOdt)
NLL <- create_calc_NLL(DO, err_obs_iid=TRUE)
NLL(metab.pars=c(GPP.daily=2, ER.daily=-2, K600.daily=25))
NLL(metab.pars=c(GPP.daily=2, ER.daily=-2, K600.daily=25), DO.mod.1=8)
NLL(metab.pars=c(GPP.daily=4, ER.daily=-7, K600.daily=15))
NLL2 <- create_calc_NLL(DO, par.names=c('GPP.daily','ER.daily'), err_obs_iid=TRUE)
NLL2(metab.pars=c(GPP.daily=2, ER.daily=-2), K600.daily=25)
NLL3 <- create_calc_NLL(DO, 
  par.names=c('GPP.daily','ER.daily','K600.daily','DO.mod.1'), err_obs_iid=TRUE)
NLL3(metab.pars=c(GPP.daily=2, ER.daily=-2, K600.daily=25, DO.mod.1=9))
nlm(NLL, p=c(GPP.daily=2, ER.daily=-2, K600.daily=25))
nlm(NLL2, p=c(GPP.daily=2, ER.daily=-2), K600.daily=31.265)
nlm(NLL3, p=c(GPP.daily=2, ER.daily=-2, K600.daily=25, DO.mod.1=9))

USGS-R/streamMetabolizer documentation built on Aug. 15, 2023, 7:50 a.m.