mm_generate_mcmc_file: Generate the models in inst/models/bayes

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

Generate the models in inst/models/bayes

Description

Generate the models in inst/models/bayes

Usage

mm_generate_mcmc_file(
  type = "bayes",
  pool_K600 = c("none", "normal", "normal_sdzero", "normal_sdfixed", "linear",
    "linear_sdzero", "linear_sdfixed", "binned", "binned_sdzero", "binned_sdfixed"),
  err_obs_iid = c(TRUE, FALSE),
  err_proc_acor = c(FALSE, TRUE),
  err_proc_iid = c(FALSE, TRUE),
  err_proc_GPP = c(FALSE, TRUE),
  ode_method = c("trapezoid", "euler"),
  GPP_fun = c("linlight", "satlight"),
  ER_fun = c("constant"),
  deficit_src = c("DO_mod", "DO_obs"),
  engine = "stan"
)

Arguments

type	character. The model type. Options: mle: maximum likelihood estimation (see also metab_mle) bayes: bayesian hierarchical models metab_bayes night: nighttime regression (see also metab_night) Kmodel: regression of daily estimates of K600.daily versus discharge, time, etc., usually for 3-phase estimation of K alone (by MLE or nighttime regression), K vs discharge (using this model), and then GPP and ER with fixed K (by MLE) (see also metab_Kmodel) sim: simulation of DO.obs 'data' for testing other models (see also metab_sim)
pool_K600	character. [How] should the model pool information among days to get more consistent daily estimates for K600? Options (see Details for more): none: no pooling of K600 normal: K600 ~ N(mu, sigma) linear: K600 ~ N(B[0] + B[1]*Q, sigma) binned: K600 ~ N(B[Q_bin], sigma) where mu ~ N(mu_mu, mu_sigma) and sigma ~ N(sigma_mu, sigma_sigma) complete: applicable only for type='Kmodel', which is generally used in conjunction with preceding estimates of K (e.g., by type='mle' or type='night') and subsequent estimates of GPP and ER (e.g., by type='mle' with daily K600 values specified)
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_acor	logical. Should autocorrelated process error (with the autocorrelation term phi fitted) be included?
err_proc_iid	logical. Should IID process error be included?
err_proc_GPP	logical. Should IID process error in GPP be included? This kind of error occurs only during the day and is used to adjust GPP before passing that adjusted GPP into the dDO/dt equation. The GPP_inst variable is the corrected GPP, and a new variable, GPP_inst_partial, contains the pre-adjustment GPP estimates
ode_method	character. The method to use in solving the ordinary differential equation for DO. Options: euler, formerly Euler: the final change in DO from t=1 to t=2 is solely a function of GPP, ER, DO, etc. at t=1 trapezoid, formerly pairmeans: the final change in DO from t=1 to t=2 is a function of the mean values of GPP, ER, etc. across t=1 and t=2. for type='mle', options also include rk2 and any character method accepted by ode in the deSolve package (lsoda, lsode, lsodes, lsodar, vode, daspk, rk4, ode23, ode45, radau, bdf, bdf_d, adams, impAdams, and impAdams_d; note that many of these have not been well tested in the context of streamMetabolizer models)
GPP_fun	character. Function dictating how gross primary productivity (GPP) varies within each day. Options: linlight: GPP is a linear function of light with an intercept at 0 and a slope that varies by day. GPP(t) = GPP.daily * light(t) / mean.light GPP.daily: the daily mean GPP, which is partitioned into timestep-specific rates according to the fraction of that day's average light that occurs at each timestep (specifically, mean.light is the mean of the first 24 hours of the date's data window) satlight: GPP is a saturating function of light. GPP(t) = Pmax * tanh(alpha * light(t) / Pmax) Pmax: the maximum possible GPP alpha: a descriptor of the rate of increase of GPP as a function of light satlightq10temp: GPP is a saturating function of light and an exponential function of temperature. GPP(t) = Pmax * tanh(alpha * light(t) / Pmax) * 1.036 ^ (temp.water(t) - 20) Pmax: the maximum possible GPP alpha: a descriptor of the rate of increase of GPP as a function of light NA: applicable only to type='Kmodel', for which GPP is not estimated
ER_fun	character. Function dictating how ecosystem respiration (ER) varies within each day. Options: constant: ER is constant over every timestep of the day. ER(t) = ER.daily ER.daily: the daily mean ER, which is equal to instantaneous ER at all times q10temp: ER at each timestep is an exponential function of the water temperature and a temperature-normalized base rate. ER(t) = ER20 * 1.045 ^ (temp.water(t) - 20) ER20: the value of ER when temp.water is 20 degrees C NA: applicable only to type='Kmodel', for which ER is not estimated
deficit_src	character. From what DO estimate (observed or modeled) should the DO deficit be computed? Options: DO_mod: the DO deficit at time t will be (DO.sat(t) - DO_mod(t)), the difference between the equilibrium-saturation value and the current best estimate of the true DO concentration at that time DO_obs: the DO deficit at time t will be (DO.sat(t) - DO.obs(t)), the difference between the equilibrium-saturation value and the measured DO concentration at that time DO_obs_filter: applicable only to type='night': a smoothing filter is applied over the measured DO.obs values before applying nighttime regression NA: applicable only to type='Kmodel', for which DO deficit is not estimated
engine	character. With which function or software should the model fitting be done? for type='mle': nlm only (the default) for type='bayes': stan only (the default), an external software package that runs MCMC chains for Bayesian models (see http://mc-stan.org) for type='night': lm only (the default) for type='Kmodel': mean, lm, or loess enable different types of relationships between daily K600 and its predictors (nothing, discharge, time, etc.) for type='sim': rnorm only (the default)

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