cnp_model_mcmc: A function to predict N and P excretion, CNP egestion, CNP...

In fishflux: Model Elemental Fluxes in Fishes

A function to predict N and P excretion, CNP egestion, CNP ingestion rate, using MCMC and stan

Description

This function combines MTE and stoichiometric theory in order to predict nescessary ingestion and excretion processes. A probability distribution is obtained by including uncertainty of parameters and using MCMC sampling with stan.

Usage

cnp_model_mcmc(
  TL,
  param,
  iter = 1000,
  cor = list(ro_Qc_Qn = 0.5, ro_Qc_Qp = -0.3, ro_Qn_Qp = -0.2, ro_Dc_Dn = 0.2, ro_Dc_Dp
    = -0.1, ro_Dn_Dp = -0.1, ro_lwa_lwb = 0.9, ro_alpha_f0 = 0.9),
  ...
)

Arguments

TL	Total length(s) in cm
param	List of all parameter means (add "_m") and standard deviations (add "_sd") Default parameters are set with very low sd's. parameters: Qc_m, Qc_sd: percentage C of dry mass fish Qn_m, Qn_sd: percentage N of dry mass fish Qp_m, Qp_sd: percentage P of dry mass fish Dc_m, Dc_sd: percentage C of dry mass food Dn_m, Dn_sd: percentage N of dry mass food Dp_m, Dp_sd: percentage P of dry mass food ac_m, ac_sd: C-specific assimilation efficiency an_m, an_sd: N-specific assimilation efficiency ap_m, ap_sd: P-specific assimilation efficiency linf_m, linf_sd: Von Bertalanffy Growth parameter, theoretical maximum size in TL (cm) k_m, k_sd: Von Bertalanffy Growth parameter, growth rate (yr^-1) t0_m, tO_sd: Von Bertalanffy Growth parameter (yr) lwa_m, lwa_sd: Parameter length-weight relationship (g cm^-1) lwb_m, lwb_sd: Parameter length-weight relationship mdw_m, wprop_sd: Ratio between dry weight and wet weight of fish F0nz_m, F0nz_sd: N-specific turnover rate F0pz_m, F0pz_sd: P-specific turnover rate f0_m, f0_sd: Metabolic normalisation constant independent of body mass (g C g^-alpha d^-1) alpha_m, alpha_sd: Metabolic rate mass-scaling exponent theta_m, theta_sd: Activity scope r_m, r_sd: Aspect ratio of caudal fin h_m, h_sd: Trophic level v_m, v_sd: Environmental temperature (degrees celcius)
iter	A positive integer specifying the number of iterations. The default is 2000.
cor	A list of correlations between certain parameters: ro_Qc_Qn, ro_Qc_Qp, ro_Qn_Qp, ro_Dc_Dn, ro_Dc_Dp, ro_Dn_Dp, ro_lwa_lwb, ro_alpha_f0
...	Additional arguments rstan::sampling, see ?rstan:sampling

Value

Returns a list with two objects: A stanfit object and a data.frame with a summary of all model components. See extract to extract a summary of predicted variables and limitation to get information on the limiting element.

Examples

library(fishflux)
model <- cnp_model_mcmc(TL = 10, param = list(
Qc_m = 40, Qn_m = 10, Qp_m = 4, theta_m = 3))

fishflux documentation built on May 6, 2022, 9:06 a.m.