sample_from: Generate samples from a network model

In isotracer: Isotopic Tracer Analysis Using MCMC

Generate samples from a network model

Description

Generate samples from a network model

Usage

sample_from(
  nm,
  at,
  dt = NULL,
  grid_size = NULL,
  end = NULL,
  error.draws = 1,
  cached_ts = NULL,
  cached_ee = NULL
)

Arguments

nm	A networkModel object.
at	Vector of time values at which the samples should be taken.
dt, grid_size	Time step size or grid points, respectively.
end	Final timepoint used in the projections.
error.draws	Integer, number of draws from the error distribution for each sample (default: 1).
cached_ts, cached_ee	Used for optimization by other functions, not for use by the package user.

Value

A tibble containing the generated samples.

Examples

library(magrittr)
mod <- new_networkModel() %>%
   set_topo("NH4 -> algae -> daphnia -> NH4")
inits <- tibble::tribble(
     ~comps, ~sizes, ~props, ~treatment,
      "NH4",    0.2,    0.8,    "light",
    "algae",      1,  0.004,    "light",
  "daphnia",      2,  0.004,    "light",
      "NH4",    0.5,    0.8,     "dark",
    "algae",    1.2,  0.004,     "dark",
  "daphnia",    1.3,  0.004,     "dark")
mod <- set_init(mod, inits, comp = "comps", size = "sizes",
                prop = "props", group_by = "treatment")
mod <- add_covariates(mod, upsilon_NH4_to_algae ~ treatment)
mod <- mod %>%
  set_params(c("eta" = 0.2, "lambda_algae" = 0, "lambda_daphnia" = 0,
               "lambda_NH4" = 0, "upsilon_NH4_to_algae|light" = 0.3,
               "upsilon_NH4_to_algae|dark" = 0.1,
               "upsilon_algae_to_daphnia" = 0.13,
               "upsilon_daphnia_to_NH4" = 0.045, "zeta" = 0.1))
spl <- mod %>% sample_from(at = 1:10)
spl

isotracer documentation built on Sept. 22, 2023, 1:07 a.m.