aquarium_mod: A simple aquarium network model, ready to run

In isotracer: Isotopic Tracer Analysis Using MCMC

A simple aquarium network model, ready to run

Description

This network model is the model used in the Quick Start tutorial vignette. It is ready to be run at once with run_mcmc.

Usage

aquarium_mod

Format

An object of class networkModel (inherits from tbl_df, tbl, data.frame) with 1 rows and 4 columns.

Details

The code used to built the model is given in the example section below.

The aquarium_run dataset is a corresponding MCMC run.

Examples

library(tidyverse)
exp <- tibble::tribble(
  ~time.day,  ~species, ~biomass, ~prop15N,
          0,   "algae",     1.02,  0.00384,
          1,   "algae",       NA,   0.0534,
        1.5,   "algae",    0.951,       NA,
          2,   "algae",    0.889,   0.0849,
        2.5,   "algae",       NA,   0.0869,
          3,   "algae",    0.837,   0.0816,
          0, "daphnia",     1.74,  0.00464,
          1, "daphnia",       NA,  0.00493,
        1.5, "daphnia",     2.48,       NA,
          2, "daphnia",       NA,  0.00831,
        2.5, "daphnia",     2.25,       NA,
          3, "daphnia",     2.15,   0.0101,
          0,     "NH4",    0.208,     0.79,
          1,     "NH4",    0.227,       NA,
        1.5,     "NH4",       NA,    0.482,
          2,     "NH4",    0.256,    0.351,
        2.5,     "NH4",       NA,    0.295,
          3,     "NH4",     0.27,        NA
  )
inits <- exp %>% filter(time.day == 0)
obs <- exp %>% filter(time.day > 0)

aquarium_mod <- new_networkModel() %>%
    set_topo("NH4 -> algae -> daphnia -> NH4") %>%
    set_init(inits, comp = "species", size = "biomass",
             prop = "prop15N") %>%
    set_obs(obs, comp = "species", size = "biomass",
                  prop = "prop15N", time = "time.day")

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