solve_numerically {isobxr}

Numerically solve stable isotope box models

Description

A numerical solver of the system of ordinary differential equations (ODES),
describing the evolution of stable isotope ratios in all boxes of a system.
Not intended for manual use.
The numerical solver uses the deSolve::ode function to integrate the stable isotopes ratios over time in each box. It allows the calculation of the evolution of stable isotope ratio in the case of unbalanced outward and inward fluxes of element X in a given box resulting in the accumulation or loss of element X.

Usage

solve_numerically(IN, paths, to_DIGEST_csv = FALSE, return_results = FALSE)

Arguments

IN

input data, edited by sim.single_run (list of dataframes)

paths

paths object edited by sim.single_run (list of characters)

to_DIGEST_csv

if TRUE, edits csv outputs to DIGEST directory
Default is FALSE.

return_results

if TRUE, results returned as a list of R objects.
Default is FALSE.

Value

Numerically determined evolution of stable isotope compositions
and masses of element X in all boxes over the run duration as specified in INPUT file.

Run outputs are stored in a temporary directory and not exported by solve_numerically.

The outputs of the run are stored in the rds output file in the SERIES directory with the following file name structure:
SERIES_ID + RUN_n.rds

Optional csv outputs to DIGEST directory are as follows

1. OUT data file storing initial and final size and delta values in all boxes.
   (file name structure: out_1_N_OUT + RUN name + .csv)

2. evS data file storing the evolution with time of the sizes (masses of element X) of all boxes.
   (file name structure: out_2_N_evS + RUN name + .csv)

3. evD data file storing the evolution with time of the delta values in all boxes.
   (file name structure: out_3_N_evD + RUN name + .csv)