plot_relaxation: plot relaxation

In isobxr: Stable Isotope Box Modelling in R

plot relaxation

Description

A function to plot the relaxation of isotope ratios in a system, including characteristic times

Usage

plot_relaxation(
  workdir,
  flux_list,
  coeff_list,
  spiked_boxes,
  spike.max_delta = 100,
  n_steps = 10000,
  hidden_boxes = NULL,
  show.residence_time = TRUE,
  show.facets = FALSE,
  time_landmarks = NULL,
  time_as_log10 = TRUE,
  isobxr_master_file = "0_ISOBXR_MASTER",
  time.resolution_cut = NULL
)

Arguments

workdir	Working directory of isobxr excel master file and where output files will be stored if exported by user. (character string)
flux_list	Name of the list of fluxes and initial box sizes to be used for the run, calling (by its header name) a single column of the FLUXES sheet of the isobxr excel master file. (character string)
coeff_list	Name of the list of fractionation coefficients to be used for the run, calling (by its header name) a single column of the COEFFS sheet of the isobxr excel master file. (character string)
spiked_boxes	Vector of box names ("BOX_ID") to be spiked. If several boxes are listed, initial spike will be evenly distributed from 0 to spike.max_delta value.
spike.max_delta	Value of the maximum spike isotope composition (in permil on the delta scale). Default is 100 permil.
n_steps	Number of calculation steps. Determines the resolution of the run. Default is 10000.
hidden_boxes	Vector of boxes to hide from plots. For instance c("SOURCE", "SINK"). Default is NULL.
show.residence_time	If TRUE, displays box-specific residence times on plot. Default is FALSE.
show.facets	If TRUE, displays results in box-specific facets. Default is FALSE.
time_landmarks	Vector of time landmarks to display on x-axis (numerical values).
time_as_log10	If TRUE, uses logarithmic time scale in plot. Default is TRUE.
isobxr_master_file	Name of isobxr excel master file. Default is "0_ISOBXR_MASTER".
time.resolution_cut	Time below which resolution is increased. Default is NULL.

Value

A plots showing the evolution of the isotopic ratios in the system until full relaxation,
defined as the maximum relaxation time multiplied by 10.

Examples

## Not run: 
plot_relaxation(workdir = "/Users/username/Documents/1_ABC_tutorial",
                flux_list = "Fx6_ABC_open_bal",
                coeff_list = "a0",
                n_steps = 1000,
                spiked_boxes = c("SOURCE"))

## End(Not run)

isobxr documentation built on Aug. 23, 2023, 5:06 p.m.