sweep.dyn_2D: Sweep the space of two parameters during the response to a...
In isobxr: Stable Isotope Box Modelling in R

sweep.dyn_2D

R Documentation

Sweep the space of two parameters during the response to a perturbation

Description

A function to assess the influence of two parameters (varying over a range of values) on dynamic evolution of a system in response to a given perturbation.

Usage

sweep.dyn_2D(
  workdir,
  SERIES_ID,
  plot.time_unit = NULL,
  isobxr_master_file = "0_ISOBXR_MASTER",
  sweep_master_file,
  swept_param_1,
  swept_param_2,
  export.data_as_csv_xlsx = TRUE,
  show.delta_plot = TRUE,
  save_outputs = FALSE,
  ask_confirmation = TRUE,
  keep_single_run_rds = FALSE
)

Arguments

`workdir`	Working directory of *0_ISOBXR_MASTER.xlsx* master file, of the dynamic sweep master file (e.g., *0_EXPLO_DYN_MASTER.xlsx*) and where output files will be stored if saved by user. (character string)
`SERIES_ID`	Name of the sweep series belongs to. It determines the folder in which the output files will be stored inside workdir. (character string)
`plot.time_unit`	Time unit to use on plot if different from native time unit. Character string, to be selected among the following: micros, ms, s, min, h, d, wk, mo, yr, kyr, Myr, Gyr Default is NULL.
`isobxr_master_file`	Name of *isobxr excel master file*. Default is "0_ISOBXR_MASTER".
`sweep_master_file`	Name of *sweep.dyn_2D excel master file*. (without file "xlsx" extension).
`swept_param_1`	Set of values of sweeping parameter 1. Formatted data frame, see vignette for further details.
`swept_param_2`	Set of values of sweeping parameter 2. Formatted data frame, see vignette for further details.
`export.data_as_csv_xlsx`	If TRUE, exports full sweep result data as csv and xlsx fo full to sweep digest directory. Default is TRUE.
`show.delta_plot`	If TRUE, prints delta and size time evolution plots in R. Default is TRUE.
`save_outputs`	If TRUE, saves all run outputs to local working directory (workdir). By default, run outputs are stored in a temporary directory and erased if not saved. Default is FALSE.
`ask_confirmation`	If TRUE, asks confirmation to run in interactive sessions. Default is TRUE.
`keep_single_run_rds`	If TRUE, keeps single runs outputs (rds files in SERIES directory). Default is FALSE.

Value

Delta values and box sizes as a function of time in response to a perturbation, in a 2D space of parameters sweep.dyn_2D outputs are saved to workdir if save_outputs = TRUE.

sweep.dyn_2D outputs consist of

single run results in SERIES directory: all single runs results as rds files
(keep_single_run_rds = TRUE)
sweep digest in sweep DIGEST directory (SERIES/DIGEST):
1. isobxr master file archive as xlsx (export.data_as_csv_xlsx = TRUE)
2. sweep.dyn_2D master file archive as xlsx (export.data_as_csv_xlsx = TRUE)
3. sweep.dyn_2D LOG excerpt as csv (export.data_as_csv_xlsx = TRUE)
4. delta_size_vs_t csv of delta and size vs time in 2D space (export.data_as_csv_xlsx = TRUE)
5. plot of delta and size vs. time in 2D space as pdf
6. sweep.dyn_2D results data set as rds, containing:
  1. delta_size_vs_t data frame of delta and size as a function of time
  2. sweeep_master list containing all inputs from sweep master file
  3. sweep_log data frame of sweep specific LOG excerpt
  4. isobxr_master list containing all inputs from isobxr master file
  5. paths list of sweep specific paths

Examples

## Not run: 
sweep.dyn_2D(workdir = "/Users/username/Documents/1_ABC_tutorial",
             SERIES_ID = "sweep_dyn_test",
             isobxr_master_file = "0_ISOBXR_MASTER",
             sweep_master_file = "0_SWEEP_DYN_demo",
             swept_param_1 = data.frame(FROM = c("A"),
                                        TO = c("C"),
                                        ALPHA_MIN = 0.999,
                                        ALPHA_MAX = 1,
                                        ALPHA_STEPS = 0.0005,
                                        EXPLO_TYPES = "EXPLO_1_ALPHA"),
             swept_param_2 = data.frame(BOX_ID = c("B"),
                                        SIZE_MIN = 2100,
                                        SIZE_MAX = 3000,
                                        SIZE_STEPS = 300,
                                        EXPLO_TYPES = "EXPLO_1_SIZE"),
             ask_confirmation = FALSE)

## End(Not run)

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