collate_run: Collate Vortex .run output files

In carlopacioni/vortexR: Post Vortex Simulation Analysis

Collate Vortex .run output files

Description

collate_run collates all Vortex output files with extension .run matching the project and scenario name in a given directory into one named list.

Usage

collate_run(
  project,
  scenario,
  npops = 1,
  dec_sep = ".",
  dir_in = NULL,
  save2disk = TRUE,
  dir_out = "ProcessedData",
  verbose = TRUE
)

Arguments

project	The Vortex project name to be imported
scenario	The scenario name
npops	The total number of simulated populations including the metapopulation
dec_sep	Decimal separator (default ".")
dir_in	The local folder containing Vortex files, default: NULL. If not specified, will fall back to use current working directory.
save2disk	Whether to save the data as rda and csv, default: TRUE
dir_out	The local path to store the output. Default: ProcessedData
verbose	Progress messages, default: TRUE

Details

dir_in may contain other files; only files matching the project and the scenario name will be read.

dir_out is created within the working directory unless a full path is provided.

If no matching files are found in the given directory, an error is reported.

When verbose=TRUE the progress (i.e. the file being read) is reported on screen.

Value

a list with two elements: run, a data.frame with data from all Vortex files and lrun, where the same data are re-arranged in long format

Examples

# Using Pacioni et al. example files. See ?pacioni for more details.
pac.dir <- system.file('extdata', 'pacioni', package='vortexRdata')
# Run collate_run on all .run of the project 'Pacioni_et_al' and
run <- collate_run('Pacioni_et_al', 'ST_LHS', 1, dir_in=pac.dir,
                   save2disk=FALSE)

carlopacioni/vortexR documentation built on May 6, 2022, 12:07 p.m.