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Read simulation run configurations from file

Source: R/utilities.R
read_config.Rd

The format of the configuration file is expected to contain 6 space-separated columns representing, in order:

site_name

Name of simulated site. This is used, for example, when an output file is created.

run_name

Name of this simulation run. Used to differentiate between different runs at the same site. Can be - to indicate no particular name, in which case nothing will be appended in the resulting output file.

year(s)

Specification of years to be simulated. Either a single number or a sequence in R's : notation, i.e. 2013:2022 to indicate all years from 2013 to (including) 2022.

param_file

Filename (not full path) of parameter file to use. The file is assumed to be located in input_dir (confer documentation for that parameter).

weather_file

Filename (not full path) of weather file. See also param_file.

management_file

Filename (not full path) of management file. See also param_file. Can be set to high, middle, low or - if no management data is to be used and the autocut routine shall be employed to simulate cutting events.

Rows starting with a # are skipped.

Usage

read_config(config_file, input_dir = NULL)

Arguments

config_file

Path to the configuration file to be read.

input_dir

Path to directory where input files are located. Defaults to getOptions("growR.input_dir", default = file.path("input")).

Value

A list of ModvegeEnvironment instances corresponding to the configurations in the order they appear in config_file.

Examples

# First, we set up the expected directory structure in a temporary place
tmp = file.path(tempdir(), "test-read_config")
dir.create(tmp)

# We need `force = TRUE` here in order to make the example work in 
# non-interactive settings.
setup_directory(root = tmp, include_examples = TRUE, force = TRUE)
#> [INFO]Initialized directory structure in `/tmp/RtmpxPgtzx/test-read_config`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/posieux_weather.txt` to `/tmp/RtmpxPgtzx/test-read_config/input/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/posieux_parameters.csv` to `/tmp/RtmpxPgtzx/test-read_config/input/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/posieux_management1.txt` to `/tmp/RtmpxPgtzx/test-read_config/input/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/posieux_management2.txt` to `/tmp/RtmpxPgtzx/test-read_config/input/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/sorens_weather.txt` to `/tmp/RtmpxPgtzx/test-read_config/input/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/sorens_parameters.csv` to `/tmp/RtmpxPgtzx/test-read_config/input/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/sorens_management1.txt` to `/tmp/RtmpxPgtzx/test-read_config/input/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/sorens_management2.txt` to `/tmp/RtmpxPgtzx/test-read_config/input/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/posieux1.csv` to `/tmp/RtmpxPgtzx/test-read_config/data/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/posieux2.csv` to `/tmp/RtmpxPgtzx/test-read_config/data/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/sorens1.csv` to `/tmp/RtmpxPgtzx/test-read_config/data/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/sorens2.csv` to `/tmp/RtmpxPgtzx/test-read_config/data/`.
#> [INFO]Copying `/home/runner/work/_temp/Library/growR/extdata/example_config.txt` to `/tmp/RtmpxPgtzx/test-read_config`.
#> [INFO]Copied example files to respective directories.

# Now we can test `read_config`.
read_config(file.path(tmp, "example_config.txt"),
            input_dir = file.path(tmp, "input"))
#> [[1]]
#> <ModvegeEnvironment>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     get_environment_for_year: function (year) 
#>     initialize: function (site_name, run_name = "-", years = NULL, param_file = "-", 
#>     input_dir: /tmp/RtmpxPgtzx/test-read_config/input
#>     load_inputs: function () 
#>     make_filename_for_run: function (run_name) 
#>     management: ManagementData, R6
#>     management_file: sorens_management1.txt
#>     param_file: sorens_parameters.csv
#>     parameters: ModvegeParameters, R6
#>     run_name: -
#>     run_name_in_filename: 
#>     set_run_name: function (run_name) 
#>     site_name: sorens1
#>     weather: WeatherData, R6
#>     weather_file: sorens_weather.txt
#>     years: 2013 2014 2015
#> 
#> [[2]]
#> <ModvegeEnvironment>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     get_environment_for_year: function (year) 
#>     initialize: function (site_name, run_name = "-", years = NULL, param_file = "-", 
#>     input_dir: /tmp/RtmpxPgtzx/test-read_config/input
#>     load_inputs: function () 
#>     make_filename_for_run: function (run_name) 
#>     management: ManagementData, R6
#>     management_file: posieux_management1.txt
#>     param_file: posieux_parameters.csv
#>     parameters: ModvegeParameters, R6
#>     run_name: -
#>     run_name_in_filename: 
#>     set_run_name: function (run_name) 
#>     site_name: posieux1
#>     weather: WeatherData, R6
#>     weather_file: posieux_weather.txt
#>     years: 2013 2014 2015
#>