Please not that not everything is fully automated or well organized.
In command line:
Rscript run_r_pops_slf_simple.R
The other R scripts have currently some hardcoded paths which work only in Docker and need to be adjusted for a native run. (This should be fixed in the future.)
docker build -t rpopstests .
docker run -v /your/local/dir:/outputs -it rpopstests
The comparison script can be executed, e.g., using:
grass --tmp-location XY --exec ./run_comparison_pops_t10x10.sh
The script also executes the GRASS GIS part.
The latest version of the module is in a separate Git repository (unknown to GRASS GIS) and it contains submodules, so we need to do the download part of the process manually using Git.
url="https://github.com/ncsu-landscape-dynamics/r.pops.spread"
git clone --recursive $url
grass --tmp-location XY --exec g.extension r.pops.spread url=r.pops.spread
- Spotter lantern fly: See
run_r_pops_slf_simple.Rfor a work-in-progress script which should be replaced byrun_r_pops_slf.R.
A data directory needs to be placed in the current directory (whatever
is the current directory for the R, GRASS GIS, or Docker execution).
The expected content of the data directory is:
data/
├── slf
│ ├── avg_spread_crit_temp_slf_2018_2022_pm.tif
│ ├── avg_spread_temp_coefficient_slf_2018_2022_pm.tif
│ ├── initial_infections_2018_single_count_pm_prop.tif
│ ├── total_hosts.tif
│ └── tree_of_heaven_0.50.tif
├── t100x100
│ ├── all_plants.tif
│ ├── host.tif
│ ├── initial_infections_multi.tif
│ ├── initial_infections_single.tif
│ ├── temp_all.tif
│ ├── temp_none.tif
│ ├── temp_some.tif
│ ├── weather_0dot25.tif
│ ├── weather_0dot25.tif.aux.xml
│ ├── weather_0dot50.tif
│ ├── weather_0dot50.tif.aux.xml
│ ├── weather_0dot75.tif
│ ├── weather_0dot75.tif.aux.xml
│ ├── weather_0.tif
│ ├── weather_0.tif.aux.xml
│ ├── weather_1.tif
│ ├── weather_1.tif.aux.xml
│ ├── weather.tif
│ └── weather.tif.aux.xml
└── t10x10
├── ...
- The native run will use whatever you have installed.
- The Docker for R installs the latests version.
- A custom wrapper around PoPS package is in
pops_multiple.R. - Docker for GRASS GIS is missing.
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