GRASS GIS manual: r.spread.sod

NAME

r.spread.sod - Stochastic landscape spread model of forest pathogen - Sudden Oak Death (SOD)

KEYWORDS

SYNOPSIS

r.spread.sod

r.spread.sod --help

r.spread.sod [-s] species=name lvtree=name infected=name output=name [output_series=basename] [stddev=name] [stddev_series=basename] [outside_spores=name] wind=string [moisture_file=name] [temperature_file=name] [weather_file=name] [weather_value=integer] start_time=integer end_time=integer [seasonality=string] [spore_rate=float] [radial_type=string] [scale_1=float] [scale_2=float] [kappa=float] [gamma=float] [random_seed=integer] [runs=integer] [nprocs=integer] [--overwrite] [--help] [--verbose] [--quiet] [--ui]

Flags:

-s: Generate random seed (result is non-deterministic); Automatically generates random seed for random number generator (use when you don't want to provide the seed option)
--overwrite: Allow output files to overwrite existing files
--help: Print usage summary
--verbose: Verbose module output
--quiet: Quiet module output
--ui: Force launching GUI dialog

Parameters:

species=name [required]: Input infected species raster map
lvtree=name [required]: Input live tree (all) raster map
infected=name [required]: Initial sources of infection raster map
output=name [required]: Name for output raster map
output_series=basename: Basename for output series
stddev=name: Standard deviations
stddev_series=basename: Basename for output series of standard deviations
outside_spores=name: Name for output vector map
wind=string [required]: Prevailing wind direction; NONE means that there is no wind; Options: N, NE, E, SE, S, SW, W, NW, NONE
moisture_file=name: Input file with one moisture map name per line; Moisture coefficient
temperature_file=name: Input file with one temperature map name per line; Temperature coefficient
weather_file=name: Text file with weather; Moisture and temperature
weather_value=integer: Value to be used as weather coeficient; Spatially and temporally constant weather coeficient (usually moisture times temperture)
start_time=integer [required]: Start year for the simulation; The first day of the year will be used
end_time=integer [required]: End year for the simulation; The last day of the year will be used
seasonality=string: Seasonal spread; Spread limited to certain months (season); Options: yes, no; Default: yes
spore_rate=float: Spore production rate per week for each infected tree; Default: 4.4
radial_type=string: Radial distribution type; Options: cauchy, cauchy_mix; Default: cauchy
scale_1=float: Scale parameter for the first Cauchy distribution; Default: 20.57
scale_2=float: Scale parameter for the second Cauchy distribution
kappa=float: Concentration parameter for the von Mises distribution; Default: 2
gamma=float: Gamma parameter for Bernoulli distribution; Probability of using the first Cauchy distribution; Options: 0-1
random_seed=integer: Seed for random number generator; The same seed can be used to obtain same results or random seed can be generated by other means.
runs=integer: Number of simulation runs; The individual runs will obtain different seeds and will be avaraged for the output
nprocs=integer: Number of threads for parallel computing; Options: 1-

DESCRIPTION
NOTES
EXAMPLES
REFERENCES
SEE ALSO
AUTHORS

DESCRIPTION

r.spread.sod simulates spread of a plant pathogen, specifically it simulates spread of Sudden Oak Death disease in California and Oregon (USA).

NOTES

The directions of wind consider north (N) to be grid north, if your true north is different direction, you need to make an adjustment.

EXAMPLES

Example of creating file with list of input maps (unix-like command line):

g.list type=raster pattern="moisture_*" mapset=PRISM -m > moistures.txt
g.list type=raster pattern="temperature_*" mapset=PRISM -m > temperatures.txt

Note that the above assumes that the names will be ordered by time. You may need to pipe the result through sort with -n (| sort -n) to achieve this if filenames contain ordinal numbers but are not zero-padded (temperature_001 versus temperature_1). Example of the run of the model (unix-like command line):

r.spread.sod species=lide lvtree=all infected=infected_2005 \
    moisture_file=moistures.txt temperature_file=temperatures.txt \
    output=spread_sod start_time=2005 end_time=2010 \
    rtype=cauchy wind=NE rseed=4

REFERENCES

Ross K. Meentemeyer, Nik J. Cunniffe, Alex R. Cook, Joao A. N. Filipe, Richard D. Hunter, David M. Rizzo, and Christopher A. Gilligan 2011. Epidemiological modeling of invasion in heterogeneous landscapes: spread of sudden oak death in California (1990-2030). Ecosphere 2:art17. DOI: 10.1890/ES10-00192.1
Tonini, Francesco, Douglas Shoemaker, Anna Petrasova, Brendan Harmon, Vaclav Petras, Richard C. Cobb, Helena Mitasova, and Ross K. Meentemeyer. Tangible geospatial modeling for collaborative solutions to invasive species management. Environmental Modelling & Software 92 (2017): 176-188. DOI: 10.1016/j.envsoft.2017.02.020

AUTHORS

Francesco Tonini* (original R version)
Zexi Chen* (C++ version)
Vaclav Petras* (parallelization, GRASS interface)
Anna Petrasova* (single species simulation)

* Center for Geospatial Analytics, NCSU

SOURCE CODE

Available at: r.spread.sod source code (history)