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NAME

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

KEYWORDS

raster, spread, model, disease

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-

Table of contents

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

SEE ALSO

r.spread

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)


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