NAME
r.fidimo performs analysis of fish dispersal based on
leptokurtic dispersal kernels. It calculates fish dispersal along river
corridors based on a users stream network input, fish source populations
and species-specific dispersal parameters.
OPTIONS
Stream parameters
- river
- Name of input stream network map (thinned raster map) on which the
calculations of dispersal is performed. In cases of very maeandering rivers
(with bends narrower than the spatial resolution of the analyis (cell size)
it is recommended to run v.generalize and r.thin and/or to use
r.fidimo.river in advance. The stream network should only consist
of tree like structures, as braiding rivers and networks with two-side
connected side arms will not work. Check the raster beforehand carefully!
- outflow_point
- Name of the outflow point txt-file (single point) for the calculation
of the flow direction within the provided river network. The text-file
must only contain a single |-separeted coordinate pair (X|Y; same
coordinate system as the river network raster). The file should not
contain any headings etc. E.g the content of the file can look like:
- barriers
- Name of input barrier text-file indicating the geographical position
and passability of barriers e.g. weirs. The file should contain the
X and Y coordinate and a value for passability (0-1 where 0 is
impassable and 1 is 100% passable). The values must be |-separated:
3543350.8001|6064831.9001|1
3535061.5179|6064457.5321|0.3
Source populations
The source populations can be provided either as random points (flag -r),
or as fixed source population raster (flag -f).
- n_source
- For the random locations; number or percentage of cells containing
source populations. The model selects randomly cell (number specified
by the user) and assigns a starting density of 1 to each occupied cell.
- source_populations
- Input raster map indicating the starting density per cell. All
cells with densities > 0 will act as source populations for the model.
The raster map must have the resolution as the river raster and all
source population cells must also be part of the river raster.
Dispersal parameters
- species
- Selected species with predefined L and AR (see R-package 'fishmove').
- L
- Length of fish which should be modelled. Increasing L is positively
correlated with larger dispersal distances. Setting L will overwrite any
species-settings (see R-package 'fishmove').
- AR
- Aspect ratio of the caudal fin of a fish which should be modelled.
Increasing AR is positively correlated with larger dispersal distances.
etting AR will overwrite any species-settings (see R-package 'fishmove').
- T
- Time interval for one modelling step. The dispersal kernel is time
dependent and increasing T is positively correlated with larger dispersal
istances (see R-package 'fishmove').
- p
- Share of the stationary component of the population. The value is
set to 0.67 by default (my Paper).
Output
- output
- The base name of the output file(s). The output raster files will
be %output%_fit respectively %output%_lwr and %output%_upr if a
statistical interval is set.
- statistical_interval
- Statistical interval (confidence or prediction) derived from the
regression analyis (see R-package 'fishmove'). If a statistical interval
is set, three output maps will be created (fit, lwr and upr).
Dependencies
- RPy2
- NumPy
- SciPy
- Sqlite3
- r.stream.order
SEE ALSO
r.stream.order,
r.watershed
REFERENCES
Fidimo-paper
AUTHOR
Johannes Radinger, Leibniz-Institute of Freshwater Ecology and Inland
Fisheries, Berlin (Germany)
Last changed: (Mo, Sept 20, 2011)