r.fidimo

Calculating fish dispersal in a river network from source populations with species specific dispersal parameters

Command linePython (grass.script)

r.fidimo [-bar] [river=string] [coors=x,y] [barriers=string] [passability_col=name] [n_source=number[%]] [source_populations=string] [species=string] [l=integer] [ar=float] [t=integer] [p=float] [habitat_attract=string] [habitat_p=string] [truncation=string] [seed1=integer] [seed2=integer] [output=name] [statistical_interval=name] [--overwrite] [--verbose] [--quiet] [--qq] [--ui]

Example:

r.fidimo

grass.script.run_command("r.fidimo", river=None, coors=None, barriers=None, passability_col=None, n_source=None, source_populations=None, species=None, l=None, ar=None, t=30, p=0.67, habitat_attract=None, habitat_p=None, truncation="0.99", seed1=None, seed2=None, output="fidimo_out", statistical_interval="no", flags=None, overwrite=False, verbose=False, quiet=False, superquiet=False)

Example:

gs.run_command("r.fidimo")

Parameters

Command linePython (grass.script)

river=string
    River network (raster, e.g. output from r.watershed)
coors=x,y
    River networks' outlet coordinates: E,N
barriers=string
    Barrier point file (vector map)
passability_col=name
    Column name indicating passability value (0-1) of barrier
n_source=number[%]
    Either: Number of random cells with source populations
source_populations=string
    Or: Source population raster (relative or absolute occurrence)
species=string
    Select fish species
    Allowed values: Custom species, Catostomus commersoni, Moxostoma duquesnii, Moxostoma erythrurum, Ambloplites rupestris, Lepomis auritus, Lepomis cyanellus, Lepomis macrochirus, Lepomis megalotis, Micropterus dolomieui, Micropterus punctulatus, Micropterus salmoides, Pomoxis annularis, Cottus bairdii, Cottus gobio, Abramis brama, Barbus barbus, Cyprinus carpio carpio, Gobio gobio, Leuciscus idus, Rutilus rutilus, Squalius cephalus, Tinca tinca, Esox lucius, Fundulus heteroclitus heteroclitus, Ameiurus natalis, Ictalurus punctatus, Morone americana, Etheostoma flabellare, Etheostoma nigrum, Perca fluviatilis, Percina nigrofasciata, Sander lucioperca, Oncorhynchus mykiss, Oncorhynchus gilae, Salmo salar, Salmo trutta fario, Salvelinus fontinalis, Salvelinus malma malma, Thymallus thymallus, Aplodinotus grunniens, Salmo trutta, Gobio gobio, Rutilus rutilus
l=integer
    Fish Length [mm] (If no species is given, range=39-810)
ar=float
    Aspect Ratio of Caudal Fin (If no species is given) (valid range 0.51 - 2.29)
t=integer
    Time interval for model step [d]
    Allowed values: 1-3650
    Default: 30
p=float
    Share of the stationary component (valid range 0 - 1)
    Default: 0.67
habitat_attract=string
    Attractiveness of habitat used as weighting factor (sink effect, habitat-dependent dispersal)
habitat_p=string
    Spatially varying and habitat-dependent p factor (float: 0-1, source effect, habitat-dependent dispersal)
truncation=string
    kernel truncation criterion (precision)
    Allowed values: 0.9, 0.95, 0.99, 0.995, 0.999, 0.99999, 0.999999999, inf
    Default: 0.99
seed1=integer
    fixed seed for generating dispersal parameters
seed2=integer
    fixed seed for multinomial realisation step
output=name
    Base name for output raster
    Default: fidimo_out
statistical_interval=name
    Statistical Intervals
    Allowed values: no, Confidence Interval, Prediction Interval, Random Value within Confidence Interval
    Default: no
-b
    Don't keep basic vector maps (source_points, barriers)
-a
    Keep all temporal vector and raster maps
-r
    Source population input are real fish counts per cell. Backtransformation into fish counts will be performed.
--overwrite
    Allow output files to overwrite existing files
--help
    Print usage summary
--verbose
    Verbose module output
--quiet
    Quiet module output
--qq
    Very quiet module output
--ui
    Force launching GUI dialog

river : str, optional
    River network (raster, e.g. output from r.watershed)
    Used as: input, raster
coors : tuple[str, str] | list[str] | str, optional
    River networks' outlet coordinates: E,N
    Used as: x,y
barriers : str, optional
    Barrier point file (vector map)
    Used as: input, vector
passability_col : str, optional
    Column name indicating passability value (0-1) of barrier
    Used as: name
n_source : str, optional
    Either: Number of random cells with source populations
    Used as: number[%]
source_populations : str, optional
    Or: Source population raster (relative or absolute occurrence)
    Used as: input, raster
species : str, optional
    Select fish species
    Allowed values: Custom species, Catostomus commersoni, Moxostoma duquesnii, Moxostoma erythrurum, Ambloplites rupestris, Lepomis auritus, Lepomis cyanellus, Lepomis macrochirus, Lepomis megalotis, Micropterus dolomieui, Micropterus punctulatus, Micropterus salmoides, Pomoxis annularis, Cottus bairdii, Cottus gobio, Abramis brama, Barbus barbus, Cyprinus carpio carpio, Gobio gobio, Leuciscus idus, Rutilus rutilus, Squalius cephalus, Tinca tinca, Esox lucius, Fundulus heteroclitus heteroclitus, Ameiurus natalis, Ictalurus punctatus, Morone americana, Etheostoma flabellare, Etheostoma nigrum, Perca fluviatilis, Percina nigrofasciata, Sander lucioperca, Oncorhynchus mykiss, Oncorhynchus gilae, Salmo salar, Salmo trutta fario, Salvelinus fontinalis, Salvelinus malma malma, Thymallus thymallus, Aplodinotus grunniens, Salmo trutta, Gobio gobio, Rutilus rutilus
l : int, optional
    Fish Length [mm] (If no species is given, range=39-810)
ar : float, optional
    Aspect Ratio of Caudal Fin (If no species is given) (valid range 0.51 - 2.29)
t : int, optional
    Time interval for model step [d]
    Allowed values: 1-3650
    Default: 30
p : float, optional
    Share of the stationary component (valid range 0 - 1)
    Default: 0.67
habitat_attract : str, optional
    Attractiveness of habitat used as weighting factor (sink effect, habitat-dependent dispersal)
    Used as: input, raster
habitat_p : str, optional
    Spatially varying and habitat-dependent p factor (float: 0-1, source effect, habitat-dependent dispersal)
    Used as: input, raster
truncation : str, optional
    kernel truncation criterion (precision)
    Allowed values: 0.9, 0.95, 0.99, 0.995, 0.999, 0.99999, 0.999999999, inf
    Default: 0.99
seed1 : int, optional
    fixed seed for generating dispersal parameters
seed2 : int, optional
    fixed seed for multinomial realisation step
output : str, optional
    Base name for output raster
    Used as: output, , name
    Default: fidimo_out
statistical_interval : str, optional
    Statistical Intervals
    Used as: name
    Allowed values: no, Confidence Interval, Prediction Interval, Random Value within Confidence Interval
    Default: no
flags : str, optional
    Allowed values: b, a, r
    b
        Don't keep basic vector maps (source_points, barriers)
    a
        Keep all temporal vector and raster maps
    r
        Source population input are real fish counts per cell. Backtransformation into fish counts will be performed.
overwrite: bool, optional
    Allow output files to overwrite existing files
    Default: False
verbose: bool, optional
    Verbose module output
    Default: False
quiet: bool, optional
    Quiet module output
    Default: False
superquiet: bool, optional
    Very quiet module output
    Default: False

DESCRIPTION

r.fidimo performs analysis of fish dispersal based on leptokurtic dispersal kernels. It calculates fish dispersal along river corridors based on a user's 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 meandering rivers (with bends narrower than the spatial resolution of the analysis (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 |-separated 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:

545287.44|1942020.18

• 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 distances (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 analysis (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

Radinger, J., Kail, J., & Wolter, C. (2014). FIDIMO — A free and open source GIS-based dispersal model for riverine fish. Ecological Informatics, 24, 238–247. https://doi.org/10.1016/j.ecoinf.2013.06.002.

AUTHOR

Johannes Radinger, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin (Germany)

SOURCE CODE

Available at: r.fidimo source code (history)
Latest change: Thursday Mar 20 21:36:57 2025 in commit 7286ecf