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Note: This document is for an older version of GRASS GIS that will be discontinued soon. You should upgrade, and read the current manual page.

Note: This addon document is for an older version of GRASS GIS that will be discontinued soon. You should upgrade your GRASS GIS installation, and read the current addon manual page.


r.fidimo - Calculating fish dispersal in a river network from source populations with species specific dispersal parameters


Fish Dispersal Model


r.fidimo --help
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] [--help] [--verbose] [--quiet] [--ui]


Don't keep basic vector maps (source_points, barriers)
Keep all temporal vector and raster maps
Source population input are real fish counts per cell. Backtransformation into fish counts will be performed.
Allow output files to overwrite existing files
Print usage summary
Verbose module output
Quiet module output
Force launching GUI dialog


River network (raster, e.g. output from r.watershed)
River networks' outlet coordinates: E,N
Barrier point file (vector map)
Column name indicating passability value (0-1) of barrier
Either: Number of random cells with source populations
Or: Source population raster (relative or absolute occurence)
Select fish species
Options: 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
Fish Length [mm] (If no species is given, range=39-810)
Aspect Ratio of Caudal Fin (If no species is given) (valid range 0.51 - 2.29)
Time interval for model step [d]
Options: 1-3650
Default: 30
Share of the stationary component (valid range 0 - 1)
Default: 0.67
Attractiveness of habitat used as weighting factor (sink effect, habitat-dependent dispersal)
Spatially varying and habitat-dependent p factor (float: 0-1, source effect, habitat-dependent dispersal)
kernel truncation criterion (precision)
Options: 0.9, 0.95, 0.99, 0.995, 0.999, 0.99999, 0.999999999, inf
Default: 0.99
fixed seed for generating dispersal parameters
fixed seed for multinomial realisation step
Base name for output raster
Default: fidimo_out
Statistical Intervals
Options: no, Confidence Interval, Prediction Interval, Random Value within Confidence Interval
Default: no

Table of contents


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.


Stream parameters

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!
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:
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:

Source populations

The source populations can be provided either as random points (flag -r), or as fixed source population raster (flag -f).
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.
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

Selected species with predefined L and AR (see R-package 'fishmove').
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').
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').
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').
Share of the stationary component of the population. The value is set to 0.67 by default (my Paper).


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 (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).


SEE ALSO, r.watershed




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

Last changed: (Mo, Sept 20, 2011)


Available at: r.fidimo source code (history)

Latest change: Monday Jun 28 07:54:09 2021 in commit: 1cfc0af029a35a5d6c7dae5ca7204d0eb85dbc55

Note: This document is for an older version of GRASS GIS that will be discontinued soon. You should upgrade, and read the current manual page.

Note: This addon document is for an older version of GRASS GIS that will be discontinued soon. You should upgrade your GRASS GIS installation, and read the current addon manual page.

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