NAME
r.fidimo - Calculating fish dispersal in a river network from source populations with species specific dispersal parametersKEYWORDS
Fish Dispersal ModelSYNOPSIS
r.fidimo
r.fidimo --helpr.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]
Flags:
- -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
- --ui
- Force launching GUI dialog
Parameters:
- 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
- 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
- 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]
- Options: 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)
- Options: 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
- Options: no, Confidence Interval, Prediction Interval, Random Value within Confidence Interval
- Default: no
Table of contents
NAME
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.watershedREFERENCES
Fidimo-paperAUTHOR
Johannes Radinger, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin (Germany)SOURCE CODE
Available at: r.fidimo source code (history)
Latest change: Monday Jan 30 19:52:26 2023 in commit: cac8d9d848299297977d1315b7e90cc3f7698730
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