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.
NAME
r.pi.energy - Individual-based dispersal model for connectivity analysis - energy based.
KEYWORDS
raster
SYNOPSIS
r.pi.energy
r.pi.energy --help
r.pi.energy [-abdi] input=name [costmap=string] [suitability=string] output=name [out_immi=string] [immi_matrix=string] [mig_matrix=string] [binary_matrix=string] [threshold=float] keyval=integer step_length=integer [step_range=float] [perception=integer] [multiplicator=float] n=integer energy=float percent=float [out_freq=integer] [title="phrase"] [--overwrite] [--help] [--verbose] [--quiet] [--ui]
Flags:
- -a
- Set for 8 cell-neighbors. 4 cell-neighbors are default
- -b
- Set if individuals should be set back after leaving area
- -d
- Output diversity map
- -i
- Output Shannon- and Simpson-index
- --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:
- input=name [required]
- Name of input raster map
- costmap=string
- Name of the costmap
- suitability=string
- Name of the suitability raster with values from 0-100
- output=name [required]
- Name for output raster map
- out_immi=string
- Name of the optional raster file for patch immigrants count
- immi_matrix=string
- Name for immigrants matrix ASCII-file
- mig_matrix=string
- Name for migrants matrix ASCII-file
- binary_matrix=string
- Name for binary immigrants(migrants) matrix ASCII-file
- threshold=float
- Percentage of individuals which must have immigrated(migrated) successfully to be considered for the binary immigrants(migrants) matrix
- keyval=integer [required]
- Category value of the patches
- step_length=integer [required]
- Length of a single step measured in pixels
- step_range=float
- Range to choose the next step direction from, in degrees [default = 180°]
- perception=integer
- Perception range
- multiplicator=float
- Attractivity of patches [1-inf]
- n=integer [required]
- Number of individuals
- energy=float [required]
- Initial energy of the individuals
- percent=float [required]
- Percentage of finished individuals desired before simulation ends
- out_freq=integer
- Output an intermediate state of simulation each [out_freq] steps
- title="phrase"
- Title for resultant raster map
Isolation or connectivity of singular patches of a defined landcover
class using individual-based dispersal models. This function is based
on a maximum amount of energy for each individuals dispersing through
the landscape which is deminished by a fricition or cost map. Unlike
the related function
r.pi.energy does this function allows
individuals to stay or move within a patch until the energy is
depleted.
Amount of successful immigrants or emigrants are not taken individual
into account which emigrated from and immigrated into the same patch
(pseudo immigration).
The suitability matrix impacts the step direction, while the costmap
relates to the depletion of assigned energy.
If individuals are moving beyond the mapset borders the indivuals are
set back to their original source patches.
An example for the North Carolina sample dataset:
The amount of successful emigrants (*_emi), immigrants (*_imi), the
percentage of immigrants per patch (*_imi_percent), the amount of lost
indivuals (*_lost), the amount of migrants (*_mig), successful
(*_mig_succ) and unsuccessful migrants (_mig_unsucc) can be retrieved
using this command:
r.pi.energy input=landclass96 output=energy1 keyval=5 n=1000 step_length=5 energy=10 percent=80
introducing costs for movement results in different immigration counts:
r.mapcalc "cost_raster = if(landclass96==5,1,if(landclass96 == 1, 10, if (landclass96==3,2, if(landclass96==4,1,if(landclass96==6,100)))))"
r.pi.energy input=landclass96 output=energy1 keyval=5 n=1000 step_length=5 energy=10 percent=80 costmap=cost_raster
introducing a suitability for the movement:
# the suitability for the next step selection is defined as: class 5
# and 3 (forest and grassland) have a high suitability, while shrubland
# (class 4) only a moderate and water and developed areas (class 6 and 1)
# have a very low suitability:
r.mapcalc "suit_raster = if(landclass96==5,100,if(landclass96 == 3, 100, if (landclass96==1,1, if(landclass96==6,1,if(landclass96==4,50)))))"
r.pi.energy input=landclass96 output=energyiter3 keyval=5 n=1000 step_length=5 energy=10 percent=80 suitability=suit_raster
further settings can be changed and information retrieved:
setting the perception range to 10 pixel:
r.pi.energy input=landclass96 output=energyiter keyval=5 n=1000 step_length=5 energy=10 percent=80 perception=10
increasing the attraction to move towards patches to 10:
r.pi.energy input=landclass96 output=energyiter keyval=5 n=1000 step_length=5 energy=10 percent=80 stats=average multiplicator=10
output of each movement location for a defined step frequency. Here
every 10th step is provided as output raster:
r.pi.energy input=landclass96 output=energyiter keyval=5 n=1000 step_length=5 energy=10 percent=80 stats=average out_freq=10
r.pi.energy.pr,
r.pi.energy,
r.pi
Programming: Elshad Shirinov
Scientific concept: Dr. Martin Wegmann
Department of Remote Sensing
Remote Sensing and Biodiversity Unit
University of Wuerzburg, Germany
Port to GRASS GIS 7: Markus Metz
SOURCE CODE
Available at:
r.pi.energy source code
(history)
Latest change: Mon Jun 28 07:54:09 2021 in commit: 1cfc0af029a35a5d6c7dae5ca7204d0eb85dbc55
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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GRASS Development Team,
GRASS GIS 7.8.8dev Reference Manual