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NAME
r.pi.searchtime - Individual-based dispersal model for connectivity analysis (time-based)
KEYWORDS
raster,
landscape structure analysis,
connectivity analysis
SYNOPSIS
r.pi.searchtime
r.pi.searchtime --help
r.pi.searchtime [-acdi] input=name [suitability=string] output=name [out_immi=string] [immi_matrix=string] [binary_matrix=string] [threshold=float] keyval=integer step_length=integer [step_range=float] [perception=integer] [multiplicator=float] n=integer percent=float stats=string[,string,...] [maxsteps=integer] [out_freq=integer] [title="phrase"] [--overwrite] [--help] [--verbose] [--quiet] [--ui]
Flags:
- -a
- Set for 8 cell-neighbors. 4 cell-neighbors are default
- -c
- Include cost of the path in the calculation of steps
- -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
- suitability=string
- Name of the costmap 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
- binary_matrix=string
- Name for binary immigrants matrix ASCII-file
- threshold=float
- Percentage of individuals which must have immigrated successfully to be considered for the binary immigrants 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
- percent=float [required]
- Percentage of individuals which must have arrived successfully to stop the model-run
- stats=string[,string,...] [required]
- Statistical method to perform on the values
- Options: average, variance, standard deviation, median, min, max
- maxsteps=integer
- Maximum steps for each individual
- out_freq=integer
- Output an intermediate state of simulation each [out_freq] steps
- title="phrase"
- Title for resultant raster map
Individual-based dispersal model for connectivity analysis (time-based)
This module provides information about the isolation or connectivity
of individual fragments derived of a landcover classification. Unlike
r.pi.energy this module provides information about the time
from emigration to immigration. The individual based dispersal model
results are based on the step length and range, the perception distance
and the attractivity to move towards patches.
The suitability matrix impacts the step direction of individuals. 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 connectivity of patches of the landclass96 class 5 are
computed using the time from emigration to immigration. The step length
is set to 5 pixel, the output statistics are set to average
time and variance of searchtime. For each patch 1000
individuals were released and the model stopped when at least 80% of
all individuals sucessfully immigrated:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000
constrain the angle of forward movement to 10 degrees:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 step_range=10
setting the perception range to 10 pixel:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 perception=10
increasing the attraction to move towards patches to 10:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 multiplicator=10
limiting the amount of steps to 10:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 maxsteps=10
output of each movement location for a defined step frequency. Here
every 10th step is provided as output raster:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 out_freq=10
output of a raster which immigration counts:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 out_immi=immi_counts
output of a binary immigration matrix. Each patch emigration and
immigration for all patch combinations is recorded as 0 or 1:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 binary_matrix=binary_matrix.txt
output of a matrix with immigration counts for each patch:
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 immi_matrix=immi_counts.txt
the previous examples assumed a homogeneous matrix, a heterogenous
matrix can be included using a raster file which values are taken as
costs for movement (0-100):
# it is assumed that our species is a forest species and cannot move
# through water, hence a cost of 100, does not like urban areas
# (class: 6, cost: 10) but can disperse through shrubland (class 4,
# cost=1) better than through grassland (class 3, cost: 2):
r.mapcalc "suit_raster = if(landclass96==5,1,if(landclass96 == 1, 10, if (landclass96==3,2, if(landclass96==4,1,if(landclass96==6,100)))))"
r.pi.searchtime input=landclass96 output=searchtime1 keyval=5 step_length=5 stats=average,variance percent=80 n=1000 suitability=suit_raster
r.pi.searchtime.pr,
r.pi.searchtime.mw,
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.searchtime source code
(history)
Latest change: Tuesday Sep 19 09:59:22 2023 in commit: e76c325998c8cd9053ce012a5adbb79f33ab0779
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GRASS Development Team,
GRASS GIS 8.3.3dev Reference Manual