Animover 1 - Revision history

Rsalter at 17:25, 29 December 2023

2023-12-29T17:25:51Z

← Older revision		Revision as of 17:25, 29 December 2023
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	[https://6db9fc8aec9da0846939-3276ccc2b20695183db7791dd451b756.ssl.cf1.rackcdn.com/NMBStudio/Ramps/Ani1CR3.nms '''Download RAMP''']		[https://6db9fc8aec9da0846939-3276ccc2b20695183db7791dd451b756.ssl.cf1.rackcdn.com/NMBStudio/Ramps/Ani1CR3.nms '''Download RAMP''']

	Click [https://www.biorxiv.org/content/10.1101/2023.12.27.573450v1\|here] for a publication describing this RAMP in detail.		Click [https://www.biorxiv.org/content/10.1101/2023.12.27.573450v1 here] for a publication describing this RAMP in detail.

	==About Animover 1==		==About Animover 1==

Rsalter at 17:25, 29 December 2023

2023-12-29T17:25:18Z

← Older revision		Revision as of 17:25, 29 December 2023
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	[https://6db9fc8aec9da0846939-3276ccc2b20695183db7791dd451b756.ssl.cf1.rackcdn.com/NMBStudio/Ramps/Ani1CR3.nms '''Download RAMP''']		[https://6db9fc8aec9da0846939-3276ccc2b20695183db7791dd451b756.ssl.cf1.rackcdn.com/NMBStudio/Ramps/Ani1CR3.nms '''Download RAMP''']

	Click here for a publication describing this RAMP in detail.		Click [https://www.biorxiv.org/content/10.1101/2023.12.27.573450v1\|here] for a publication describing this RAMP in detail.

	==About Animover 1==		==About Animover 1==

Rsalter at 17:21, 22 December 2023

2023-12-22T17:21:28Z

← Older revision		Revision as of 17:21, 22 December 2023
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	The initial pool is defined for each kernel type by the blue annulus shown in the figure. It uses the parameters ''r<sub>min</sub>'', ''r<sub>max</sub>'' and ''ψ'', specified on the Parameter Page and by sliders (with ''θ'' representing the agent's current trajectory), to define a global prototype for that kernel type.		The initial pool is defined for each kernel type by the blue annulus shown in the figure. It uses the parameters ''r<sub>min</sub>'', ''r<sub>max</sub>'' and ''ψ'', specified on the Parameter Page and by sliders (with ''θ'' representing the agent's current trajectory), to define a global prototype for that kernel type.

	Kernels are specified as a sequence of ''phases'', ''&~~rho~~;<sub>i</sub>'', each of which may substitute values of		Kernels are specified as a sequence of ''phases'', ''Φ<sub>i</sub>'', each of which may substitute values of
	''r<sub>min</sub>'', ''r<sub>max</sub>'' and ''ψ'', whose values may depend on the global prototype, to specify its candidate pool ; i.e.,		''r<sub>min</sub>'', ''r<sub>max</sub>'' and ''ψ'', whose values may depend on the global prototype, to specify its candidate pool ; i.e.,

	:''K<sub>type</sub>'' = [''&~~rho~~;<sub>0</sub>''(''r<sub>0,min</sub>, r<sub>0,max</sub>, ψ<sub>0</sub>''), ''&~~rho~~;<sub>1</sub>''(''r<sub>1,min</sub>, r<sub>1,max</sub>, ψ<sub>1</sub>''), ...]		:''K<sub>type</sub>'' = [''Φ<sub>0</sub>''(''r<sub>0,min</sub>, r<sub>0,max</sub>, ψ<sub>0</sub>''), ''Φ<sub>1</sub>''(''r<sub>1,min</sub>, r<sub>1,max</sub>, ψ<sub>1</sub>''), ...]

	Each phase attempts to create a non-empty set of potential targets, but a phase may fail. Phases are tried in sequence until one succeeds. Since the kernel is expected to succeed at making a selection, the last phase in each kernel must be guaranteed to succeed.		Each phase attempts to create a non-empty set of potential targets, but a phase may fail. Phases are tried in sequence until one succeeds. Since the kernel is expected to succeed at making a selection, the last phase in each kernel must be guaranteed to succeed.

Rsalter at 17:14, 22 December 2023

2023-12-22T17:14:47Z

← Older revision		Revision as of 17:14, 22 December 2023
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			[https://www.numerusinc.com/studio/ Download Numerus Studio]

	[https://6db9fc8aec9da0846939-3276ccc2b20695183db7791dd451b756.ssl.cf1.rackcdn.com/NMBStudio/Ramps/Ani1CR3.nms '''Download RAMP''']		[https://6db9fc8aec9da0846939-3276ccc2b20695183db7791dd451b756.ssl.cf1.rackcdn.com/NMBStudio/Ramps/Ani1CR3.nms '''Download RAMP''']

Rsalter at 17:13, 22 December 2023

2023-12-22T17:13:32Z

← Older revision		Revision as of 17:13, 22 December 2023
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	'''Download RAMP'''		[https://6db9fc8aec9da0846939-3276ccc2b20695183db7791dd451b756.ssl.cf1.rackcdn.com/NMBStudio/Ramps/Ani1CR3.nms '''Download RAMP''']

	Click here for a publication describing this RAMP in detail.		Click here for a publication describing this RAMP in detail.

Rsalter: /* Resource Extraction, Depletion and Regrowth */

2023-12-19T17:29:33Z

Resource Extraction, Depletion and Regrowth

← Older revision		Revision as of 17:29, 19 December 2023
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	[[file:extraction2.png\|thumb\|Alternative 2]]		[[file:extraction2.png\|thumb\|Alternative 2]]
	Alternative 2 is the same as Alternative 1 except it has 20 percent metabolic efficiency (not 100 percent), regrowth is reduced by a factor of 10 to deal with too many decimal points in the slider, and size-dependent traveling efficiency has been added.		Alternative 2 is the same as Alternative 1 except it has 20 percent metabolic efficiency (not 100 percent), regrowth is reduced by a factor of 10 to deal with too many decimal points in the slider, and size-dependent traveling efficiency has been added.
			<br sides="both">

Rsalter: /* Resource Extraction, Depletion and Regrowth */

2023-12-19T17:28:29Z

Resource Extraction, Depletion and Regrowth

← Older revision		Revision as of 17:28, 19 December 2023
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	[[file:extraction1.png\|thumb\|Alternative 1]]		[[file:extraction1.png\|thumb\|Alternative 1]]
	In ~~alternative~~ 1, regrowth is equal to the regrowth rate <tt>k_grw</tt> times the amount of resource remaining in the cell.		In Alternative 1, regrowth is equal to the regrowth rate <tt>k_grw</tt> times the amount of resource remaining in the cell.

			[[file:extraction2.png\|thumb\|Alternative 2]]
			Alternative 2 is the same as Alternative 1 except it has 20 percent metabolic efficiency (not 100 percent), regrowth is reduced by a factor of 10 to deal with too many decimal points in the slider, and size-dependent traveling efficiency has been added.

Rsalter: /* Resource Extraction, Depletion and Regrowth */

2023-12-19T17:18:33Z

Resource Extraction, Depletion and Regrowth

← Older revision		Revision as of 17:18, 19 December 2023
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	==Resource Extraction, Depletion and Regrowth==		==Resource Extraction, Depletion and Regrowth==
	[[file:extraction0.png\|thumb\|Default]]		[[file:extraction0.png\|thumb\|Default]]
	The agent "burns" its resource as it moves across the landscape. Resources are transferred to the agent when it occupies a cell containing resources; correspondingly, a cell's resource may experience regrowth. These dynamics are handled by the Extraction RAM, with 3 possible supplied settings, to which the user may add his or her own versions.		The agent "burns" its resource as it moves across the landscape. Resources are transferred to the agent when it occupies a cell containing resources; correspondingly, a cell's resource may experience regrowth. These dynamics are handled by the Extraction RAM, with 3 possible supplied settings, to which the user may add his or her own versions. This RAM is used to choose among models that compute the next values of the individuals energy/size variable,
			''h<sub>t</sub>'' and the cell resource variables ''c<sub>ab,t</sub>'', encoded respectively as <code>next_h</code> and <code>next_c</code>. Current value
			''h<sub>t</sub>'' is encoded as <code>agent.h()</code>, and ''c<sub>ab,t</sub>'' is encoded as <code>cell.c()</code>.

			In the default version, agent resource increases by the smaller of <tt>k_add</tt> and the amount remaining in the cell, and is depleted by the burn rate <tt>k_sub</tt> times the distance traveled. There is no regrowth.

			[[file:extraction1.png\|thumb\|Alternative 1]]
			In alternative 1, regrowth is equal to the regrowth rate <tt>k_grw</tt> times the amount of resource remaining in the cell.

Rsalter: /* Resource Acquisition, Depletion and Regrowth */

2023-12-19T17:01:47Z

Resource Acquisition, Depletion and Regrowth

← Older revision		Revision as of 17:01, 19 December 2023
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	#If the aging computation indicates that the kernel should switch, then the switch takes place.		#If the aging computation indicates that the kernel should switch, then the switch takes place.

	==Resource ~~Acquisition~~, Depletion and Regrowth==		==Resource Extraction, Depletion and Regrowth==
			[[file:extraction0.png\|thumb\|Default]]
	The agent "burns" its resource as it moves across the landscape. Resources are transferred to the agent when it occupies a cell containing resources; correspondingly, a cell's resource may experience regrowth. These dynamics are handled by the Extraction RAM, with 3 possible supplied settings, to which the user may add his or her own versions.		The agent "burns" its resource as it moves across the landscape. Resources are transferred to the agent when it occupies a cell containing resources; correspondingly, a cell's resource may experience regrowth. These dynamics are handled by the Extraction RAM, with 3 possible supplied settings, to which the user may add his or her own versions.

Rsalter at 16:58, 19 December 2023

2023-12-19T16:58:48Z

← Older revision		Revision as of 16:58, 19 December 2023
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	'''Download ~~Ramp~~'''		'''Download RAMP'''

	Click here for a publication describing this ~~Ramp~~ in detail.		Click here for a publication describing this RAMP in detail.

	==About Animover 1==		==About Animover 1==
	'''Animover 1''' is the first in a series of models simulating animal movement over a territory containing resources. In Animover 1 a single agent is foraging over the landscape with the ability to detect and consume a single resource. The amount of resource contained in the agent is depleted by the agent's movement, and the agent will cease moving if its resource level ever reaches 0. The resource appears in ~~clumps~~ randomly across the landscape.		'''Animover 1''' is the first in a series of models simulating animal movement over a territory containing resources. In Animover 1 a single agent is foraging over the landscape with the ability to detect and consume a single resource. The amount of resource contained in the agent is depleted by the agent's movement, and the agent will cease moving if its resource level ever reaches 0. The resource appears in patches randomly across the landscape.

	Movement is governed by a kernel data structure, which selects a set of acceptable target locations for the agent from a set of candidates, based on a number of criteria. The kernel then uses a selection algorithm <ref>Animover 1 uses multinomial selection based on fitness criteria described later.</ref> to determine the actual target. Kernels draw from an initial pool of potential next locations. This pool is a segment of an annulus defined by radii ''r<sub>min</sub>'', ''r<sub>max</sub>'' and angle ''ψ'', as described [[#Kernel Definitions and Rules\|below]].		Movement is governed by a kernel data structure, which selects a set of acceptable target locations for the agent from a set of candidates, based on a number of criteria. The kernel then uses a selection algorithm <ref>Animover 1 uses multinomial selection based on fitness criteria described later.</ref> to determine the actual target. Kernels draw from an initial pool of potential next locations. This pool is a segment of an annulus defined by radii ''r<sub>min</sub>'', ''r<sub>max</sub>'' and angle ''ψ'', as described [[#Kernel Definitions and Rules\|below]].

	Two kernel types are employed, depending on the agent's current circumstances: ''Between Patches (BP)'' and '' Within Patches (WP)''. Generally, an agent using the ''BP'' kernel will try to find a site within a resource ~~clump~~ of maximal utility. When using a ''WP'' kernel, the agent will tend to move within the ~~clump~~ as long as the ~~clump~~'s resource level is above a threshold, and the length of the stay is not too great.		Two kernel types are employed, depending on the agent's current circumstances: ''Between Patches (BP)'' and '' Within Patches (WP)''. Generally, an agent using the ''BP'' kernel will try to find a site within a resource patch of maximal utility. When using a ''WP'' kernel, the agent will tend to move within the patch as long as the patch's resource level is above a threshold, and the length of the stay is not too great.

	The simulation starts with the agent in an initial location, with an initial trajectory ''θ'' and an initial kernel. The current kernel selects the next location and the next kernel. Because selecting the next location may require more than one simulation clock tick, a separate model clock is maintained which advances only when the agent actually moves.		The simulation starts with the agent in an initial location, with an initial trajectory ''θ'' and an initial kernel. The current kernel selects the next location and the next kernel. Because selecting the next location may require more than one simulation clock tick, a separate model clock is maintained which advances only when the agent actually moves.
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	<br clear="both">		<br clear="both">

	==~~Ramp~~ Controls==		==RAMP Controls==
	[[File:console1.png\|800px\|thumb\|Animover 1 Console]]		[[File:console1.png\|800px\|thumb\|Animover 1 Console]]

	===Parameter Sliders===		===Parameter Sliders===
	Sliders belong to one of three groups, determined by their color.		Sliders belong to one of three groups, determined by their color.
	;~~Clump~~ Creation (orange)		;Patch Creation (orange)
	:Resource ~~clumps~~ are laid down randomly over multiple passes when the simulation is reset. These parameters determine the number of passes and control the density of resources within ~~clumps~~, and ~~clumps~~ throughout the landscape.		:Resource patches are laid down randomly over multiple passes when the simulation is reset. These parameters determine the number of passes and control the density of resources within patches, and patches throughout the landscape.
	;Kernel Specifications (yellow)		;Kernel Specifications (yellow)
	:Determines the min and max radii and the angles associated with the ''BP'' and ''WP'' Kernels.		:Determines the min and max radii and the angles associated with the ''BP'' and ''WP'' Kernels.
	;Resource Energy and Regrowth (purple)		;Resource Energy and Regrowth (purple)
	:Determines the agent's initial energy, its consumption and expended energy per time unit, and the resource growth rate. All of these are used by the equations used in the ~~resource consumption and burn ram~~.		:Determines the agent's initial energy, its consumption and expended energy per time unit, and the resource growth rate. All of these are used by the equations used in the Extraction RAM.

	===Buttons===		===Buttons===
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	:The '''CSV''' button saves the current run in a file uniquely identified with the run. Alternatively, selecting '''CSV Auto''' causes the previous run to be saved on reset.		:The '''CSV''' button saves the current run in a file uniquely identified with the run. Alternatively, selecting '''CSV Auto''' causes the previous run to be saved on reset.

	;~~Clump~~ Initialization (orange)		;Patch Initialization (orange)
	:'''Initialization Algorithm''' selects either a random irregular or regular shape. When a regular shape is selected, '''Neighborhood''' determines whether a Moore or Von Neumann neighborhood is used.		:'''Initialization Algorithm''' selects either a random irregular or regular shape. When a regular shape is selected, '''Neighborhood''' determines whether a Moore or Von Neumann neighborhood is used.

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	<br clear="both">		<br clear="both">
	===''BP'' Kernel Description===		===''BP'' Kernel Description===
	The ''BP'' kernel consists of 2 phases, ''Vision'' and ''Movement''. The Vision phase searches for a resource ~~clump~~ and the Movement phase is deployed when no ~~clump~~ is found. If a ~~clump~~ is found, it must pass a resource level test detailed below in order to be acceptable.		The ''BP'' kernel consists of 2 phases, ''Vision'' and ''Movement''. The Vision phase searches for a resource patch and the Movement phase is deployed when no patch is found. If a patch is found, it must pass a resource level test detailed below in order to be acceptable.

	;Vision		;Vision
	[[File:vision0.png\|right\|Vision]]		[[File:vision0.png\|right\|Vision]]
	[[File:vision1.png\|right\|Vision]]		[[File:vision1.png\|right\|Vision]]
	#Computes a candidate pool with ''r<sub>min</sub>'' = 0 and ''ψ'' = ''π'' /2 (''r<sub>max</sub>'' is the same as in the global prototype. If the candidate pool fails to intersect a resource ~~clump~~, proceed to Movement.		#Computes a candidate pool with ''r<sub>min</sub>'' = 0 and ''ψ'' = ''π'' /2 (''r<sub>max</sub>'' is the same as in the global prototype. If the candidate pool fails to intersect a resource patch, proceed to Movement.
	#Determine ''c<sub>max</sub>'', a cell with maximal resource value within the intersection.		#Determine ''c<sub>max</sub>'', a cell with maximal resource value within the intersection.
	#Sum the resources in ''c<sub>max</sub>'' plus the resources in the Moore neighborhood of ''c<sub>max</sub>''.		#Sum the resources in ''c<sub>max</sub>'' plus the resources in the Moore neighborhood of ''c<sub>max</sub>''.
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	===''WP'' Kernel Description===		===''WP'' Kernel Description===
	The ''WP'' kernel consists of 3 phases, ''Consuming'', ''Seeking'' and ''Rim''. The Consuming phase uses a small candidate pool and continues foraging within a ~~clump~~. The Seeking phase is uses a disk for its candidate pool to expand the foraging range. The Rim phase uses a thin, distant region to jump out of the resource patch.		The ''WP'' kernel consists of 3 phases, ''Consuming'', ''Seeking'' and ''Rim''. The Consuming phase uses a small candidate pool and continues foraging within a patch. The Seeking phase is uses a disk for its candidate pool to expand the foraging range. The Rim phase uses a thin, distant region to jump out of the resource patch.

	;Consuming		;Consuming
	[[File:consuming.png\|right\|Consuming]]		[[File:consuming.png\|right\|Consuming]]
	#Computes a candidate pool with a global prototype in which ''r<sub>min</sub>'' = 0, ''r<sub>max</sub>'' is small, and ''ψ = π / 4''		#Computes a candidate pool with a global prototype in which ''r<sub>min</sub>'' = 0, ''r<sub>max</sub>'' is small, and ''ψ = π / 4''
	#Succeeds if the intersection with the current ~~clump~~ passes the same resource test as described above with the ''BP'' kernel; otherwise move to the Seeking phase.		#Succeeds if the intersection with the current patch passes the same resource test as described above with the ''BP'' kernel; otherwise move to the Seeking phase.
	#If successful, choose the target using the multinomial selection process described above.		#If successful, choose the target using the multinomial selection process described above.
	<br sides="both">		<br sides="both">