I am modeling diffusion in my model, but I think I am getting a calculation artifact due to NetLogo sequentially updating individual patches. I will not be using the diffuse command (due to inaccurate diffusion). However, much like how this command works, I would like to update all the calculations of the patches simultaneously, rather than sequentially. I have a slight recollection of seeing some sample code that used values at the beginning of the tick, however I can´t seem to find it now.
Specifically, I need help programming a way to store patch values at the turn of each tick, and then carry out a simultaneous calculation based on these stored values.
Great question. As you indicate, basically you want to calculate the new value of the variable in one ask block, but store it in a separate variable, and then update the actual value of the variable in a second ask block, like so:
turtles-own [
value
new-value
]
...
to go
ask patches [
;; Change this line to however you want the diffusion to work
set new-value 0.5 * value + sum [ 0.5 * value / 4 ] of neighbors4
]
ask patches [
set value new-value
]
end
This way all patches calculate their updated values from the same information, and then actually update the values themselves simultaneously.
Related
I am working on a model which is supposed to act like a human tissue. It is composed of only patches which represent the human cells. The cells replicate over time, and I want to introduce unique IDs to each of the individual patches (cells). These IDs should also carry over to the daughter cells after the replication. I cannot seem to find a good starting point for this and not sure how to approach it.
This is the code I tried but it is not working to even at least give each patch a unique ID. Track clones is supposed to give each of the patches an ID and I will later introduce more to the code to track individual patches and their division over time.
to track-clones
; let patch-list patches
; let patch-count count patches
; foreach patch-list [
; set id ?1
; ]
end
This will have each patch take unique and sequential IDs:
to assign-ids
ask patches [
set id (max [id] of patches + 1)
]
end
That said, it is not clear to me what you mean, in model's terms, when you say
These IDs should also carry over to the daughter cells after the replication.
given that we don't know how such replication is supposed to take place - but it seems this is a separate issue to address.
PS: the syntax using ? for anonymous procedures is no longer accepted, make sure to check the latest NetLogo Dictionary.
You can quickly assign an initial ID based on the patch coordinates
Ask patches [ set patch-id (pxcor - min-pxcor ) + (pycor - min-pxcor) * world-width
]
Alternately, you can use the patch itself as the patch ID:
Ask patches [ set patch-id self ]
This might make other operations relating to the progenitor patch simpler.
Picture of my behaviourspace menu
I'm working on an agent based model where a variable (agentvariable1) owned by all agents changes every tick. I want to report a time series for the values of this variable for every agent using Behaviourspace.
However, when I measure runs using the following reporter
[agentvariable1] of turtles
the values that are reported for agentvariable1 are randomly shuffled, because "turtles" calls all turtles in a random order, which is different every tick. Because of this the data that is exported is not usable to create a time-series.
Is it posstible to create a reporter in Behaviourspace that reports the values of the agentvariable1 in a sequence that remains the same every tick?
Using sort on an agentset creates a list of those agents sorting them by some criteria. In the case of turtles, they are sorted by their who which means that their relative order will always be the same.
However you cannot directly do [agentvariable1] of sort turtles, because of expects an agent/agentset but you are giving it a list.
What you can do is creating a global variable as a list: at each tick the list is emptied, and later all turtles (sorted as per sort) will append their value to the list.
That list is what you will report in your Behavior Space.
globals [
all-values
]
turtles-own [
my-value
]
to setup
clear-all
reset-ticks
create-turtles 5
end
to go
set all-values (list)
ask turtles [
set my-value random 10
]
foreach sort turtles [
t ->
ask t [
set all-values lput my-value all-values
]
]
show all-values
tick
end
As an alternative to Matteo's answer (which is perfectly suitable and directly addresses your intention, I just present another option depending on preference) you could also pair the variable of interest with some turtle identifier and report that as a list of lists. This adds a bit of flexibility in cases where the number of turtles increases or decreases. In this example, I use who and xcor for simplicity, but you may want to create your own unique turtle identifier for more explicit tracking. With this toy model:
to setup
ca
crt 5
reset-ticks
end
to go
ask turtles [
rt random 30 - 15
fd 1
]
tick
end
to-report report-who-x
report list who xcor
end
At any point, you can call the list with [report-who-x] of turtles to get a list of lists. With a behaviorspace setup such as:
you get an output that would look something like:
I have one doubt:
Context: I have a code in which, briefly, turtles have an integer variable (energy-collected) and from that, patches update their own variable (energy-of-my-agent), as described in the code snippet below.
Problem: The turtle variable is of type int (-1, for example), but the patch variable is a one-element list ( [-1] ).
Question: Should this happen? Otherwise, how can I make the patch variable just an integer value?
ask turtles
[
set energy-collected (energy - euse)
]
ask patches
[
set energy-of-my-agent [energy-collected] of turtles-here
]
Thanks in advance
The main thing you have to consider is what of reports.
In your case turtles-here is an agentset, not a specific agent.
This is because, although you might have a single turtle on a patch, you may also have multiple turtles on a patch. Therefore turtles-here reports an agentset, even if that agentset may be made of a single turtle.
It follows that a collection of values from an agentset, obtained with of (and [energy-collected] of turtles-here is exactly that), will be a list of values - even if that list contains only one element.
Therefore I would say:
Is your model made in such a way that each patch cannot have more than one turtle at a time? Then you could do:
ask patches [
if any? turtles-here [
set energy-of-my-agent [energy-collected] of one-of turtles-here
]
]
In the code above, one-of turtles-here reports a specific agent - not an agentset anymore.
So its variable's value, obtained with of, will be stored as a single value (provided that the agent's variable is not a list itself, but that's not your case).
Can it happen that your patches have more than one turtle at a time? Then, if you're interested in the single patch holding "its" turtles' values, dealing with lists is probably necessary.
Update
I made a connection between this question and your other one suggesting that you want to use patches as elements of matrices.
Maybe this is useful to your case: if your model allows for the possibility of having more than one turtle on the same patch, you might be interested in doing something like:
ask patches [
set energy-of-my-agent sum [energy-collected] of turtles-here
]
As you can see, sum takes a list as input and reports a number. Each patch will take the sum of all the values of energy-collected by turtles standing there, or you can change the calculation using whatever you want (e.g. mean, max etc).
Actually, you can use this approach regardless: this way, even when you have a single turtle on a patch, sum (or any other function taking a lost and returning a value) will give you a single value where before you had a list of one value.
In NetLogo: suppose the model has
a turtle (0) of breed A with undirected links with 3 turtles (1, 2 and 3) of breed B;
the turtle 0 has an attribute named "number-of-links" that equals 3.
Now, let one of the 3 neighbors of 0 dies..
How can I program turtle 0 to change its number-of-links automatically to 2?
If all you want is a way of keeping track of the number links, use count my-links instead of a custom variable.
In general, the least bug prone way of having a value update when the number of links changes is to compute that value when you need it. For number of links, this is simply count my-links. For more complicated things, wrap them in a reporter:
to-report energy-of-neighbors
report sum [ energy ] of link-neighbors
end
If this doesn't work for whatever reason (agents need to react to a link disappearing or you're seeing a serious, measurable performance hit from calculating on the fly), you'll have to make the updates yourself when the number of links change. The best way to do this is to encapsulate the behavior in a command:
to update-on-link-change [ link-being-removed ] ;; turtle procedure
; update stuff
end
and then encapsulate the things that can cause the number of links to change (such as turtle death) in commands as well:
to linked-agent-death ;; turtle procedure
ask links [
ask other-end [ update-on-link-change myself ]
]
die
end
As part of the setup procedure I am trying to use a slider to set the density of patches which will be displayed and assigned a random value. The slider on the interface for density ranges 0 to 100 and the random value of the patch is set using an input on the interface. This will normally be set in the region go 4. So, if 50% is set the the procedure will assign 50% of the patches with a random value.
When i do i get the following error: "Expected command" and the variable 'error-count' is highlighted in the code.
;; The density of patches to be set with a random value is set using variable init-errors on interface.
;; Every patch uses a task which reports a random value.
;; The random value is set using variable error-count on interface
to setup-random
ask patches [
if (random-float 100.0) < init-errors
[setup task random error-count]
]
end
You need to change:
setup task random error-count
to
setup task [ random error-count ]
Anytime the task body isn't just a single primitive (the "concise task syntax"), it needs to be surrounded by square brackets. The error message you're getting happens because task random is valid syntax; NetLogo interprets it as short for task [ random ? ]. Then it doesn't know what to do with the following error-count, hence the error.
I am not entirely clear on the task syntax you are using (in particular, why setup is at the beginning of that line) or why you want to use a task here - but that could be a difference in coding style. But the NetLogo compiler is letting you know that it expected a command after the word random but got a value. Since random does expect a value after, I think it's something to do with the setup and task elements. Here's an alternative way of doing what you want, which might be easier. I have also turned the non-zero error patches green so you can see them. This code assumes you have the two sliders you defined in your problem description.
patches-own [errors]
to setup-random
ask patches [
if (random-float 100.0) < init-errors
[ set errors random error-count
set pcolor green ]
]
end