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.
Related
I want place 1 million fish in a lake at random to do so i have this.
ask patches[ if sum [peces] of patches < 1000000 [ask one-of patches with [mallor = 1][set peces peces + 1]]]
This is taking too long, how would you suggest to make it quicker? I know it´s the sum part as it has to always check, but i dont know how else to do it
A first thing I noticed is that you have the construction:
ask patches [ if ... [ ask one-of patches [...]]]
That first ask patches is completely redundant here. It lets each patch direct another random patch to make a fish. Since you use one-of the second time around I don't expect that the speed impact is too big but it should still help
Next, I suggest counting the fish you have already placed with a single local variable, instead of using sum [peces] of patches 1000000 times. Getting variables from an agent (with of or with) takes a lot of time if you have a lot of agents, and I remember from your previous questions that your number of patches is pretty huge.
Then thirdly, you also check for which patches the mallor = 1 condition is true 1000000 times. That one can also be grouped into a local agentset
let fish-placed 0
let mallor_patches patches with [mallor = 1 ]
while [fish-placed < 1000000] [
ask one-of mallor_patches [
set peces peces + 1
set fish-placed fish-placed + 1
]
]
Disclaimer, I haven't tested any of this code in Netlogo since I don't have the bigger model to test the code in. However I expect it will run a many times faster than what you originally wrote.
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.
I've got a doozy of a Netlogo question. If I have two different breeds of turtles, can the sum of a specified number of one breed's variables BE THE VARIABLE of the other breed?
Here is my train of thought. I’d like to model water usage of multiple households, but that water usage of a household needs to be dependent on a) the fixed values of the house (like water used by a faucet) * b) frequency of use of faucet by a person. With each household containing either 1 or more person (people) and that frequency of use can vary person to person.
The idea of using two turtle breeds would allow me to see how the decisions made by one breed affects the other.
Here is my pseudo code to help illustrate what I was thinking (not intended to be a working code)
globals []
breed [People person]
breed [Community household]
People-own [frequency]
Community-own [waterusefacuet HouseholdWaterUse]
;; =================================================================================================================
;; =================================================================================================================
to setup
clear-all
HouseholdCreation
PersonCreation
reset-ticks
end
to go
ask Community [WaterConsumption]
tick
end
;; =================================================================================================================
;; =================================================================================================================
to HouseholdCreation
ask patches [ sprout-Community n of 1 [
set size 1.0 set shape "square" set color blue
set waterusefacuet (1)
] ]
end
to PersonCreation
ask Community [ hatch-People 1 [
set size 0.5 set shape "circle" set color red
set frequency (1 + random 4)
]]
end
to WaterConsumption
Set HouseholdWaterUse (waterusefacuet * (frequency * # of people) )
end
Why not simply make each patch a household, have each patch have one or more turtles (persons), and then calculate household factors as patch factors? To define communities one could place patches into zones (e.g., if pxcor >= 5 and pxcor <=8 and pycor >=3 and pycor <= 6 set zone 1) <== not meant to be code, just the idea.
You could set patch size to make each patch small and specify a large zone of patches.
can the sum of a specified number of one breed's variables BE THE VARIABLE of the other breed?
Absolutely.
snipsnip for clarification : In my code here, I do not let the water use of people who live in a household BE the water use variable of that household. And generally I would recommend against a solution that lets the state of one (or more) agents be the state of another variable - unless there is a very good reason for it. Having states depend on each other is dangerous because you always have to make sure that you sync the values between agents. More importantly, it's often unnecessary. In my solution here, each person belongs to a household, and when that households calculates its total water use, it asks all its inhabitants to send them their use on that day, and then returns the sum of all those numbers. I hope that makes sense. If not, please do ask.
*< /snipsnip>
You need to use the of keyword though. of allows you direct access to variables from the context/perspective of one or more individual agent. So, let's say we have households and people, and people (because we all have different water use habits) have some frequency of water tap uses. In fact, we could have people draw the amount of water they use every day from a a normal distribution that is unique to them. Let's do that:
breed [people person]
breed [households household]
people-own [
mean-use-per-day ;; mean use per day
sd-use-per-day ;; standard dev per day
my-household ;; the household to which a person belongs
]
to setup
create-households 10 [
hatch-people random 4 + 1 [ ;; between 1 and 4 people in a household
set mean-use-per-day random 5 + 5 ;; mean 5-9
set sd-use-per-day random-float 3 ;; sd 0.00-2.99
set my-household myself ;; we set the person's household to the household that hatched them
]
]
to-report household-water-use ;; household reporter
report sum [random-normal mean-use-per-day sd-use-per-day] of people with [my-household = myself] ;; this creates a list of water uses based on the random use of each person in the household.
end
in order to run this code, you can simply call
show [household-water-use] of households
from the command center. This will give you a list of the water use of each household. Or if you want to just see the water use of one household on one random day, you can try
show [household-water-use] of one-of households
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
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.