I'm trying to load data from R to Netlogo. I always get the error
Cannot move turtle beyond the worlds edge.
error while turtle 8 running SET
called by procedure LOAD-DATA
called by procedure SETUP
called by Button 'Setup'
I defined the world edge
let minworldx r:get "min(dataTurtle$bcx)"
let maxworldx r:get "max(dataTurtle$bcx)"
letminworldy r:get "min(dataTurtle$bcy)"
let maxworldy r:get "max(dataTurtle$bcy)"
resize-world minworldx maxworldx minworldy maxworldy
The turtles are defined as follows
set dataTurt r:get "dataTurtle" ; transfers data to Netlogo
print dataTurt ; just to test
ask turtles ; reads in data to the variables
[ set color 14
set heading 1
set xcor item who Item 1 dataTurt
set ycor item who Item 2 dataTurt
set label item who Item 0 dataTurt
set P_FertSpace 2000 ; just a value test value
]
How can I ensure that all turtles that I create get the assinged data?
The loop is stopping because there's an error. The error message tells you that the error is because you are trying to put a turtle in a place that doesn't exist.
Does this fix it?
let minworldx floor r:get "min(dataTurtle$bcx)" - 1
let maxworldx ceiling r:get "max(dataTurtle$bcx)" + 1
let minworldy floor r:get "min(dataTurtle$bcy)" - 1
let maxworldy ceiling r:get "max(dataTurtle$bcy)" + 1
resize-world minworldx maxworldx minworldy maxworldy
I have used floor and ceiling to round down and up respectively, and then added or subtracted 1 for extra safety. This should make sure the turtles don't get positioned outside the world boundaries.
Related
I am trying to write a procedure where a turtle of a certain breed asks turtles of the same breed, within a certain distance, the value of a certain variable. The asking turtle will then capture the values add them to it's own, map + them and then reduce + to a single number. Here's the code
ask Teams
[ if AsgnE = "E 1"
[
ask Teams with [ distance myself < 25]
[
; assuming that there are no more then 2 teams within distance
let Val1 []
let Val2 []
let Val3 []
set Val1 Value
set Val2 Value
set Val3 [Value] of self
let Val4 (map + Val1 Val2 Val3)
set Val4 (reduce + Val4)
set Storys1 [Stories] of Epic 0
if Storys1 > 0 [ set TotValue1 Val4 ]
]
]
]
The values of each Team continuously update as long as the go button is pressed. The issue is that the resulting number never matches the aggregate of all the values. As the number updates they never match the totals of the separate Teams. Sometimes the number drops to a lower number (I'm assuming it's representing a single teams value) before jumping back to a higher number.
Any idea on how to fix this?
Thanks
Rudy
My guess is that it's a synchronicity problem. The ask will iterate (in random order) through all the turtles. Let's say it starts with turtle 1 - so turtle 1 updates its value to be the sum of its old value and all the values of the nearby turtles. Then the ask moves on to turtle 2, and turtle 2 happens to be nearby to turtle 1. That means turtle 2 adds all the numbers again, with turtle 1 having its adjusted value. With just these two turtles, the value for turtle 2 gets added in twice because turtle 1 also has it hidden in its new value.
If this is not the behaviour you want, the easiest thing to do is to have an extra variable called something like next-value. Calculate next-value for each turtle as the appropriate sum. Then, in a new ask, get each turtle to set value next-value to update them all at the same time.
Also, your map and reduce seems unnecessarily complicated. If what you are trying to achieve is to add the value of a variable over a bunch of turtles, then you can simply do a sum of the variable after constructing the relevant turtle agentset. But it may be that you simplified for the purposes of the question, in which case just ignore this!
UPDATE ---- added complete model example
turtles-own
[ team
myval
nextval
]
to setup
clear-all
create-turtles 20
[ setxy random-xcor random-ycor
set team one-of ["A" "B"]
set myval 1
]
reset-ticks
end
to go
ask turtles
[ let myteam turtles with [team = [team] of myself]
set nextval sum [myval] of myteam
]
type "total before: " print sum [myval] of turtles
ask turtles
[ set myval nextval
]
type "total after: " print sum [myval] of turtles
end
I am trying to move the turtles one patch to the right if the value of their label is bigger than the previous value, from the previous tick.
How can I do this?
From your comment, your calculation is:
to calculate-value
ask n-of (count turtles * 0.5) turtles
[ set value value + 100
ifelse show-value?
[ set label value ]
[ set label " " ]
]
end
So, you have half the turtles increase their value (which is also their label) by 100 and the other half have no change. Since the turtles that increase their value are the same turtles as the ones that you want to move to the right, you can simply add the instructions for moving inside the code block, something like this:
to calculate-value
ask n-of (count turtles * 0.5) turtles
[ set value value + 100
set heading 90
forward 1
ifelse show-value?
[ set label value ]
[ set label " " ]
]
end
I'm doing a model of some chains of cells (as part of a larger DNA string model). They wiggle around on screen, and when they wiggle so much, that they come close to a cell of the same type in the same string, they must create a link with that cell.
Code below.
It kinda works.... But after I introduced the linking behavior described above, the string breaks into pieces after a short while. I can't figure out why :-) Any ideas?
Thanks,
Palle
breed [cells cell]
cells-own [paired?]
globals [chains]
to setup
clear-all
set chains []
addchain
reset-ticks
end
to go
foreach chains [c -> movechain c]
ask cells [if any? other cells-here with [label = [label] of myself and paired? = false] [
let makker one-of other cells-here with [label = [label] of myself and paired? = false]
create-link-with makker [tie]
set color red
set paired? true
ask makker [set color red set paired? true]
print word label " was found!"
]]
tick
end
to addchain
set chains lput makechain chains
end
to movechain [mylist]
let antalfollowers length mylist - 1
let i antalfollowers
repeat antalfollowers [
ask item i mylist [
move-to (item (i - 1) mylist)
]
set i i - 1
]
ask first mylist [
right random-float wigglefactor
left random-float wigglefactor
fd 1
]
end
to-report makechain
let mylist []
let text "MGIVEQCCTSICSRYQ"
let startx random-xcor / -3
let starty random-ycor / -3
let i 0
repeat length text [
create-cells 1 [
set color green
set shape "circle"
set label item i text
set paired? false
set mylist lput self mylist
setxy startx + i * .75 starty + i * .75
]
set i i + 1
]
report mylist
end
OK - I finally figured out what's going on. This was hard to see. The tricks I used
in order to see it are listed at the bottom of this post.
In the case of a single strand of synthetic DNA floating around,
when two cells of the same type hit and stick, at that point there will
be a loop of all the cells that were between the moving cell and the
cell that got run into in the list of the sequence of cells.
What you need to do is to:
(a) take the cell that just got run into and link it and tie it to the moving
cell, making the moving cell the MASTER of the link [tie]. You do that
already.
(b) remove the cell you just made a SLAVE from the list of cells your code
has to move, because it will now be moved automatically when the master cell
moves.
AND ... importantly ...
(c) repeat steps (a) and (b) for EVERY cell on the list in positions between
the two cells that just collided and stuck.**
That will effectively freeze the configuration of the entire loop and make it
into a single large unit that will move as one unit when the master cell is
moved by your code.
The User Manual states in the subsection on TIE in the section on LINKS:
When the root turtle turns right or left, the leaf turtle rotates
around the root turtle the same amount as if a stiff were attaching
the turtles. When tie-mode is set to “fixed” the heading of the leaf
turtle changes by the same amount.
I think that you do want to set tie-mode to FIXED so the whole cluster will rotate when the master cell rotates.
I think, but have not looked at it, that this algorithm will work even if the linked cell is the very first or very last one on the chain. Better check it though. Maybe the cell that should be the MASTER is the one that got hit, not the one doing the moving.
In the case of two different strands of DNA intersecting,
basically forming an X, or more complicated cases ... I leave it up to you to figure out what you want the larger connected structure to do, and how hit should move. Do BOTH of the leading cells of each strand tug on it at once? Do you need to shut off one of them so there is only one cell moving the crowd? Will you need to change your code that moves the chain to insert one of the chains entirely into the middle of the other chain on the list that moves them in sequence? I don't know!
By the way, to figure this out, I had to:
slow down the motion and
set the color of the cells to [0 255 0 125] which is a half-transparent green
so I could see through them and see through them overlap, and
use the "watch" feature of the Inspector to follow one of the cells I knew
was going to get linked up, and
use the slider in the inspector to zoom up as far as it would go, and
put a 500 millisecond "wait" in side the innermost loop of the motion.
I'm working on your question and have made some progress -- at least I have a revision of your code with some troubleshooting additions to it, and a revision of the Interface. I can't figure out how to attach a model here, or an image of the view you will see when you run it, so I posted the full model and a PNG file in the netlogo-users Google Group.
The revisions do not fully answer your question about how to solve the breaking up of the chain, but they provide a reproducible version of the model that you can be sure will break at step 746 and that you can turn on dense printing and slow action and watch what is going on with attempted moves after that.
Maybe if we both look at that it will be obvious why this is breaking.
One thing I think may be happening is that, once two cells link and tie, your move algorithm no longer is the correct logic for how the knotted chain should move.
Here's the changes that I made:
I added a random-seed command in setup so that the model can be repeatedly run with exactly the same choices in random variables, so we can both look at the results.
I added a "verbose?" switch on the Interface to turn on or off detailed printing of what's going on.
I added a "clear-stop" button that will allow the "stop" commands I put in the model to stop the running using a stop-requested? flag, which the code sets and this button resets so that "go" and "one step" work again after a stop and the ticks counter keeps on incrementing.
I added a msec-per-tick slider to put a fixed number of milliseconds at the end of the go step so the model will run at a speed that is usable for debugging. I don't know how other people can do it -- when I try to use the built-in slider at the top of the interface to control speed, either it's way too slow, or it's way too fast, and I can't seem to be able to tweak it to just right. So I added this kludge.
I guessed what limits you had on your wigglefactor slider on your interface and made one that goes from 0 to 90 (degrees). It works ok and reproduces your bug.
I added some additional tests to prevent the two C-cells that are adjacent in your choice of cells from linking to each other when they discover, as they do sometimes, that they are on the same patch. With a random seed of 23456 your original code ties its own CC adjacent pair together in tick 2 for instance.
(
Here's the revised code, and comments as to how to use it are in the posted model (in netlogo-users) and below after the code as well.
breed [cells cell]
cells-own [paired?]
globals [
chains
stop-requested? ;;//////////////////////////////////////////////////
]
to setup
clear-all
;; random-seed 12345 ;; /////////////// breaks at either step 35 or 45 ////
;; random-seed 23456 ;; ////////////////// ties its own CC in tick 2 ///
random-seed 34567 ;; /////////////////// ties own cc in tick 84 , ties C at 746 and breaks in 6 steps
;;// wow -- it SNIPS TSIC out of the middle of the chain!! snips out CTIS, turtles 7 8 9 and 10
;; cell 6 C is directly followed by cell 11 -- also C
set chains []
addchain
set stop-requested? FALSE ;; ////////////////////////////////////////
reset-ticks
end
to go
if stop-requested? [ stop ] ;;////////////////////////////////////////////
foreach chains [c -> movechain c]
ask cells [if any? other cells-here with [label = [label] of myself and paired? = false
and who != [who] of myself + 1
and who != [who] of myself - 1
] [
let makker one-of other cells-here with [label = [label] of myself and paired? = false]
create-link-with makker [tie]
set color red
set paired? true
ask makker [set color red set paired? true]
print ( word label " was found at tick " ticks)
set stop-requested? TRUE ;;/////////////////////////////////////////////
]]
wait ( msec-per-tick / 1000 ) ;;////////////////////////////////////////
tick
end
to addchain
set chains lput makechain chains
end
to movechain [mylist]
if verbose? [print ( word "\n\nin code at tick " ticks " starting movechain") ];;//////////////
;;if verbose? [ show mylist ]
let antalfollowers length mylist - 1
let i antalfollowers
repeat antalfollowers [
ask item i mylist [
if verbose? [
;;print (word " asking item " i " on mylist to move to item " (i - 1) )
let mover [label] of item i mylist
let moveto [label] of item (i - 1) mylist
let mover-color [color] of item i mylist
let moveto-color [color] of item (i - 1) mylist
;; BLUE one moves TO the YELLOW ONE at the end of this second
print (word " move " mover " to " moveto )
ask item i mylist [set color blue set shape "square" set size 2]
ask item (i - 1) mylist [set color yellow set shape "square" set size 2]
display
wait 4
ask item i mylist [set color mover-color set shape "circle" set size 1]
ask item (i - 1) mylist [set color moveto-color set shape "circle" set size 1]
display
]
move-to (item (i - 1) mylist)
;;print word "just moved follower " i ;;//////////////////////////
;; wait 0.1 ;;////////////////////////////////////////////////////
]
set i i - 1
]
ask first mylist [
right random-float wigglefactor
left random-float wigglefactor
fd 1
]
end
to-report makechain
let mylist []
let text "MGIVEQCCTSICSRYQ" ;; NOTE - this has a repeat of CC in it which SOMETIMES gets tied (23456 tick 2)
let startx random-xcor / -3
let starty random-ycor / -3
let i 0
repeat length text [
create-cells 1 [
set color green
set shape "circle"
set label item i text
set paired? false
set mylist lput self mylist
setxy startx + i * .75 starty + i * .75
]
set i i + 1
]
report mylist
end
to clear-stop ;;////////////////////////////////
set stop-requested? FALSE ;;////////////////////////////////
end ;;////////////////////////////////
Anyway, here's how to run it to reproduce the problem and examine it
in fine detail very closely.
WHAT IS IT?
model of DNA in motion modified for troubleshooting. When a "C" cell
touches another "C" cell in step 746, and sets a link between the two
C cells and ties them to move as one, the algorithm for motion
breaks somehow. This may help figure out why,
HOW IT WORKS
This has added to it a msec-per-tick slider, default 50, to set the
display speed about right if you leave the usual speed slider at the
very top in the middle (normal).
I also added a button ("clear stop") and a switch ( verbose?)
normally off. With verbose? ON, the model runs very very slowly and
color codes which cell is about to move to which cell ( blue is moving
to yellow ) and they both temporarily change to squares.
HOW TO USE IT
1) set msecs-per-tick to 50 2) shut off verbose?, click SETUP, click
GO. The model will run 746 ticks. ( thats with the random-seed set to
a value of 34567 in globals. )
3) After it stops at tick 746. click clear-stop.
NOTICE the CTI group at the upper right. This is logically BETWEEN the
two C-cells which have linked up. This group will be snipped-out of
the moving DNA It has who numbers 7, 8, 9 and 10 as you can see by
inspecting it.
4) click one-step 6 times to advance to where you can see more clearly
that the two groups have become separate. Then turn on verbose? and
click one-step once to watch the gory details with a 4 second pause
between cell-moves and the running commentary in the Command Center
telling which cells are about to move.
I don't understand why something appened in my netlogo code, but finally I found that a global variables change values from turtles to turtles, is this possible?
I noticed this because I have 2 print value in my code like this:
breed [players player]
breed [balls ball]
globals [
TURNS;
TEAM-OWNER
]
to setup
clear-all
reset-ticks
set TURNS 0
setup-players
setup-ball
end
to setup-ball
create-balls 1 [
setxy 0 0
set color orange
set shape "bug"
set size 2.5
]
end
to setup-players
create-players 5 [
setxy 0 0
set color white
set shape "bug"
set size 2.5
]
end
to go
set TURNS TURNS + 1
print word "this is the turns " TURNS
print ( word " values " TEAM-OWNER)
if ticks >= 1000 [ stop ]
ask players [
print ( word " values " TEAM-OWNER)
fd 2
set TEAM-OWNER "red"
]
ask balls [
fd 2
set TEAM-OWNER "black"
]
end
Is this possible? Global values doesn't change it values in all turtles?
This is the print that I got:
this is the turns 1
values 0
values 0
values red
values red
values red
values red
this is the turns 2
values black
values black
values red
values red
values red
values red
It has not be like black 1 times ? and red the other times? And Why I get 2 blacks?
A global variable is global - there is only ONE copy of it and all turtles retrieve and modify the same copy.
Look at this piece of your code:
ask players [
print ( word " values " TEAM-OWNER)
fd 2
set TEAM-OWNER "red"
]
ask balls [
fd 2
set TEAM-OWNER "black"
]
First, every one of your players moves forward two distance units, then sets the value of TEAM-OWNER to "red". If you have 10 players, then the global variable TEAM-OWNER is being set to red 10 times. Then every one of your balls moves forward two distance units and sets the variable TEAM-OWNER to "black". As long as you have one (or more) balls, then the global variable will be overwritten.
A global variable is used for something that is the same for every turtle in your model.
I'm new in Netlogo . I'm trying to use the code included in the Many Regions Example of the library. But I get one error in this procedure
to keep-in-region [ which-region ]
if region != which-region [
let region-min-pxcor first item (which-region - 1) region-boundaries
let region-max-pxcor last item (which-region - 1) region-boundaries
let region-width (region-max-pxcor - region-min-pxcor) + 1
ifelse xcor < region-min-pxcor [
set xcor xcor + region-width ]
[if xcor > region-max-pxcor [
set xcor xcor - region-width
]
]
]
The error I get is .... any advices? Thanks in advance
-1 no esta mas que o iqual a cero.
error while a-seller 31 running ITEM
called by procedure KEEP-IN-REGION
called by procedure ADJUST
called by procedure GO
called by Botón 'go'
The error you are getting ("-1 isn't greater than or equal to zero.", once translated to English) is caused by passing -1 as an index for the item primitive.
There are two lines in the code that make use of item:
let region-min-pxcor first item (which-region - 1) region-boundaries
let region-max-pxcor last item (which-region - 1) region-boundaries
As you can see (which-region - 1) is the expression passed to item as index. If you are getting -1, it must be because which-region = 0.
In the "Many Regions Example" model, region 0 is reserved for the patches that are not part of any regions, namely, the patches that act as region boundaries. The regions themselves are numbered from 1.
Look in your code for the place where keep-in-region is called and make sure that you are using a region number that is between 1 and the number of regions you have (inclusively).
Disclaimer: I originally wrote the "Many Regions" code example. Maybe I could have used a value like nobody for the patches outside of any region and number the actual regions starting from 0 instead of one, but I don't remember if I actively decided against it or just didn't think of it.