New babies born outside the home range of mother

GoogleCodeExporter commented 9 years ago

I am breaking this out of Nicks original post as it is a separate issue.

Original issue reported on code.google.com by ran...@mwwb.net on 6 Oct 2009 at 11:44

GoogleCodeExporter commented 9 years ago

Original comment by ran...@mwwb.net on 6 Oct 2009 at 12:10

Added labels: Priority-High
Removed labels: Priority-Medium

GoogleCodeExporter commented 9 years ago

I am not sure if this will help or not. I ran a test where I started with 
initial 
residents and then swapped out the social map (mostly testing other issue). 
When I 
looked at the breeding in animal.log, though I saw something that seemed odd to 
me:

11:02:51:648:  inside winter kill for resident number 20
11:02:51:648:  inside winter kill with roll of 0.791891629710743
11:02:51:648:  my chance of winter kill is 0
11:05:25:304:  inside set inital sleeptime curr time is 10/5/2010  6:00 AM
11:05:25:304:  inside calc sleep getting the number of hours before I go to 
sleep
11:05:25:304:  get the mean and sd for this rest time
11:05:25:304:  inside getDurationMeanAndSD for  0
11:05:25:304:  the mean is 12 sd = 0
11:05:25:304:  new duration id is 1
11:05:25:304:  I will be active for 12
11:05:25:304:  so I will go to sleep at 10/5/2010 6:00 PM
11:05:25:304:  inside setInitialValues for animal 21
11:05:26:117:  
11:05:26:117:  my sex is female
11:05:26:117:  
11:05:26:117:  inside animal dump
11:05:26:117:  My ID number is 21
11:05:26:117:  my X Location is 457509.296079115 my y location is 
632739.010238576
11:05:26:117:  My prob of capturing food is 1
11:05:26:117:  My prob of getting killed is 0
11:05:26:117:  My movement speed is 300
11:05:26:117:  My move tortuosity is 0.5
11:05:26:117:  My current use of food is 1
11:05:26:117:  My perception range is 0.400000005960464
11:05:26:117:  leaving animal dump
11:05:26:117:  
11:05:26:226:  inside breed for resident 
11:05:26:226:  rolling the dice returned 0.0302119041002411
11:05:26:226:  percent breed is 1
11:05:26:226:  my mean is 1
11:05:26:226:  my SD is 0
11:05:26:226:  we are going to have a litter with 1

So in this snippet we finish up the winter kill of residents loop and move into 
breeding. The weird thing is that animal #21 is created before we ever do the 
breeding for a resident. This seems to be an extra animal (in this year I had 
one 
more offspring than expected) and is the only one that was not born in the 
center of 
a mother's HR. Perhaps this is what is leading to animals outside of their 
mother's 
HRs? I have attached the xml. I believe you have all of the maps already but 
just in 
case I have updated test_maps.zip on the FTP site.

Original comment by bpa...@purdue.edu on 27 Oct 2009 at 3:32

Attachments:

hr_swap.xml

GoogleCodeExporter commented 9 years ago

ok so I did see something.

Original comment by ran...@mwwb.net on 27 Oct 2009 at 4:34

GoogleCodeExporter commented 9 years ago

I looked back at v88_time_test results that first had this problem of animals 
being 
born outside HRs (animal log pasted below) and did NOT see an extra animal 
being 'born' after winter kill and before resident breeding. 

So, perhaps the issues are not directly linked? Regardless, version 88 did not 
have 
the issue described by Ben and did in version 104B.

1:26:53:709:  my chance of winter kill is 0
11:26:53:709:  inside winter kill for resident number 3
11:26:53:709:  inside winter kill with roll of 0.125703990052316
11:26:53:709:  my chance of winter kill is 0
11:26:53:709:  inside winter kill for resident number 4
11:26:53:709:  inside winter kill with roll of 0.701440694602877
11:26:53:709:  my chance of winter kill is 0
11:26:53:709:  inside winter kill for resident number 6
11:26:53:709:  inside winter kill with roll of 0.502374214354145
11:26:53:709:  my chance of winter kill is 0
11:26:53:709:  inside winter kill for resident number 7
11:26:53:709:  inside winter kill with roll of 0.940188848385675
11:26:53:709:  my chance of winter kill is 0
11:26:53:709:  inside winter kill for resident number 8
11:26:53:709:  inside winter kill with roll of 0.380896982448593
11:26:53:709:  my chance of winter kill is 0

11:26:53:725:  inside breed for resident 0
11:26:53:725:  rolling the dice returned 0.0821866556453456
11:26:53:725:  percent breed is 1
11:26:53:725:  my mean is 50
11:26:53:725:  my SD is 0
11:26:53:725:  we are going to have a litter with 50
11:26:53:725:  percent chance of having a female is 1
11:26:53:725:  rolling the dice returned 0.516575136928156
11:26:53:725:  rolling the dice returned 0.795440485605709
11:26:53:725:  rolling the dice returned 0.285703809599254
11:26:53:725:  rolling the dice returned 0.663528621040065
11:26:53:725:  rolling the dice returned 0.221528828712892
11:26:53:725:  rolling the dice returned 0.38481293776

Original comment by nmcc...@purdue.edu on 28 Oct 2009 at 4:35

GoogleCodeExporter commented 9 years ago

Ok. I looked at my v88_time_test run again, and a re-run of the same XML.

I had the proper # of offspring born in year 2. More importantly, the 1st 
offspring 
was born inside a female HR in year 2. I was incorrect when I said the v88 run 
had 
animal 10 born outside any female HR. I had the incorrect social map in the 
background when examining this. (I incorrectly thought that the Social Map 
shapefile 
with the highest # was also the newest, depicting all HRs.)

So, Ben's run, with a Social Swap, is the only run I am aware of that had 
offspring 
born outside of female HRs AND incorrect numbers of offspring.

Original comment by nmcc...@purdue.edu on 28 Oct 2009 at 5:16

GoogleCodeExporter commented 9 years ago

I re-ran the time_test XML; this time adding 1 female resident to the initial 
social 
map.

I had proper numbers of offspring, and the 9 offspring I looked at (1 for each 
surviving female resident) started in female home ranges. Good!

This run did not have any swaps. Ben's run above had intitial residents -and- a 
swap. Perhaps the swap is what fouled-up the ordering of breeding Ben saw? Not 
sure.

Original comment by nmcc...@purdue.edu on 29 Oct 2009 at 4:57

GoogleCodeExporter commented 9 years ago

I re-ran teh time_test XML with 1 resident at the start of year 1 (as above), 
and 
now adding an annual social map swap (HR_swap map Ben used). 

Results for breeding were good. Proper number of offspring in year 2, and at 
least 1 
born in each living female's HR in year 2.

Bottom line: adding the swap did not re-create the problem Ben saw. I am going 
to re-
run Ben's test to see if I can re-create the issue; then tweek the run to see 
where 
it is corrected.

Original comment by nmcc...@purdue.edu on 30 Oct 2009 at 4:42

GoogleCodeExporter commented 9 years ago

I re-ran Ben's 10/27 HR_swap run and had the same results he observed: 1 
'extra' 
female (#21) offspring born outside any female reident's home range (actually 
inside 
Male 110's HR, though not in the center).

Note that this problem occurs between years 1 and 2 (2009 and 2010), but not 
between 
2 and 3 (2010 and 2011; when the 'empty' textfiles were written for offspring 
born 
in the last year). So in 2011, we have 8 offspring (empty textfiles) whereas in 
2010 
we have 9 offspring. We should have 8 each year; so 2011 is correct.

Here is the place in the animal.log output where the issue occurs (2009-10) and 
does 
not occur (2010-2011, scroll down):

*********
2009-2010
winter kill, then #21 born, then residents breed
*********
12:53:49:828:  my chance of winter kill is 0
12:56:35:785:  inside set inital sleeptime curr time is 10/5/2010  6:00 AM
12:56:35:785:  inside calc sleep getting the number of hours before I go to 
sleep
12:56:35:785:  get the mean and sd for this rest time
12:56:35:785:  inside getDurationMeanAndSD for  0
12:56:35:785:  the mean is 12 sd = 0
12:56:35:785:  new duration id is 1
12:56:35:785:  I will be active for 12
12:56:35:785:  so I will go to sleep at 10/5/2010 6:00 PM
12:56:35:785:  inside setInitialValues for animal 21
12:56:36:550:  
12:56:36:550:  my sex is female
12:56:36:550:  
12:56:36:550:  inside animal dump
12:56:36:550:  My ID number is 21
12:56:36:550:  my X Location is 457509.296079115 my y location is 
632739.010238576
12:56:36:550:  My prob of capturing food is 1
12:56:36:550:  My prob of getting killed is 0
12:56:36:550:  My movement speed is 300
12:56:36:550:  My move tortuosity is 0.5
12:56:36:550:  My current use of food is 1
12:56:36:550:  My perception range is 0.400000005960464
12:56:36:550:  leaving animal dump
12:56:36:550:  
12:56:36:628:  inside breed for resident 
12:56:36:628:  rolling the dice returned 0.0217090686884285
12:56:36:628:  percent breed is 1
12:56:36:628:  my mean is 1
12:56:36:628:  my SD is 0

*********
2010-2011
winter kill, then residents breed, so correct I think
*********
01:05:50:014:  my chance of winter kill is 0
01:05:50:014:  inside winter kill for resident number 16
01:05:50:014:  inside winter kill with roll of 0.265927842476372
01:05:50:014:  my chance of winter kill is 0
01:05:50:014:  inside winter kill for resident number 17
01:05:50:014:  inside winter kill with roll of 0.390097476257988
01:05:50:014:  my chance of winter kill is 0
01:05:50:014:  inside winter kill for resident number 18
01:05:50:014:  inside winter kill with roll of 0.575778346311198
01:05:50:014:  my chance of winter kill is 0
01:05:50:014:  inside breed for resident 
01:05:50:014:  rolling the dice returned 0.410860332851699
01:05:50:014:  percent breed is 1
01:05:50:014:  my mean is 1
01:05:50:014:  my SD is 0
01:05:50:014:  we are going to have a litter with 1
01:05:50:014:  percent chance of having a female is 1
01:05:50:014:  rolling the dice returned 0.79312703050353
01:05:50:014:  we have 0 males
01:05:50:014:  we have 1 females
01:05:50:014:  inside set inital sleeptime curr time is 10/5/2011  6:00 AM
01:05:50:014:  inside calc sleep getting the number of hours before I go to 
sleep
01:05:50:014:  get the mean and sd for this rest time
01:05:50:014:  inside getDurationMeanAndSD for  0
01:05:50:014:  the mean is 12 sd = 0
01:05:50:014:  new duration id is 1
01:05:50:014:  I will be active for 12
01:05:50:014:  so I will go to sleep at 10/5/2011 6:00 PM
01:05:50:014:  inside setInitialValues for animal 30
01:05:50:592:  
01:05:50:592:  my sex is female
01:05:50:592:  
01:05:50:592:  inside animal dump
01:05:50:592:  My ID number is 30

Original comment by nmcc...@purdue.edu on 2 Nov 2009 at 1:11

GoogleCodeExporter commented 9 years ago

Stupid, stupid stupid! I finally figured out why we were getting animals born 
outside of their mothers' HRs. I completely overlooked the fact that I had 
included 
a yearly release of a single animal in the xml that I was basing all of my runs 
off 
(and having Nick base his runs off). So the animal "born" outside the HRs that 
we 
kept seeing was, in fact, released at the correct location. Sorry for the waste 
of 
time Nick and Bob. Now we can get back to actual issues.

Original comment by bpa...@purdue.edu on 2 Nov 2009 at 2:57

Changed state: Invalid

cday41 / paz-search

New babies born outside the home range of mother #40