RMark uneven primary and secondary time intervals

posts related to the RMark library, which may not be of general interest to users of 'classic' MARK

RMark uneven primary and secondary time intervals

Postby NI01 » Mon Oct 08, 2018 12:46 am

Hi everyone,

I am very new to coding and Mark, so I apologise in advance if this is a simple question. :oops: :cry:

Currently I am attempting to run a CJS model (null model to begin with).

My data was collected historically (2011-2017) at very unequal time intervals between primary sessions, additionally secondary sessions run for an unequal period of time.

My capture history (`ch`) is very large (n=2392 days) as is continuous with ‘0’s in-between primary sessions.
To account for this in my model, I calculated the time intervals between each primary session as per the number of discussions I have read online, example of what I have written in RMark:

I first specify the duration between each (primary?) occasion (in our case the number of days),
I then specify the vector in the process.data() function:

Code: Select all
 time.intervals <-c(0,13,55,44,52,26,50,35,146,63,92,45,91,9,57,12,104,109,60,98,99,49,140,48,123,83,97,87,51,39,184,92)

process=process.data(ch, begin.time=1, model="CJS", time.intervals=time.intervals)


I then get an error:

Code: Select all
Error in process.data- Incorrect number of time intervals.


What am I missing here?

If anyone could post some example code for a similar issue, provide some advice or point me in the right direction I would be extremely grateful! I posted sample of my data also.

Code: Select all
Date   ID
24.01.2011   13
27.01.2011   14
10.02.2011   7
10.02.2011   8
14.02.2011   9
14.02.2011   10
15.02.2011   11
15.02.2011   12
12.04.2011   23
13.04.2011   24
13.04.2011   25
20.04.2011   26
20.04.2011   27
20.04.2011   28
4.06.2011   29
4.06.2011   30
4.06.2011   31
5.06.2011   32
5.06.2011   33
5.06.2011   34
5.06.2011   35
28.07.2011   15
28.07.2011   16
28.07.2011   17
30.07.2011   18
30.07.2011   19
30.07.2011   20
30.07.2011   21
30.07.2011   22
1.09.2011   1
2.09.2011   6A290D7
2.09.2011   6A2A31C
2.09.2011   6A29854
3.09.2011   6A2A7C0
3.09.2011   6A290D7
3.09.2011   6A2A31C
3.09.2011   6A29854
23.10.2011   2
23.10.2011   6A2A9D9
23.10.2011   6A2847F
24.10.2011   6A29854
24.10.2011   3
24.10.2011   6A2882F
24.10.2011   6A29854
24.10.2011   6A283B5
25.10.2011   6A2847F
25.10.2011   4
25.10.2011   6A2991C
1.12.2011   6A2847F
1.12.2011   6A29854
2.12.2011   6A29854
2.12.2011   6A2A31C
2.12.2011   6A290D7
3.12.2011   6A2A7C0
3.12.2011   6A29854
3.12.2011   6A2A7C0
3.12.2011   6A2A31C
4.12.2011   6A28670
10.02.2012   6A29854
10.02.2012   5
11.02.2012   6A2A7C0
12.02.2012   6A2A7C0
12.02.2012   6A28E80
12.02.2012   6A29854
10.02.2012   69C42F2
10.02.2012   6A283B5
11.02.2012   6A283B5
11.02.2012   6A2991C
12.02.2012   6
29.04.2012   6A28789
29.04.2012   6A2A800
29.04.2012   6A2A31C
30.04.2012   6A2B5A3
30.04.2012   6A29811
30.04.2012   6A29304
30.04.2012   36
30.04.2012   6A28789
30.04.2012   6A288C5
1.05.2012   6A2A5AD
1.05.2012   6A2B5A3
1.05.2012   6A2A800
1.05.2012   6A29304
1.05.2012   6A28BB3
1.05.2012   6A2A7C0
2.05.2012   6A28789
2.05.2012   6A2A7C0
2.05.2012   6A29811
2.05.2012   6A2A31C
2.05.2012   6A2A5AD
2.05.2012   6A28BB3
2.05.2012   6A29304
2.05.2012   6A290D6
2.05.2012   6A2AB20
2.05.2012   6A28942
2.05.2012   6A288C5
1.05.2012   6A28789
1.05.2012   6A2A31C
5.07.2012   6A28092
5.07.2012   6A2A800
5.07.2012   6A29304
5.07.2012   6A28BB3
5.07.2012   6A2A5AD
5.07.2012   6A2AB1C
5.07.2012   6A29B00
5.07.2012   6A2B418
7.07.2012   6A2A5AD
7.07.2012   6A29304
7.07.2012   6A28027
7.07.2012   6A28BB3
7.07.2012   6A29B00
7.07.2012   6A2A4B9
7.07.2012   6A289AF
7.07.2012   6A29BDE
7.07.2012   6A281DC
7.07.2012   6A29178
7.07.2012   6A28D24
8.07.2012   6A28789
8.07.2012   6A27F1D
8.07.2012   6A28A9F
8.07.2012   6A2A4B9
8.07.2012   6A28027
8.07.2012   6A29B00
8.07.2012   6A2A455
8.07.2012   6A28BB3
8.07.2012   6A2A5AD
8.07.2012   6A29811
8.07.2012   6A29304
9.09.2012   6A29304
9.09.2012   6A28BB3
9.09.2012   6A2A31C
9.09.2012   37
10.09.2012   6A27F9D
10.09.2012   6A29304
10.09.2012   6A28BB3
10.09.2012   6A29811
10.09.2012   6A2B310
10.09.2012   6A2A31C
10.09.2012   6A28A9F
10.09.2012   6A29BDE
10.09.2012   6A27F1D
10.09.2012   6A288C5
10.09.2012   6A29811
10.09.2012   6A27F9D
10.09.2012   6A28BB3
10.09.2012   6A28027
10.09.2012   6A28A9F
10.09.2012   6A2A31C
11.09.2012   6A29304
11.09.2012   6A28027
11.09.2012   6A2A31C
11.09.2012   38
11.09.2012   6A27F9D
12.09.2012   6A28BB3
12.09.2012   6A29304
12.09.2012   6A27F9D
12.09.2012   6A2A1A0
10.09.2012   6A2B422
10.09.2012   6A27F1D
10.09.2012   6A288C5
11.09.2012   6A2B422
11.09.2012   6A288C5
12.09.2012   6A28D24
27.11.2012   6A2A1A0
27.11.2012   6A28BB3
27.11.2012   6A29304
27.11.2012   6A28092
27.11.2012   6A2A31C
28.11.2012   6A28BB3
28.11.2012   6A29304
28.11.2012   6A299F7
28.11.2012   6A2A31C
28.11.2012   6A28A9F
29.11.2012   6A2A1A0
29.11.2012   6A29D60
29.11.2012   6A28BB3
29.11.2012   6A29304
29.11.2012   6A28092
29.11.2012   6A299F7
29.11.2012   6A2A31C
30.11.2012   6A28BB3
30.11.2012   6A28092
30.11.2012   6A2A31C
30.11.2012   6A29304
2.03.2013   6A29304
3.03.2013   6A28092
3.03.2013   6A27EEB
3.03.2013   6A29304
3.03.2013   6A2AB98
3.03.2013   6A27E1E
3.03.2013   6A2A916
3.03.2013   6A2B422
4.03.2013   6A28092
4.03.2013   6A29304
4.03.2013   6A2A31C
4.03.2013   6A27EEB
4.03.2013   6A27E1D
4.03.2013   6A288C5
5.03.2013   39
5.03.2013   40
5.03.2013   6A29304
5.03.2013   6A27EEB
5.03.2013   41
5.03.2013   6A27E1D
5.03.2013   42
5.03.2013   6A2B422
5.03.2013   43
5.03.2013   44
5.03.2013   6A29BDE
5.03.2013   45
15.03.2013   6A29304
15.03.2013   6A289AB
15.03.2013   6A27EEB
15.03.2013   6A2A31C
15.03.2013   6A288C5
15.03.2013   6A29BDE
15.03.2013   6A27F1D
15.03.2013   6A2A5FF
12.06.2013   6A2AABD
12.06.2013   6A28B9D
12.06.2013   6B35060
13.06.2013   6A28B9D
13.06.2013   6A27F1D
13.06.2013   6B35060
14.06.2013   6A27E1E
14.06.2013   6B35060
14.06.2013   6A288C5
14.06.2013   6A28B9D
14.06.2013   6A2AABD
27.06.2013   6A29906
27.06.2013   6A280E7
27.06.2013   6A2B422
27.06.2013   6A2AABD
27.06.2013   6A28B9D
30.06.2013   6A29FF4
30.06.2013   6A28370
30.06.2013   6A29883
30.06.2013   6A2AABD
30.06.2013   6A28B9D
27.06.2013   6A29304
27.06.2013   46
27.06.2013   6A27EEB
27.06.2013   6A28EF8
30.06.2013   6A289AB
30.06.2013   6A29304
30.06.2013   6A27EEB
30.06.2013   6A29386
30.06.2013   6A2A31C
12.09.2013   6A289AB
12.09.2013   6A29304
12.09.2013   6B35CED
12.09.2013   6A27EEB
12.09.2013   47
12.09.2013   6A2AEA3
12.09.2013   6B36A56
12.09.2013   6A2A31C
12.09.2013   6A29386
12.09.2013   6B34D54
13.09.2013   6B39C28
13.09.2013   6A289AB
13.09.2013   6A27EEB
13.09.2013   6B20CA4
13.09.2013   6B39A7A
13.09.2013   6A29386
14.09.2013   6A29304
14.09.2013   6A289AB
14.09.2013   6A27EEB
14.09.2013   6E20CA4
14.09.2013   6B35CED
14.09.2013   6B39A7A
14.09.2013   6A29386
21.09.2013   6B35CED
21.09.2013   6A27EEB
21.09.2013   6A289AB
21.09.2013   6A29304
22.09.2013   6B35CED
22.09.2013   6A289AB
22.09.2013   6A29304
25.09.2013   6A29304
25.09.2013   6A27EEB
25.09.2013   6B35CED
25.09.2013   6B39A7A
26.09.2013   6E229BB
26.09.2013   68289AB
26.09.2013   6B35CED
26.09.2013   6B39A7A
26.09.2013   48
26.09.2013   49
26.09.2013   6B35CED
26.09.2013   6A2A31C
26.09.2013   6A29304
26.09.2013   6A2AEA3
26.09.2013   6A27EEB
26.09.2013   6A29386
14.01.2014   6A283DA
14.01.2014   6A289AB
14.01.2014   6B39A7A
NI01
 
Posts: 2
Joined: Thu Oct 04, 2018 9:37 pm

Re: RMark uneven primary and secondary time intervals

Postby jlaake » Mon Oct 08, 2018 8:40 am

You don't have capture histories. You need to turn your raw data into capture histories before using process.data. Please see Cooch and White electronic book.
jlaake
 
Posts: 1021
Joined: Fri May 12, 2006 12:50 pm
Location: Escondido, CA

Re: RMark uneven primary and secondary time intervals

Postby cooch » Mon Oct 08, 2018 9:48 am

jlaake wrote:You don't have capture histories. You need to turn your raw data into capture histories before using process.data. Please see Cooch and White electronic book.


Specifically, chapter 2 (but if this is an indication of the 'level' you're at, then I'd suggest chapters 1 -> 7 at minimum, since even after ytou have your data formatted, you probably want to have a fair idea of what you're doing with them. ;-)

The book can be found at: http://www.phidot.org/software/mark/docs/book/
cooch
 
Posts: 1338
Joined: Thu May 15, 2003 4:11 pm
Location: Cornell University

Re: RMark uneven primary and secondary time intervals

Postby jlaake » Mon Oct 08, 2018 5:56 pm

You can use table function in R to help turn your current data into a capture history. If your data are in dataframe x then use something like

chmat= table (x $ID, x $Date)
chmat[chmat>0]=1
ch=apply (chmat,1,paste,collapse="")
jlaake
 
Posts: 1021
Joined: Fri May 12, 2006 12:50 pm
Location: Escondido, CA

Re: RMark uneven primary and secondary time intervals

Postby NI01 » Mon Oct 08, 2018 6:12 pm

Hi!
Thanks for your response, although perhaps I did not word my question correctly.

I do have capture histories- I have only attached a snip below since it is a huge file. I have also read through the book.

My question was more specific about uneven primary and uneven secondary intervals. I was hoping someone else had run into the problem also and had some example code or an additional helpful resource.

Thank you





Code: Select all
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NI01
 
Posts: 2
Joined: Thu Oct 04, 2018 9:37 pm

Re: RMark uneven primary and secondary time intervals

Postby jlaake » Mon Oct 08, 2018 10:17 pm

I'm very confused. You are using cjs model which only has primary occasions. If you have primary and secondary then you should be using a robust model and then secondary are closed so secondary time intervals are 0. But none of this affects your error which is likely because you don't have the correct number of time intervals relative to number of occasions.
jlaake
 
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