Problems with reading capture data text file

questions concerning anlysis/theory using program DENSITY and R package secr. Focus on spatially-explicit analysis.

Problems with reading capture data text file

Postby ehileman » Thu Nov 14, 2013 12:47 pm

Hi all,
I am attempting to use program DENSITY 5.0 for the first time and I am having difficulties having the program read my capture data text file. I have checked the forum postings and help files and cannot seem to figure out what I am doing wrong. I am getting the following error:
Capture file contains record of ID 138 in session 1 with trap ID SB8 (sample 2) that is not in trap site file.
I double checked the trap file and it does indeed have trap SB8 (see below). Furthermore, when I delete this entry from both files, I get a similar message for another ID.
Here is a snippet of my capture file:
# session, animal ID, occasion, trapID
1 364 2 SF-11
1 198 2 SX3
1 345 2 SJJ-10
1 138 2 SB8
1 432 3 SVV4
1 345 3 SJJ-10
1 415 3 SJJ-4

Here is a snippet of my trap file:
#Trap ID, x, y
Sb6 417101 4804675
Sb-6 417095 4804863
Sb7 417101 4804659
Sb-7 417095 4804879
Sb8 417101 4804642
Sb-8 417093 4804896
Sb9 417101 4804626

My trap file seems to be working fine as I was able to use it in the simulator. Any suggestion as to what I might be doing wrong would be greatly appreciated.

Best regards,

Eric
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Re: Problems with reading capture data text file

Postby James Russell » Thu Nov 14, 2013 1:40 pm

Case sensitivity? Capture file is in capitals while trap file is in lower case, for all entries.
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Re: Problems with reading capture data text file

Postby ehileman » Thu Nov 14, 2013 2:26 pm

Thanks, James! That was it. I thought I read somewhere that the text file source data were not case sensitive. Obviously, I was mistaken. Thanks again!

Eric
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Re: Problems with reading capture data text file

Postby murray.efford » Thu Nov 14, 2013 3:09 pm

Hmm. The Help does say "Density is not case-sensitive", but a bug may have slipped into 5.0. I'll have to look into that.
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Re: Problems with reading capture data text file

Postby murray.efford » Thu Nov 14, 2013 9:09 pm

I can confirm that Density is case-sensitive with respect to TrapID in both the trap layout and capture files, and that this is a longstanding bug (at least 4.4 and 5.0). Funny that it hasn't caused problems before. I suggest we just live with it until there's a strong reason to put out a new version. Other identifiers are converted to uppercase internally. Thanks for spotting this, James.
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Re: Problems with reading capture data text file

Postby ehileman » Fri Nov 15, 2013 3:15 pm

Hi Murray,

Thank you for looking into the matter and for making me aware of the bug. The case sensitivity is easy enough to work with, but I was initially a bit perplexed as to why I couldn't get the program to read my capture text file. Thanks for clearing things up.

Cheers!

Eric
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Posts: 51
Joined: Sat Nov 26, 2011 6:40 pm
Location: West Virginia University


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