error messages for secr.fit density analyses

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

error messages for secr.fit density analyses

Postby cdevens226 » Wed Apr 19, 2017 7:42 am

Hi Murray,
I'm running secr.fit to determine density estimates for three different regional leopard surveys. Two of my three regions were run with no issue, but my third (and smallest) region seems to just throw error message after error message at me. I'm running it with 5 different buffers: 15, 20, 25, 30, 35km2, and there are 2 errors I consistently get. I've gone back to the drawing board and recreated my input files from scratch, adding a few additional capture events and occurrence detector locations where I can in an attempt to beef up the capture input file as much as is possible, but it doesn't seem to have helped anything.

If you could please help me understand these error messages and how to fix the problem!

Code: Select all
overberg_REDO_nocovar <- read.capthist(captfile = 'overberg_capture_REDO_2017.csv', trapfile = 'overberg_trap_REDO_2017.csv', detector = 'count', fmt = 'trapID', covnames = 'Sex')

secr.fit(overberg_REDO_nocovar, model=list(g0 ~ b, g0 ~ T), trace = FALSE, buffer=15000, verify = FALSE)


15km, 20km, 25km buffer runs:
Warning messages:
1: In bias.D(buffer, temptrps, detectfn = output$detectfn, detectpar = dpar, :
bias.D() does not allow for variable effort (detector usage)
2: In bufferbiascheck(output, buffer, biasLimit) :
predicted relative bias exceeds 0.01 with buffer = 15000


30km and 35km buffer runs
Warning message:
In bias.D(buffer, temptrps, detectfn = output$detectfn, detectpar = dpar, :
bias.D() does not allow for variable effort (detector usage)



I've read all the help info for suggest.buffer and bias.D and have tried run them many times but haven't come right with them yet (R script writing is an ongoing struggle).

I ran the other regional surveys with 90 day phases, but this survey was more on the ad hoc side and cameras were left for sometimes 4 to 8 months. I'm attempting to maintain the 90day survey period for this region as well, but this region has the smallest leopard identification sample size and number of capture occurrences spread across almost a year, so my input file data is very limited within 90 days phases. Would running the region over 200 or more days be a problem for the closure assumption?

Additionally, are these warning messages indicating that the numbers produced are unusable without the fix, or still relatively what they would be? (aka: how screwed am I with this region?!)

I apologize if this seems like a very fundamental question... If you could just dumb the problem and (hopefully) the fix down for me I'd be SO GRATEFUL! Just feeling very stuck at the moment...!

All the best,
Carolyn
cdevens226
 
Posts: 10
Joined: Mon Mar 03, 2014 1:10 pm
Location: Pretoria, South Africa

Re: error messages for secr.fit density analyses

Postby cdevens226 » Wed Apr 19, 2017 8:28 am

Hi Murray!
My apologies, I looked back and just realized you had answered this question for me a couple years ago! I can't seem to figure out how to delete this post! sorry about that...

I just ran it with the biasLimit = NA and it was 100% and same results!

best,
carolyn
cdevens226
 
Posts: 10
Joined: Mon Mar 03, 2014 1:10 pm
Location: Pretoria, South Africa


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