secr

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Welcome to this Google Group for discussion on spatially explicit capture-recapture methods for animal populations, and for questions related to the Windows software DENSITY and the R package 'secr'. The scope overlaps with the Density | secr forum at www.phidot.org/forums. Note the search tool on the group website.

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Sarah Darrah, Murray Efford3

Jul 24

Error in makeStart

3 individuals make of the 26 detections. The code worked for the first fit. This error pops up when I

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Error in makeStart

3 individuals make of the 26 detections. The code worked for the first fit. This error pops up when I

Jul 24

Rui Peres dos Santos, Murray Efford2

Jul 24

Seeking Advice on Reducing Data Size for openCR Analysis of Marine Mammals in the Open Sea

Hi Rui Peres Yes, that data structure is way too large for openCR (even if it didn't hit the R

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Seeking Advice on Reducing Data Size for openCR Analysis of Marine Mammals in the Open Sea

Hi Rui Peres Yes, that data structure is way too large for openCR (even if it didn't hit the R

Jul 24

Josh Mulvaney, Murray Efford2

Jul 24

No SE for Density estimate

I'm sorry that I have a backlog of my own work and can't troubleshoot for you right now.

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No SE for Density estimate

I'm sorry that I have a backlog of my own work and can't troubleshoot for you right now.

Jul 24

Sarah Darrah, Murray Efford3

Jul 14

Error in make.capthist

I am so sorry, I messed up the line. The line is suppose to look like this: MRCH <- read.capthist(

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Error in make.capthist

I am so sorry, I messed up the line. The line is suppose to look like this: MRCH <- read.capthist(

Jul 14

Jeanette Fouche, Murray Efford3

Jul 4

SECR error: "noccasions"

In files Jeanette sent I found an inconsistency between the capture and trap files (lower-case p vs

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SECR error: "noccasions"

In files Jeanette sent I found an inconsistency between the capture and trap files (lower-case p vs

Jul 4

Jul 3

The only notable change in secr 4.6.9 (now on CRAN) is a correction to the relative density code

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The only notable change in secr 4.6.9 (now on CRAN) is a correction to the relative density code

Jul 3

Ayan Sadhu, Murray Efford3

Jun 27

Error messgae specific to R & secr version

Thanks for sending the data and code. I see several problems. 1. The help for read.traps specifies

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Error messgae specific to R & secr version

Thanks for sending the data and code. I see several problems. 1. The help for read.traps specifies

Jun 27

Jun 11

New releases of secr and secrdesign

secrdesign 2.9.1 and secr 4.6.7 have been on CRAN for a while. No major changes, just a few new

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New releases of secr and secrdesign

secrdesign 2.9.1 and secr 4.6.7 have been on CRAN for a while. No major changes, just a few new

Jun 11

Fernando Mercado Malabet, … Nianfan Ding9

May 10

Using secr.fit with a habitat mask leads to error - "Warning: missing values in predictors?Error in lpred[, 1] <- Yp : replacement has length zero"

Update: For those who may also encounter this, I figured out my error was because I coded something

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Using secr.fit with a habitat mask leads to error - "Warning: missing values in predictors?Error in lpred[, 1] <- Yp : replacement has length zero"

Update: For those who may also encounter this, I figured out my error was because I coded something

May 10

May 7

Comparing density estimates

Hi, I have conducted a follow-up camera trapping study to one conducted 2-years prior in the same

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Comparing density estimates

Hi, I have conducted a follow-up camera trapping study to one conducted 2-years prior in the same

May 7

Gazmeister 101, Murray Efford7

May 6

Issues trying to learn secr coding to estimate fox densities

Attach the text data files and a text file of R code to an email sent to murray.efford at otago.ac.nz

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Issues trying to learn secr coding to estimate fox densities

Attach the text data files and a text file of R code to an email sent to murray.efford at otago.ac.nz

May 6

Carson G, … Kavya Shah13

Apr 23

Error in read.capthist(), : requires single 'captfile'

Hello Sir, Thank you for your response. I made the changes recommended, but still I am facing the

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Error in read.capthist(), : requires single 'captfile'

Hello Sir, Thank you for your response. I made the changes recommended, but still I am facing the

Apr 23

Ide Uitentuis, Murray Efford3

Apr 19

NA in density estimates if varying effort is added

Hi again Thanks for sending data. It seems that, despite having a lot of data, you have just one

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NA in density estimates if varying effort is added

Hi again Thanks for sending data. It seems that, despite having a lot of data, you have just one

Apr 19

jcl...@utk.edu, Murray Efford4

Apr 9

bk models in secr and openCR

Hi Joe I'm not sure either, and this is a bit dense for me to troubleshoot. I suggest you pare it

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bk models in secr and openCR

Hi Joe I'm not sure either, and this is a bit dense for me to troubleshoot. I suggest you pare it

Apr 9

HL Y, Murray Efford3

Mar 18

openCR survival interpretation

Dear Murray, Apologies for my late reply! I was on a trip and could not access to gmail for the last

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openCR survival interpretation

Dear Murray, Apologies for my late reply! I was on a trip and could not access to gmail for the last

Mar 18

Aline Gibson Vega, Duane Diefenbach3

Mar 13

Proximity or multi? Turning transect data into point data

Hi Duane, Thank you for that suggestion! I feel very silly that I forgotten about the 'count'

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Proximity or multi? Turning transect data into point data

Hi Duane, Thank you for that suggestion! I feel very silly that I forgotten about the 'count'

Mar 13

Cheryl Lohr, Murray Efford3

Mar 3

shareFactorLevels not working

Cheryl Thanks for sending the data. shareFactorLevels is working. You have inconsistent factor levels

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shareFactorLevels not working

Cheryl Thanks for sending the data. shareFactorLevels is working. You have inconsistent factor levels

Mar 3

mirjam....@gmail.com, … indu...@gmail.com5

Feb 28

expected AC density surface = predictDsurface()? -- Durbach et al., 2024, Biometrics

Thank you very much for this comment and confirmation, Ian! These technical papers often come a bit

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expected AC density surface = predictDsurface()? -- Durbach et al., 2024, Biometrics

Thank you very much for this comment and confirmation, Ian! These technical papers often come a bit

Feb 28

h.tr...@gmx.de, … Lukas Scholz10

Feb 26

Using hcov in secr.fit for polygon data causes R session abort

Hey Murray, perfect, will try it with the latest working version directly. Also, a massive thank you

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Using hcov in secr.fit for polygon data causes R session abort

Hey Murray, perfect, will try it with the latest working version directly. Also, a massive thank you

Feb 26

Tomas T., Murray Efford4

Feb 24

openCR: how to represent missing data?

And the 'usage' attribute handles that comprehensively for spatial analyses. Strata can be

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openCR: how to represent missing data?

And the 'usage' attribute handles that comprehensively for spatial analyses. Strata can be

Feb 24

Erica Hendrikse, Murray Efford2

Feb 18

Question about suitable buffer width

Erica I assume you have seen secr-habitatmasks.pdf and tried esa.plot() (much faster than repeated

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Question about suitable buffer width

Erica I assume you have seen secr-habitatmasks.pdf and tried esa.plot() (much faster than repeated

Feb 18

stefano palmero, Murray Efford2

Feb 18

Large scale simulations of lynx

Stefano I think you're right that it won't make much difference. On the plus side, it shows

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Large scale simulations of lynx

Stefano I think you're right that it won't make much difference. On the plus side, it shows

Feb 18

Chris Sutherland

Feb 6

Important ISEC dates and information

Hello friends and colleagues (and apologies for cross posting!), Here is some information and

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Important ISEC dates and information

Hello friends and colleagues (and apologies for cross posting!), Here is some information and

Feb 6

Marina Ramon, Murray Efford3

Jan 30

Discretized model instead of area search model?

Hi Murray, Great. Thanks for the detailed answer. Marina El dia dimarts, 30 de gener del 2024 a les 5

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Discretized model instead of area search model?

Hi Murray, Great. Thanks for the detailed answer. Marina El dia dimarts, 30 de gener del 2024 a les 5

Jan 30

Antonio Sampedro, Murray Efford3

Jan 30

Problem with my N-Mixture model

Hi Antonio I think you got the wrong list for this. Try unmarked. Murray On Tuesday, January 30, 2024

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Problem with my N-Mixture model

Hi Antonio I think you got the wrong list for this. Try unmarked. Murray On Tuesday, January 30, 2024

Jan 30

Jan 29

Problem with Telemetry and Impervious Surface Covariate

Hi All, I am in the last little bit of my project here and have been cruising but I hit a snag with

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Problem with Telemetry and Impervious Surface Covariate

Hi All, I am in the last little bit of my project here and have been cruising but I hit a snag with

Jan 29

Anne-Sophie Crunchant, … Nianfan Ding4

Jan 23

season as timecov and NAs parameter estimates

Hi Anne-Sophie and Murray, I'd just like to thank you both for your thoughts and sharing. I'

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season as timecov and NAs parameter estimates

Hi Anne-Sophie and Murray, I'd just like to thank you both for your thoughts and sharing. I'

Jan 23

Heather Gaya, Murray Efford6

12/22/23

Potential Bug with site-level variation

I'm glad that worked. It is not necessary for all factor levels to be represented in every

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Potential Bug with site-level variation

I'm glad that worked. It is not necessary for all factor levels to be represented in every

12/22/23

Sarah Lydia, Murray Efford2

12/20/23

Basic openCR questions about primary and secondary sessions

I would have thought each month was a primary session (allowing turnover between primary sessions,

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Basic openCR questions about primary and secondary sessions

I would have thought each month was a primary session (allowing turnover between primary sessions,

12/20/23

mirjam....@gmail.com, Murray Efford6

12/11/23

Implications of non-independence between sessions in Multi-session models

Collect lots of data, learn Nimble, and don't expect too much. On Tuesday, December 12, 2023 at 1

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Implications of non-independence between sessions in Multi-session models

Collect lots of data, learn Nimble, and don't expect too much. On Tuesday, December 12, 2023 at 1

12/11/23

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