ctmm R user group

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Welcome! This group is for questions and discussions about the ctmm: continuous-time movement modeling package for R, and topics related to the movement models and statistical methods implemented in ctmm. Here are some useful links:

ctmm FAQ: ?"ctmm-FAQ" or help("ctmm-FAQ")
ctmm package news: news(package="ctmm")
Github organization : project
Master-branch development packages can be installed from the command line: remotes::install_github("ctmm-initiative/ctmm")
Calabrese, J. M., C. H. Fleming and E. Gurarie (2016), "ctmm: an R package for analyzing animal relocation data as a continuous-time stochastic process", Methods in Ecology and Evolution, 7:9 1124–1132 (2016).
Calabrese, J. M., C. H. Fleming, M. J. Noonan, X. Dong, "ctmmweb: A Graphical User Interface for Autocorrelation‐Informed Home Range Estimation", Wildlife Society Bulletin, doi:10.1002/wsb.1154 (2021).
AniMove ctmm lectures (2022)
ctmm workshop materials: ctmmlearn

If you have encountered some errors or misbehavior with your data and want to keep them private, then feel free to message or email the data to me separately and post your inquiry here.

Below are links to project code that use ctmm:

Space Use and Movement Patterns of Moose in Southwest Alaska

0 selected

Damber, Christen Fleming3

Nov 28

Home range along road corridors

Hi Chris, Many thanks for this helpful information! It worked well. I am eagerly looking forward to

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Home range along road corridors

Hi Chris, Many thanks for this helpful information! It worked well. I am eagerly looking forward to

Nov 28

Amy Durham, Christen Fleming2

Nov 27

Range Residency and Variogram Pattern Interpretations

Hi Amy, 1-7 look pretty good, but you do want to confirm that the fitted model matches the general

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Range Residency and Variogram Pattern Interpretations

Hi Amy, 1-7 look pretty good, but you do want to confirm that the fitted model matches the general

Nov 27

Michael Gamble, Jesse Alston5

Nov 22

AKDE or KDE more appropriate?

Got it. Thanks, really appreciate the help! Michael On Wednesday, November 22, 2023 at 2:37:19 PM UTC

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AKDE or KDE more appropriate?

Got it. Thanks, really appreciate the help! Michael On Wednesday, November 22, 2023 at 2:37:19 PM UTC

Nov 22

Tyler Hodges, … Christen Fleming15

Nov 20

Range Residency in a Forest Bird with Variable Space Use

Will do, thanks Chris! On Monday, November 20, 2023 at 10:05:05 PM UTC-5 chris.h...@gmail.com wrote:

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Range Residency in a Forest Bird with Variable Space Use

Will do, thanks Chris! On Monday, November 20, 2023 at 10:05:05 PM UTC-5 chris.h...@gmail.com wrote:

Nov 20

Mairin Murphy, Christen Fleming2

Nov 20

Variogram interpretation/AKDE help

Hi Mairin, These variograms don't look range resident. At best, it looks like you might be able

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Variogram interpretation/AKDE help

Hi Mairin, These variograms don't look range resident. At best, it looks like you might be able

Nov 20

Anna Berg, Christen Fleming5

Nov 16

predict() creates straight lines of locations

Hi Anna, as.telemetry() now imports those columns correctly (on Github), but it doesn't know what

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predict() creates straight lines of locations

Hi Anna, as.telemetry() now imports those columns correctly (on Github), but it doesn't know what

Nov 16

Ryan Bourbour, Christen Fleming2

Nov 15

Troubleshooting for large confidence intervals

Hi Ryan, Did you feed in these data with raster::as.factor() to make sure that they are treated

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Troubleshooting for large confidence intervals

Hi Ryan, Did you feed in these data with raster::as.factor() to make sure that they are treated

Nov 15

Connie Kot, Christen Fleming4

Nov 14

Error when calculating pkde and mean

Thanks! I confirmed that it works now for both the example and another dataset! On Tuesday, October

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Error when calculating pkde and mean

Thanks! I confirmed that it works now for both the example and another dataset! On Tuesday, October

Nov 14

Catherine Kelly, Christen Fleming2

Nov 10

Extent of Suitability prediction

Hi Cat, Would you mind putting those objects into a dropbox folder and sending a link for me to

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Extent of Suitability prediction

Hi Cat, Would you mind putting those objects into a dropbox folder and sending a link for me to

Nov 10

Terrah Owens, Jesse Alston3

Nov 8

Home range estimates are biologically unreasonable using ctmm.select

Hi Jesse, Thank you for the quick response. I looked at the variograms, and the birds I'm having

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Home range estimates are biologically unreasonable using ctmm.select

Hi Jesse, Thank you for the quick response. I looked at the variograms, and the birds I'm having

Nov 8

Fang Chen, Christen Fleming5

Nov 4

rsf.fit() problem with categorical data

Hi Chris, Thank you very much for providing the solutions. I just realized that I did not specify the

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rsf.fit() problem with categorical data

Hi Chris, Thank you very much for providing the solutions. I just realized that I did not specify the

Nov 4

Tyler, Christen Fleming5

Nov 1

ctmm.boot error and increasing computational efficiency

Hi Chris, Thank you very much. I ran it with iterate=FALSE using eight cores and it was considerably

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ctmm.boot error and increasing computational efficiency

Hi Chris, Thank you very much. I ran it with iterate=FALSE using eight cores and it was considerably

Nov 1

Amber Litterer, Christen Fleming3

Oct 31

Issues with error and periodogram help

I forgot to answer your periodicity question. If they are roosting at night, then the better model is

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Issues with error and periodogram help

I forgot to answer your periodicity question. If they are roosting at night, then the better model is

Oct 31

Luke Emerson, … Jesse Alston33

Oct 26

Thanks Chris and Jesse for that info and advice. I had wondered if I needed to instead use MCP in

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Thanks Chris and Jesse for that info and advice. I had wondered if I needed to instead use MCP in

Oct 26

Vicki Fishlock, Christen Fleming3

Oct 26

Fitting ML with ctmm.select for elephant collars

hi Chris, Many thanks, that's really helpful. I did figure I could wrap this in a function for

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Fitting ML with ctmm.select for elephant collars

hi Chris, Many thanks, that's really helpful. I did figure I could wrap this in a function for

Oct 26

Emmeleia Nix, Christen Fleming2

Oct 25

Apples to oranges? Trouble calculating AKDEs on a consistent grid

Hi Emme, Yes, and I realize that there are numerous papers published in wildlife and ecology journals

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Apples to oranges? Trouble calculating AKDEs on a consistent grid

Hi Emme, Yes, and I realize that there are numerous papers published in wildlife and ecology journals

Oct 25

James Anderson, Christen Fleming5

Oct 23

Trouble running weighted ADKEs

Hi James, If you can send me a minimal working example (data + script, preferably with the fit

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Trouble running weighted ADKEs

Hi James, If you can send me a minimal working example (data + script, preferably with the fit

Oct 23

David Blount, Christen Fleming6

Oct 18

iRSF with multiple categorial variables

Hi David, The effective sample size should decrease with every predictor that you include in the

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iRSF with multiple categorial variables

Hi David, The effective sample size should decrease with every predictor that you include in the

Oct 18

Connie Kot, Christen Fleming12

Oct 16

ctmm.fit vs ctmm.select for mean UDs

Thanks, Chris! Please keep me posted on the updates on the tool and I'll be sure to keep

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ctmm.fit vs ctmm.select for mean UDs

Thanks, Chris! Please keep me posted on the updates on the tool and I'll be sure to keep

Oct 16

Matthew Butler, … Christen Fleming30

Oct 11

grid argument in the akde function

Hi Kristin, I can only suspect that there is a file locking issue happening, and that you need to

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grid argument in the akde function

Hi Kristin, I can only suspect that there is a file locking issue happening, and that you need to

Oct 11

Tyler Hodges, Christen Fleming7

Oct 10

"Data not in the same coordinate system"

Hello Chris, Thank you so much for your help, it's much appreciated! Manually selecting the top

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"Data not in the same coordinate system"

Hello Chris, Thank you so much for your help, it's much appreciated! Manually selecting the top

Oct 10

yu lei, … Christen Fleming20

Oct 8

How to identify residency via SVF?

Hi Soham, I do not, but its just a for loop over times. Best, Chris On Saturday, October 7, 2023 at

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How to identify residency via SVF?

Hi Soham, I do not, but its just a for loop over times. Best, Chris On Saturday, October 7, 2023 at

Oct 8

Holly Gamblin, Christen Fleming5

Oct 4

Trouble interpreting null model approach for artefactual periodicity test

Hi Holly, It looks like you aren't fitting any periodic models in your code. I would take a look

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Trouble interpreting null model approach for artefactual periodicity test

Hi Holly, It looks like you aren't fitting any periodic models in your code. I would take a look

Oct 4

Odd Jacobson, Christen Fleming7

Oct 4

Estimate Absolute Number of Encounters

Thanks Chris! On Wednesday, October 4, 2023 at 5:05:19 PM UTC+2 chris.h...@gmail.com wrote: Hi Odd,

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Estimate Absolute Number of Encounters

Thanks Chris! On Wednesday, October 4, 2023 at 5:05:19 PM UTC+2 chris.h...@gmail.com wrote: Hi Odd,

Oct 4

Marius G, Christen Fleming3

Oct 3

ctmm::meta() with scaled Homerange-sizes

Hi Chris, amazing, exactly what I was looking for. Thank you so much, Marius chris.h...@gmail.com

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ctmm::meta() with scaled Homerange-sizes

Hi Chris, amazing, exactly what I was looking for. Thank you so much, Marius chris.h...@gmail.com

Oct 3

Christen Fleming

Sep 28

Graduate student advertisement

Dear ctmm community, The Ecological Informatics Lab in the Department of Biology at the University of

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Graduate student advertisement

Dear ctmm community, The Ecological Informatics Lab in the Department of Biology at the University of

Sep 28

Christen Fleming

Sep 22

Continuous-time encounter measures and their estimation

If anyone is interested in a talk on continuous-time measures of interactions and encounters, which I

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Continuous-time encounter measures and their estimation

If anyone is interested in a talk on continuous-time measures of interactions and encounters, which I

Sep 22

Christen Fleming3

Sep 18

TWS 2023 Conference

Also at this year's TWS annual conference, I will be delivering a talk on the population

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TWS 2023 Conference

Also at this year's TWS annual conference, I will be delivering a talk on the population

Sep 18

Christen Fleming

Sep 18

Stochastic process models of animal movement, maximum entropy, and approximation theory

If anyone is interested in a more mathematical talk on the basic continuous-time stochastic process

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Stochastic process models of animal movement, maximum entropy, and approximation theory

If anyone is interested in a more mathematical talk on the basic continuous-time stochastic process

Sep 18

Wivian Neo, Christen Fleming4

Sep 17

Error message in rsf.fit Error in beta != beta.init : comparison of these types is not implemented

Hi Wivian, I'm not getting this error in the latest development version of the package. Please

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Error message in rsf.fit Error in beta != beta.init : comparison of these types is not implemented

Hi Wivian, I'm not getting this error in the latest development version of the package. Please

Sep 17

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