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")
Pre-built β release packages (on demand)
Github organization : project
Master-branch development packages can be installed from the command line: remotes::install_github("ctmm-initiative/ctmm") or devtools::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).
ctmm workshop materials: ctmmlearn
AniMove ctmm lectures (2022)

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

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adrian...@gmail.com, Christen Fleming5

Jun 2

Hi Chris, Thanks for the help. It worked. All the best, Adrian El jueves, 11 de mayo de 2023 a las 20

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Hi Chris, Thanks for the help. It worked. All the best, Adrian El jueves, 11 de mayo de 2023 a las 20

Jun 2

Tori Mezebish, Christen Fleming3

Jun 1

Segment movement data into pre- and post- home range establishment using variogram

Hi Chris, Thanks so much for your response! Exciting to hear about the path segmentation method -

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Segment movement data into pre- and post- home range establishment using variogram

Hi Chris, Thanks so much for your response! Exciting to hear about the path segmentation method -

Jun 1

Dibyendu Biswas, Christen Fleming4

May 27

aKDE or HMM for movement with clear phases

Hi Dibyendu, For the flying data that should work. For the resting data, you would have to be a

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aKDE or HMM for movement with clear phases

Hi Dibyendu, For the flying data that should work. For the resting data, you would have to be a

May 27

Devin Johnson - NOAA Federal, Christen Fleming3

May 26

mixed argos and gps data

Thanks Chris! On Friday, May 26, 2023 at 5:28:18 PM UTC-6 chris.h...@gmail.com wrote: Hi Devin, Yes,

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mixed argos and gps data

Thanks Chris! On Friday, May 26, 2023 at 5:28:18 PM UTC-6 chris.h...@gmail.com wrote: Hi Devin, Yes,

May 26

Danielle Berger, Christen Fleming2

May 26

What is the correct way to aggregate individual ODs at the population level?

Hi Dani, It depends on what you want the aggregate population OD to correspond to. The individual OD

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What is the correct way to aggregate individual ODs at the population level?

Hi Dani, It depends on what you want the aggregate population OD to correspond to. The individual OD

May 26

Lorenzo Frangini, Christen Fleming4

May 25

Code for intensity()

Hi Lorenzo, Can you send me a minimal working example to debug? Best, Chris On Thu, May 25, 2023 at 4

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Code for intensity()

Hi Lorenzo, Can you send me a minimal working example to debug? Best, Chris On Thu, May 25, 2023 at 4

May 25

Luke Emerson, Christen Fleming3

May 24

Variogram: measures for meeting asymptote and range-residency assumption

Thanks for the advice Chris, much appreciated! Cheers, Luke On Wednesday, 24 May 2023 at 01:47:42 UTC

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Variogram: measures for meeting asymptote and range-residency assumption

Thanks for the advice Chris, much appreciated! Cheers, Luke On Wednesday, 24 May 2023 at 01:47:42 UTC

May 24

Luke Emerson, Christen Fleming9

May 18

Missing PDOP/DOP/HDOP/error values/calibration data and what to do with water locations

Hi Luke, You would want to do this before importing, to not have to mess with that. I would use the

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Missing PDOP/DOP/HDOP/error values/calibration data and what to do with water locations

Hi Luke, You would want to do this before importing, to not have to mess with that. I would use the

May 18

Aidan Branney, Christen Fleming2

May 18

Pooled Variance

Hi Aidan, This should be fixed on Github. Thanks for the report. Best, Chris On Wednesday, May 17,

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Pooled Variance

Hi Aidan, This should be fixed on Github. Thanks for the report. Best, Chris On Wednesday, May 17,

May 18

Rafael Reyna, Christen Fleming2

May 16

I get a consist error in ctmm.select

Hi Rafael, What is class(eli_GUESS) here? Additionally, I don't recall an AIC argument in ctmm.

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I get a consist error in ctmm.select

Hi Rafael, What is class(eli_GUESS) here? Additionally, I don't recall an AIC argument in ctmm.

May 16

Caka Karlsson, Christen Fleming5

May 15

Questions regarding the ctmm

Hi Caka, No asymptote means either non-resident behavior or not enough data to see it. The default

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Questions regarding the ctmm

Hi Caka, No asymptote means either non-resident behavior or not enough data to see it. The default

May 15

jasone...@aol.com, Christen Fleming3

May 10

Is there Any Way to Apply Different Projections to Individuals in the Same List

Hey Chris, well this is a bit embarrassing but my code seems to be working now. I think the issue is

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Is there Any Way to Apply Different Projections to Individuals in the Same List

Hey Chris, well this is a bit embarrassing but my code seems to be working now. I think the issue is

May 10

Christen Fleming2

May 7

RSF diagnostic plots

I wanted to add that this is very early in testing (use at your own risk) and I am only announcing it

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RSF diagnostic plots

I wanted to add that this is very early in testing (use at your own risk) and I am only announcing it

May 7

Michael Taylor, Christen Fleming5

May 4

RSF with average ranges

Thanks for the clarification on workflow and weighting Chris! Its also good to learn a little more

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RSF with average ranges

Thanks for the clarification on workflow and weighting Chris! Its also good to learn a little more

May 4

Kimberley, Christen Fleming2

May 3

Hi Kimberley, The current CRAN package reference is: CH Fleming, JM Calabrese, “ctmm: Continuous-time

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Hi Kimberley, The current CRAN package reference is: CH Fleming, JM Calabrese, “ctmm: Continuous-time

May 3

Michela Coury, … Christen Fleming12

Apr 27

Coming up with IID for FIT summary

Hi Michela, The variogram is just a visual tool and if it doesn't look great because of irregular

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Coming up with IID for FIT summary

Hi Michela, The variogram is just a visual tool and if it doesn't look great because of irregular

Apr 27

abern...@gmail.com, Christen Fleming4

Apr 27

Unexpected behaviour of ctmm.select (range=false)

Hi Robin, Yeah, I think there is too much difference in the autocorrelation structure within the

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Unexpected behaviour of ctmm.select (range=false)

Hi Robin, Yeah, I think there is too much difference in the autocorrelation structure within the

Apr 27

Apr 26

Combining Multiple Odds Ratio Plots

Hello All, I hope this is an appropriate place to post this question, as it relates to the final

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Combining Multiple Odds Ratio Plots

Hello All, I hope this is an appropriate place to post this question, as it relates to the final

Apr 26

Gladys Kung'u, Christen Fleming3

Apr 26

Extracting home range sizes for multiple individuals

Hi Chris, Thank you very much for your quick response and tips. Best, Gladys. On Wednesday, April 26,

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Extracting home range sizes for multiple individuals

Hi Chris, Thank you very much for your quick response and tips. Best, Gladys. On Wednesday, April 26,

Apr 26

Kristy, Christen Fleming2

Apr 25

3D DEM for homerange

Hi Kristy, I'm not very familiar with ArcGIS, but you should be able to export what you need from

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3D DEM for homerange

Hi Kristy, I'm not very familiar with ArcGIS, but you should be able to export what you need from

Apr 25

jasone...@aol.com, Christen Fleming5

Apr 23

Error Writing a Loop to Calculate Variograms for Multiple Dataframes

Thanks so much, that did it! best, Jason On Saturday, April 22, 2023 at 3:06:07 PM UTC-5 chris.h...@

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Error Writing a Loop to Calculate Variograms for Multiple Dataframes

Thanks so much, that did it! best, Jason On Saturday, April 22, 2023 at 3:06:07 PM UTC-5 chris.h...@

Apr 23

Apr 17

stack plotting UDs

Hi Community, I have created home ranges for my animal for different years and I would like to

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stack plotting UDs

Hi Community, I have created home ranges for my animal for different years and I would like to

Apr 17

Meaghan Rupprecht, Christen Fleming2

Apr 17

Alternative applications of ctmm package

Hi Meaghan, It seems very reasonable to try. You should at least be able to see what the temporal

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Alternative applications of ctmm package

Hi Meaghan, It seems very reasonable to try. You should at least be able to see what the temporal

Apr 17

abern...@gmail.com, Christen Fleming2

Apr 15

Error Modelling, no HDOP

Hi Robin, With, at most, 1-hour data on caribou and wolves, I really doubt that you will need to

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Error Modelling, no HDOP

Hi Robin, With, at most, 1-hour data on caribou and wolves, I really doubt that you will need to

Apr 15

Wouter Waenink, Christen Fleming3

Apr 14

Weird pattern in variogram

Thanks for the answer! On Wednesday, April 5, 2023 at 10:35:06 PM UTC+2 chris.h...@gmail.com wrote:

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Weird pattern in variogram

Thanks for the answer! On Wednesday, April 5, 2023 at 10:35:06 PM UTC+2 chris.h...@gmail.com wrote:

Apr 14

Markus Milchram, Christen Fleming7

Apr 13

part-time residency

Hi Chris, okay, thank you very much! I think I know what to do now Best, Markus chris.h...@gmail.com

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part-time residency

Hi Chris, okay, thank you very much! I think I know what to do now Best, Markus chris.h...@gmail.com

Apr 13

adrian...@gmail.com, Christen Fleming2

Apr 9

Error writeShapefile.ctmm not found

Hi Adrian, The second element is not a UD object: > sapply(V.AKDE.nonbreeding,class) [1] "UD

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Error writeShapefile.ctmm not found

Hi Adrian, The second element is not a UD object: > sapply(V.AKDE.nonbreeding,class) [1] "UD

Apr 9

Iran Normande, Christen Fleming4

Mar 29

Hi Iran, occurrence() is not really something to compare because it is not a biological parameter.

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Hi Iran, occurrence() is not really something to compare because it is not a biological parameter.

Mar 29

jasone...@aol.com, Christen Fleming2

Mar 29

How to convert a telemetry object to a kml file?

Hi Jason, I haven't attempted this, but have you tried exporting to an sp object and then running

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How to convert a telemetry object to a kml file?

Hi Jason, I haven't attempted this, but have you tried exporting to an sp object and then running

Mar 29

Adam Fell, Christen Fleming26

Mar 23

Changes in sampling intervals

Hi Adam, I was just doing what you were, but with a regular for() loop. I didn't keep running it,

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Changes in sampling intervals

Hi Adam, I was just doing what you were, but with a regular for() loop. I didn't keep running it,

Mar 23

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