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

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Adelaida Pérez Cadavid, adrian...@gmail.com3

Apr 25

Applications to detect stopover sites

Hola Adrian, Thank you very much for your response. I have already reviewed the resource you sent me,

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Applications to detect stopover sites

Hola Adrian, Thank you very much for your response. I have already reviewed the resource you sent me,

Apr 25

Tristan Swartout

Apr 24

Home range: Impassable barriers within impassable barrier

Hello all, My question is regarding how to account for the sp argument when I have a hard boundary

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Home range: Impassable barriers within impassable barrier

Hello all, My question is regarding how to account for the sp argument when I have a hard boundary

Apr 24

Christen Fleming

Apr 24

Smithsonian Postdoc: Animal Tracking & Camera Trap Data Integration

https://trustcareers.si.edu/en/postings/a26327b0-475a-42b6-887c-3087178479cb The deadline is May 1st

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Smithsonian Postdoc: Animal Tracking & Camera Trap Data Integration

https://trustcareers.si.edu/en/postings/a26327b0-475a-42b6-887c-3087178479cb The deadline is May 1st

Apr 24

Apr 24

cluster() Function and Paper

Hello Chris, I am currently working on an analysis of sub-seasonal functional home ranges of elk in

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cluster() Function and Paper

Hello Chris, I am currently working on an analysis of sub-seasonal functional home ranges of elk in

Apr 24

Oliver Holt, … Tyler Hodges4

Apr 24

Home Range Size

Thanks for the clarification, Chris! Best, Tyler On Wednesday, April 24, 2024 at 12:56:21 AM UTC-4

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Home Range Size

Thanks for the clarification, Chris! Best, Tyler On Wednesday, April 24, 2024 at 12:56:21 AM UTC-4

Apr 24

Meredith VanAcker, Christen Fleming2

Apr 24

Loops for pairwise home range overlap

Hi Meredith, Could you send me a minimal working example for a pair that produce the extent error?

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Loops for pairwise home range overlap

Hi Meredith, Could you send me a minimal working example for a pair that produce the extent error?

Apr 24

Ryan Gill, Christen Fleming2

Apr 23

resampling UDs to common grid and resolution

Hi Ryan, There is no way to resample within ctmm. Assuming that the projections are the same, then

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resampling UDs to common grid and resolution

Hi Ryan, There is no way to resample within ctmm. Assuming that the projections are the same, then

Apr 23

Kerry Kilshaw, Christen Fleming3

Apr 18

Warning messages: query?

Hi Chris Yes, that sorted it, thanks, on of the column headings was slightly different! Thanks Kerry

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Warning messages: query?

Hi Chris Yes, that sorted it, thanks, on of the column headings was slightly different! Thanks Kerry

Apr 18

Mark Le Pla, Christen Fleming2

Apr 10

Diffusion rate and periods of inactivity

Hi Mark, Yes, it sounds like you have a two-state behavior and need to segment before fitting a

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Diffusion rate and periods of inactivity

Hi Mark, Yes, it sounds like you have a two-state behavior and need to segment before fitting a

Apr 10

Iran Normande, Christen Fleming2

Apr 9

RSF estimate = 0

Hi Iran, I've not seen that behavior, but if you can create a minimal working example for me (

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RSF estimate = 0

Hi Iran, I've not seen that behavior, but if you can create a minimal working example for me (

Apr 9

Feipeng Huang, Christen Fleming8

Apr 9

Outlier and model fitting

Hi Feipeng, t=c(t1,t2) would correspond to the range of times between t1 and t2, which should be

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Outlier and model fitting

Hi Feipeng, t=c(t1,t2) would correspond to the range of times between t1 and t2, which should be

Apr 9

Christina Aiello, Christen Fleming3

Apr 2

kernel argument in pkde function

Good to know! Thanks for responding with that info. Christina On Sunday, March 31, 2024 at 8:43:13 PM

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kernel argument in pkde function

Good to know! Thanks for responding with that info. Christina On Sunday, March 31, 2024 at 8:43:13 PM

Apr 2

Marian, … Christen Fleming11

Apr 1

akde with very large data sets

Hi Maria, There's vignette('error') in the package and a workshop script in the ctmm-

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akde with very large data sets

Hi Maria, There's vignette('error') in the package and a workshop script in the ctmm-

Apr 1

Rozy Bathrick, Christen Fleming3

Mar 31

pkde error: ud @ ctmm

Hi Rozy, sapply(LEYE_all_tel,class) shows 3 elements that are not UD objects but lists containing

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pkde error: ud @ ctmm

Hi Rozy, sapply(LEYE_all_tel,class) shows 3 elements that are not UD objects but lists containing

Mar 31

Chris MacColl, Christen Fleming2

Mar 24

RSF's for disparate individuals

Hi Chris, The timeout for memory (if you hit the RAM limit of rsf.fit()) should still return a result

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RSF's for disparate individuals

Hi Chris, The timeout for memory (if you hit the RAM limit of rsf.fit()) should still return a result

Mar 24

lisa king, Christen Fleming2

Mar 24

Number of individuals for population mean

Hi Lisa, The CoV returned by meta() is that of the population of home-range areas, and will stabilize

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Number of individuals for population mean

Hi Lisa, The CoV returned by meta() is that of the population of home-range areas, and will stabilize

Mar 24

Elena Pi Serra, Christen Fleming3

Mar 24

GPS and VHF (outliers, models HR, residency)

Hi Elennaa, Irregular sampling is fine with continuous-time models. If the sampled movements are

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GPS and VHF (outliers, models HR, residency)

Hi Elennaa, Irregular sampling is fine with continuous-time models. If the sampled movements are

Mar 24

Tristan Swartout, Tyler3

Mar 21

Home range with impassable bounds

Thank you so much for the help! I added the shapefile to the SP argument and now everything is

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Home range with impassable bounds

Thank you so much for the help! I added the shapefile to the SP argument and now everything is

Mar 21

Fang Chen, Christen Fleming7

Mar 18

Suitability prediction and RSF questions

Hi Fang, Would you mind sending me 3 different minimal working examples (MWEs), including: The track

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Suitability prediction and RSF questions

Hi Fang, Would you mind sending me 3 different minimal working examples (MWEs), including: The track

Mar 18

Elli Rivers, Christen Fleming2

Mar 18

OUF models during bird nesting

Hi Elli, The models in ctmm are currently stationary, so you would want to segment the data into

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OUF models during bird nesting

Hi Elli, The models in ctmm are currently stationary, so you would want to segment the data into

Mar 18

Ryan Bourbour, Christen Fleming2

Mar 18

Classified hunting locations and RSF

Hi Ryan, This is the approach that I would recommend for the moment. Especially for the perching data

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Classified hunting locations and RSF

Hi Ryan, This is the approach that I would recommend for the moment. Especially for the perching data

Mar 18

Dibyendu Biswas, Christen Fleming2

Mar 18

Is aKDE usable for entire data of a year of a migratory secies

Hi Dibyendu, It makes sense to run AKDE on the winter ranges and the summer ranges separately. It

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Is aKDE usable for entire data of a year of a migratory secies

Hi Dibyendu, It makes sense to run AKDE on the winter ranges and the summer ranges separately. It

Mar 18

Mark Le Pla, Christen Fleming2

Mar 18

Diffusion rate's relationship with different movement models

Hi Mark, The diffusion rates are maximized across time-lag to be comparable across models. There is

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Diffusion rate's relationship with different movement models

Hi Mark, The diffusion rates are maximized across time-lag to be comparable across models. There is

Mar 18

Mario Posillico2

Mar 11

Errors while loading csv data

Sorry... the date was transformed from yyyy-mm-dd hh:mm:ss into another format (dd/mm/yyyy etc.). Now

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Errors while loading csv data

Sorry... the date was transformed from yyyy-mm-dd hh:mm:ss into another format (dd/mm/yyyy etc.). Now

Mar 11

yu lei, … Christen Fleming26

Mar 10

How to identify residency via SVF?

I concur with Jesse. At the end where the variogram shoots up, the CIs also become very wide. You can

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How to identify residency via SVF?

I concur with Jesse. At the end where the variogram shoots up, the CIs also become very wide. You can

Mar 10

Chris MacColl, Christen Fleming2

Mar 10

Home range meta-analysis and hard borders

Hi Chris, Sorry for the delay. For meta() you don't need them to be on the same grid. But for

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Home range meta-analysis and hard borders

Hi Chris, Sorry for the delay. For meta() you don't need them to be on the same grid. But for

Mar 10

Karina Li, Christen Fleming2

Mar 10

Calibration data

Hi Karina, Sorry for the delay. The Argos error ellipses don't need to be calibrated. If you need

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Calibration data

Hi Karina, Sorry for the delay. The Argos error ellipses don't need to be calibrated. If you need

Mar 10

Kerry Kilshaw, … Christen Fleming7

Mar 10

trouble with writevector

Hi All, Sorry for the delay - I'm teaching a new course. I'm not getting these errors. I

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trouble with writevector

Hi All, Sorry for the delay - I'm teaching a new course. I'm not getting these errors. I

Mar 10

Tyler Hodges, … Christen Fleming35

Feb 28

Range Residency in a Forest Bird with Variable Space Use

Hello Chris, Noted, thanks! I suppose I need to dedicate some time to figuring out what is going on

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Range Residency in a Forest Bird with Variable Space Use

Hello Chris, Noted, thanks! I suppose I need to dedicate some time to figuring out what is going on

Feb 28

Chris MacColl, Christen Fleming5

Feb 27

Plotting variograms

Hi Chris, Overall, those look pretty good. I suspect 157651,150621, 37740 may deviate significantly

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Plotting variograms

Hi Chris, Overall, those look pretty good. I suspect 157651,150621, 37740 may deviate significantly

Feb 27

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