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Interface to other packages with amt

Johannes Signer

2025-08-23

About

This vignette briefly introduces how one can coerce amt track_xy* to other commonly used packages. At the moment this vignette shows methods to coerce to adehabitatHR, ctmm, and move.

Getting the data ready

First we load the required libraries and the relocation data (called deer)

library(amt)
data("deer")
class(deer)

## [1] "track_xyt"  "track_xy"   "tbl_df"     "tbl"        "data.frame"

deer

## # A tibble: 826 × 4
##          x_       y_ t_                  burst_
##  *    <dbl>    <dbl> <dttm>               <dbl>
##  1 4314068. 3445807. 2008-03-30 00:01:47      1
##  2 4314053. 3445768. 2008-03-30 06:00:54      1
##  3 4314105. 3445859. 2008-03-30 12:01:47      1
##  4 4314044. 3445785. 2008-03-30 18:01:24      1
##  5 4313015. 3445858. 2008-03-31 00:01:23      1
##  6 4312860. 3445857. 2008-03-31 06:01:45      1
##  7 4312854. 3445856. 2008-03-31 12:01:11      1
##  8 4312858. 3445858. 2008-03-31 18:01:55      1
##  9 4312745. 3445862. 2008-04-01 00:01:24      1
## 10 4312651. 3446024. 2008-04-01 06:00:54      1
## # ℹ 816 more rows

`adehbatit*`

adehabitatLT_ltraj <- as_ltraj(deer)
class(adehabitatLT_ltraj)

## [1] "ltraj" "list"

adehabitatLT_ltraj

## 
## *********** List of class ltraj ***********
## 
## Type of the traject: Type II (time recorded)
## * Time zone: UTC *
## Irregular traject. Variable time lag between two locs
## 
## Characteristics of the bursts:
##         id    burst nb.reloc NAs          date.begin            date.end
## 1 animal_1 animal_1      826   0 2008-03-30 00:01:47 2009-04-28 00:00:21
## 
## 
##  infolocs provided. The following variables are available:
## [1] "pkey"

`ctmm`

With the function as_telemetry a track_xyt can be coerced to a telemetry object used in ctmm.

ctmm_obj <- as_telemetry(deer)
class(ctmm_obj)

## [1] "telemetry"
## attr(,"package")
## [1] "ctmm"

head(ctmm_obj)

##             timestamp longitude latitude          t         x          y
## 1 2008-03-30 00:01:47  9.894014 54.11902 1206835307 787.90305  -12.44995
## 2 2008-03-30 06:00:54  9.893777 54.11867 1206856854 805.32875  -50.41657
## 3 2008-03-30 12:01:47  9.894574 54.11948 1206878507 775.82955   49.58712
## 4 2008-03-30 18:01:24  9.893642 54.11883 1206900084 786.89412  -44.95229
## 5 2008-03-31 00:01:23  9.877903 54.11946 1206921683  26.94402 -739.21455
## 6 2008-03-31 06:01:45  9.875533 54.11945 1206943305 -79.03065 -851.89042

`sf`

There are three functions that convert tracks/steps to tibbles with a geometry columns (sf-objects).

as_sf() converts a track or steps to a point geometry, by calling that the function as_sf_points(). For steps the end points of steps is used by default. Setting end = FALSE will use the start points.
as_sf_point()

It is possible to convert a track and steps to tibble with a geometry column using the function `as_sf

Todo

`move`

Session

sessioninfo::session_info()

## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.5.1 (2025-06-13)
##  os       macOS Sequoia 15.6
##  system   aarch64, darwin20
##  ui       X11
##  language (EN)
##  collate  C
##  ctype    en_US.UTF-8
##  tz       Europe/Berlin
##  date     2025-08-23
##  pandoc   3.4 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
##  quarto   1.6.40 @ /usr/local/bin/quarto
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package      * version  date (UTC) lib source
##  ade4           1.7-23   2025-02-14 [3] CRAN (R 4.5.0)
##  adehabitatLT   0.3.29   2025-06-17 [3] CRAN (R 4.5.0)
##  adehabitatMA   0.3.17   2024-09-06 [3] CRAN (R 4.5.0)
##  amt          * 0.3.0.0  2025-08-23 [1] local
##  backports      1.5.0    2024-05-23 [3] CRAN (R 4.5.0)
##  boot           1.3-31   2024-08-28 [3] CRAN (R 4.5.1)
##  bslib          0.9.0    2025-01-30 [3] CRAN (R 4.5.0)
##  cachem         1.1.0    2024-05-16 [3] CRAN (R 4.5.0)
##  checkmate      2.3.3    2025-08-18 [3] CRAN (R 4.5.0)
##  circular       0.5-1    2024-08-29 [3] CRAN (R 4.5.0)
##  class          7.3-23   2025-01-01 [3] CRAN (R 4.5.1)
##  classInt       0.4-11   2025-01-08 [3] CRAN (R 4.5.0)
##  cli            3.6.5    2025-04-23 [3] CRAN (R 4.5.0)
##  codetools      0.2-20   2024-03-31 [3] CRAN (R 4.5.1)
##  ctmm           1.3.0    2025-07-26 [3] CRAN (R 4.5.1)
##  data.table     1.17.8   2025-07-10 [3] CRAN (R 4.5.0)
##  DBI            1.2.3    2024-06-02 [3] CRAN (R 4.5.0)
##  DEoptimR       1.1-4    2025-07-27 [3] CRAN (R 4.5.0)
##  digest         0.6.37   2024-08-19 [3] CRAN (R 4.5.0)
##  dplyr        * 1.1.4    2023-11-17 [3] CRAN (R 4.5.0)
##  e1071          1.7-16   2024-09-16 [3] CRAN (R 4.5.0)
##  evaluate       1.0.4    2025-06-18 [3] CRAN (R 4.5.0)
##  farver         2.1.2    2024-05-13 [3] CRAN (R 4.5.0)
##  fastmap        1.2.0    2024-05-15 [3] CRAN (R 4.5.0)
##  fitdistrplus   1.2-4    2025-07-03 [3] CRAN (R 4.5.0)
##  generics       0.1.4    2025-05-09 [3] CRAN (R 4.5.0)
##  ggforce        0.5.0    2025-06-18 [3] CRAN (R 4.5.0)
##  ggplot2      * 3.5.2    2025-04-09 [3] CRAN (R 4.5.0)
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##  ggrepel        0.9.6    2024-09-07 [3] CRAN (R 4.5.0)
##  glue           1.8.0    2024-09-30 [3] CRAN (R 4.5.0)
##  Gmedian        1.2.7    2022-06-08 [3] CRAN (R 4.5.0)
##  graphlayouts   1.2.2    2025-01-23 [3] CRAN (R 4.5.0)
##  gridExtra      2.3      2017-09-09 [3] CRAN (R 4.5.0)
##  gtable         0.3.6    2024-10-25 [3] CRAN (R 4.5.0)
##  htmltools      0.5.8.1  2024-04-04 [3] CRAN (R 4.5.0)
##  igraph         2.1.4    2025-01-23 [3] CRAN (R 4.5.0)
##  jquerylib      0.1.4    2021-04-26 [3] CRAN (R 4.5.0)
##  jsonlite       2.0.0    2025-03-27 [3] CRAN (R 4.5.0)
##  KernSmooth     2.23-26  2025-01-01 [3] CRAN (R 4.5.1)
##  knitr        * 1.50     2025-03-16 [3] CRAN (R 4.5.0)
##  labeling       0.4.3    2023-08-29 [3] CRAN (R 4.5.0)
##  lattice        0.22-7   2025-04-02 [3] CRAN (R 4.5.1)
##  lifecycle      1.0.4    2023-11-07 [3] CRAN (R 4.5.0)
##  lubridate    * 1.9.4    2024-12-08 [3] CRAN (R 4.5.0)
##  magrittr       2.0.3    2022-03-30 [3] CRAN (R 4.5.0)
##  MASS           7.3-65   2025-02-28 [3] CRAN (R 4.5.1)
##  Matrix         1.7-3    2025-03-11 [3] CRAN (R 4.5.1)
##  memoise        2.0.1    2021-11-26 [3] CRAN (R 4.5.0)
##  mvtnorm        1.3-3    2025-01-10 [3] CRAN (R 4.5.0)
##  pillar         1.11.0   2025-07-04 [3] CRAN (R 4.5.0)
##  pkgconfig      2.0.3    2019-09-22 [3] CRAN (R 4.5.0)
##  polyclip       1.10-7   2024-07-23 [3] CRAN (R 4.5.0)
##  proxy          0.4-27   2022-06-09 [3] CRAN (R 4.5.0)
##  purrr          1.1.0    2025-07-10 [3] CRAN (R 4.5.0)
##  R6             2.6.1    2025-02-15 [3] CRAN (R 4.5.0)
##  raster         3.6-32   2025-03-28 [3] CRAN (R 4.5.0)
##  rbibutils      2.3      2024-10-04 [3] CRAN (R 4.5.0)
##  RColorBrewer   1.1-3    2022-04-03 [3] CRAN (R 4.5.0)
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##  rstudioapi     0.17.1   2024-10-22 [3] CRAN (R 4.5.0)
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##  sf             1.0-21   2025-05-15 [3] CRAN (R 4.5.0)
##  sp             2.2-0    2025-02-01 [3] CRAN (R 4.5.0)
##  survival       3.8-3    2024-12-17 [3] CRAN (R 4.5.1)
##  terra          1.8-60   2025-07-21 [3] CRAN (R 4.5.0)
##  tibble         3.3.0    2025-06-08 [3] CRAN (R 4.5.0)
##  tidygraph    * 1.3.1    2024-01-30 [3] CRAN (R 4.5.0)
##  tidyr          1.3.1    2024-01-24 [3] CRAN (R 4.5.0)
##  tidyselect     1.2.1    2024-03-11 [3] CRAN (R 4.5.0)
##  timechange     0.3.0    2024-01-18 [3] CRAN (R 4.5.0)
##  tweenr         2.0.3    2024-02-26 [3] CRAN (R 4.5.0)
##  units          0.8-7    2025-03-11 [3] CRAN (R 4.5.0)
##  utf8           1.2.6    2025-06-08 [3] CRAN (R 4.5.0)
##  vctrs          0.6.5    2023-12-01 [3] CRAN (R 4.5.0)
##  viridis        0.6.5    2024-01-29 [3] CRAN (R 4.5.0)
##  viridisLite    0.4.2    2023-05-02 [3] CRAN (R 4.5.0)
##  withr          3.0.2    2024-10-28 [3] CRAN (R 4.5.0)
##  xfun           0.53     2025-08-19 [3] CRAN (R 4.5.0)
##  yaml           2.3.10   2024-07-26 [3] CRAN (R 4.5.0)
## 
##  [1] /private/var/folders/ln/h3zng0fs2pq7mhn_hzn0d8x00000gn/T/RtmpvmiLWg/Rinst1761f5e417fe9
##  [2] /private/var/folders/ln/h3zng0fs2pq7mhn_hzn0d8x00000gn/T/RtmpfKQTmf/temp_libpath16445556b59c1
##  [3] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library
##  * ── Packages attached to the search path.
## 
## ──────────────────────────────────────────────────────────────────────────────

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Interface to other packages with amt