Interface to other packages with amt

Johannes Signer

2021-12-02

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")
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
## # … with 816 more rows

adehbatit*

adehabitatLT_ltraj <- as_ltraj(deer)
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"

move

move_obj <- as_move(deer)
move_obj
## class       : Move 
## features    : 826 
## extent      : 4309723, 4318383, 3442716, 3450713  (xmin, xmax, ymin, ymax)
## crs         : +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs 
## variables   : 1
## names       : burst_ 
## min values  :      1 
## max values  :     35 
## timestamps  : 2008-03-30 00:01:47 ... 2009-04-28 00:00:21 Time difference of 394 days  (start ... end, duration) 
## sensors     : unknown 
## indiv. data :  
## indiv. value:  
## date created: 2021-10-27 07:36:30.642356

To sf and sp

Session

sessioninfo::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 4.1.2 (2021-11-01)
##  os       Ubuntu 20.04.3 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  C                           
##  ctype    en_US.UTF-8                 
##  tz       Europe/Berlin               
##  date     2021-12-02                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package      * version date       lib source        
##  ade4           1.7-18  2021-09-16 [3] CRAN (R 4.1.1)
##  adehabitatLT   0.3.25  2020-01-19 [3] CRAN (R 4.1.1)
##  adehabitatMA   0.3.14  2020-01-13 [3] CRAN (R 4.1.1)
##  amt          * 0.1.5   2021-12-02 [1] local         
##  assertthat     0.2.1   2019-03-21 [3] CRAN (R 4.1.1)
##  backports      1.3.0   2021-10-27 [3] CRAN (R 4.1.1)
##  boot           1.3-28  2021-05-03 [6] CRAN (R 4.0.5)
##  bslib          0.3.1   2021-10-06 [5] CRAN (R 4.1.1)
##  cachem         1.0.6   2021-08-19 [3] CRAN (R 4.1.1)
##  checkmate      2.0.0   2020-02-06 [3] CRAN (R 4.1.1)
##  CircStats      0.2-6   2018-07-01 [3] CRAN (R 4.1.1)
##  circular       0.4-93  2017-06-29 [3] CRAN (R 4.1.1)
##  class          7.3-19  2021-05-03 [6] CRAN (R 4.0.5)
##  classInt       0.4-3   2020-04-07 [3] CRAN (R 4.1.1)
##  cli            3.1.0   2021-10-27 [3] CRAN (R 4.1.1)
##  codetools      0.2-18  2020-11-04 [6] CRAN (R 4.0.3)
##  colorspace     2.0-2   2021-06-24 [3] CRAN (R 4.1.1)
##  crayon         1.4.2   2021-10-29 [3] CRAN (R 4.1.1)
##  ctmm           0.6.1   2021-07-28 [3] CRAN (R 4.1.1)
##  DBI            1.1.1   2021-01-15 [3] CRAN (R 4.1.1)
##  DEoptimR       1.0-9   2021-05-24 [3] CRAN (R 4.1.1)
##  digest         0.6.28  2021-09-23 [3] CRAN (R 4.1.1)
##  dplyr        * 1.0.7   2021-06-18 [3] CRAN (R 4.1.1)
##  e1071          1.7-9   2021-09-16 [3] CRAN (R 4.1.1)
##  ellipsis       0.3.2   2021-04-29 [3] CRAN (R 4.1.1)
##  evaluate       0.14    2019-05-28 [3] CRAN (R 4.1.1)
##  fansi          0.5.0   2021-05-25 [3] CRAN (R 4.1.1)
##  farver         2.1.0   2021-02-28 [3] CRAN (R 4.1.1)
##  fastmap        1.1.0   2021-01-25 [3] CRAN (R 4.1.1)
##  fitdistrplus   1.1-6   2021-09-28 [3] CRAN (R 4.1.1)
##  generics       0.1.1   2021-10-25 [3] CRAN (R 4.1.1)
##  geosphere      1.5-14  2021-10-13 [3] CRAN (R 4.1.1)
##  ggforce        0.3.3   2021-03-05 [3] CRAN (R 4.1.1)
##  ggplot2      * 3.3.5   2021-06-25 [3] CRAN (R 4.1.1)
##  ggraph       * 2.0.5   2021-02-23 [3] CRAN (R 4.1.1)
##  ggrepel        0.9.1   2021-01-15 [3] CRAN (R 4.1.1)
##  glue           1.4.2   2020-08-27 [3] CRAN (R 4.1.1)
##  Gmedian        1.2.6   2021-04-07 [3] CRAN (R 4.1.1)
##  graphlayouts   0.7.1   2020-10-26 [3] CRAN (R 4.1.1)
##  gridExtra      2.3     2017-09-09 [3] CRAN (R 4.1.1)
##  gtable         0.3.0   2019-03-25 [3] CRAN (R 4.1.1)
##  highr          0.9     2021-04-16 [3] CRAN (R 4.1.1)
##  htmltools      0.5.2   2021-08-25 [3] CRAN (R 4.1.1)
##  httr           1.4.2   2020-07-20 [3] CRAN (R 4.1.1)
##  igraph         1.2.7   2021-10-15 [3] CRAN (R 4.1.1)
##  jquerylib      0.1.4   2021-04-26 [3] CRAN (R 4.1.1)
##  jsonlite       1.7.2   2020-12-09 [3] CRAN (R 4.1.1)
##  KernSmooth     2.23-20 2021-05-03 [6] CRAN (R 4.0.5)
##  knitr        * 1.36    2021-09-29 [3] CRAN (R 4.1.1)
##  labeling       0.4.2   2020-10-20 [3] CRAN (R 4.1.1)
##  lattice        0.20-45 2021-09-22 [6] CRAN (R 4.1.1)
##  lifecycle      1.0.1   2021-09-24 [3] CRAN (R 4.1.1)
##  lubridate    * 1.8.0   2021-10-07 [3] CRAN (R 4.1.1)
##  magrittr       2.0.1   2020-11-17 [3] CRAN (R 4.1.1)
##  MASS           7.3-54  2021-05-03 [6] CRAN (R 4.0.5)
##  Matrix         1.3-4   2021-06-01 [6] CRAN (R 4.1.0)
##  memoise        2.0.0   2021-01-26 [3] CRAN (R 4.1.1)
##  move           4.0.6   2020-11-26 [3] CRAN (R 4.1.1)
##  munsell        0.5.0   2018-06-12 [3] CRAN (R 4.1.1)
##  mvtnorm        1.1-3   2021-10-08 [3] CRAN (R 4.1.1)
##  pillar         1.6.4   2021-10-18 [3] CRAN (R 4.1.1)
##  pkgconfig      2.0.3   2019-09-22 [3] CRAN (R 4.1.1)
##  polyclip       1.10-0  2019-03-14 [3] CRAN (R 4.1.1)
##  proxy          0.4-26  2021-06-07 [3] CRAN (R 4.1.1)
##  purrr          0.3.4   2020-04-17 [3] CRAN (R 4.1.1)
##  R6             2.5.1   2021-08-19 [3] CRAN (R 4.1.1)
##  raster       * 3.5-2   2021-10-11 [3] CRAN (R 4.1.1)
##  rbibutils      2.2.4   2021-10-11 [3] CRAN (R 4.1.1)
##  Rcpp           1.0.7   2021-07-07 [3] CRAN (R 4.1.1)
##  Rdpack         2.1.2   2021-06-01 [3] CRAN (R 4.1.1)
##  rgdal          1.5-27  2021-09-16 [3] CRAN (R 4.1.1)
##  rgeos          0.5-8   2021-09-22 [3] CRAN (R 4.1.1)
##  rlang          0.4.12  2021-10-18 [3] CRAN (R 4.1.1)
##  rmarkdown      2.11    2021-09-14 [3] CRAN (R 4.1.1)
##  robustbase     0.93-9  2021-09-27 [3] CRAN (R 4.1.1)
##  RSpectra       0.16-0  2019-12-01 [3] CRAN (R 4.1.1)
##  rstudioapi     0.13    2020-11-12 [5] CRAN (R 4.0.3)
##  sass           0.4.0   2021-05-12 [5] CRAN (R 4.0.5)
##  scales         1.1.1   2020-05-11 [3] CRAN (R 4.1.1)
##  sessioninfo    1.1.1   2018-11-05 [3] CRAN (R 4.1.1)
##  sf             1.0-3   2021-10-07 [3] CRAN (R 4.1.1)
##  sp           * 1.4-5   2021-01-10 [3] CRAN (R 4.1.1)
##  stringi        1.7.5   2021-10-04 [3] CRAN (R 4.1.1)
##  stringr        1.4.0   2019-02-10 [3] CRAN (R 4.1.1)
##  survival       3.2-13  2021-08-24 [6] CRAN (R 4.1.1)
##  terra          1.4-11  2021-10-11 [3] CRAN (R 4.1.1)
##  tibble         3.1.5   2021-09-30 [3] CRAN (R 4.1.1)
##  tidygraph    * 1.2.0   2020-05-12 [3] CRAN (R 4.1.1)
##  tidyr          1.1.4   2021-09-27 [3] CRAN (R 4.1.1)
##  tidyselect     1.1.1   2021-04-30 [3] CRAN (R 4.1.1)
##  tweenr         1.0.2   2021-03-23 [3] CRAN (R 4.1.1)
##  units          0.7-2   2021-06-08 [3] CRAN (R 4.1.1)
##  utf8           1.2.2   2021-07-24 [3] CRAN (R 4.1.1)
##  vctrs          0.3.8   2021-04-29 [3] CRAN (R 4.1.1)
##  viridis        0.6.2   2021-10-13 [3] CRAN (R 4.1.1)
##  viridisLite    0.4.0   2021-04-13 [3] CRAN (R 4.1.1)
##  withr          2.4.2   2021-04-18 [3] CRAN (R 4.1.1)
##  xfun           0.27    2021-10-18 [3] CRAN (R 4.1.1)
##  xml2           1.3.2   2020-04-23 [3] CRAN (R 4.1.1)
##  yaml           2.2.1   2020-02-01 [3] CRAN (R 4.1.1)
## 
## [1] /tmp/RtmpXBk6U6/Rinst292653af4766d
## [2] /tmp/RtmpURq9WN/temp_libpath2126b766c140d
## [3] /home/jsigner/R/x86_64-pc-linux-gnu-library/4.1
## [4] /usr/local/lib/R/site-library
## [5] /usr/lib/R/site-library
## [6] /usr/lib/R/library