Interpolate GPS locations at a set time interval using a continuous time correlated random walk (ctcrw) model

This function is a wrapper for momentuHMM::crawlWrap(), which uses the crawl package to fit ctcrw model to GPS tracks at a user-defined time interval. The function is currently designed to handle GPS data from central place foraging birds. It takes tracking data, where trips have been identified and classified using OPPTools::opp_get_trips(). The function returns a list with four objects: (1) original tracking data (as SPDF), (2) colony location (as SPDF), (3) interpolated locations (as SPDF), and (4) a list of CRAWL fits for each trip. All spatial objects are in the same custom Lambert equal area projection centered on the colony.

Usage

ctcrw_interpolation(
  data,
  site,
  type,
  timestep,
  interpolateGaps = TRUE,
  showPlots = TRUE,
  plotsPerPage = 4,
  theta = c(8, 2),
  quiet = TRUE
)

Arguments

data: Trip data ouptut from OPPTools::opp_get_trips().
site: Vector containing coordinates of the study site, in the same format as site information returned by OPPtools::opp2KBA or track2KBA::move2KBA.
type: List indicating the types of trips to include in interpolation. Possible values are: 'Complete', 'Incomplete', 'Gappy', and 'Non-trip'. Default is 'Complete'.
timestep: string indicating time step for track interpolation, eg. '10 min', '1 hour', '1 day'
showPlots: TRUE/FALSE should plots of interpolated tracks against original data be produced
plotsPerPage: Numeric indicating the number of individuals to include in a single plot. Defaults to 4.
theta: starting values for ctcrw parameter optimization, see ?crawl::crwMLE for details

Examples

my_data <- opp_download_data(study = c(1247096889),login = NULL, start_month = NULL,
                            end_month = NULL,season = NULL)
#> Warning: 0 location(s) is/are removed by removeDuplicatedTimestamps

my_track2kba <- opp2KBA(data = my_data)

my_trips <- opp_get_trips(data = my_track2kba, innerBuff  = 5, returnBuff = 20,
                         duration  = 2, gapLimit = 100, gapTime = 2, gapDist = 5,
                         showPlots = TRUE)
#> Registered S3 methods overwritten by 'adehabitatMA':
#>   method                       from
#>   print.SpatialPixelsDataFrame sp  
#>   print.SpatialPixels          sp  
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html



#> Use back arrow in plot pane to browse all plots




my_interp <- ctcrw_interpolation(data = my_trips,
                   site = my_track2kba$site,
                   type = c('Complete','Incomplete','Gappy'),
                   timestep = '10 min',
                   interpolateGaps = T,
                   showPlots = T,
                   plotsPerPage = 2,
                   theta = c(8,2)
)
#> crawl 2.2.1 (2018-09-12) 
#>  Demos and documentation can be found at our new GitHub repository:
#>  https://dsjohnson.github.io/crawl_examples/
#> Loading required package: foreach
#> Loading required package: rngtools
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Warning: CRS object has comment, which is lost in output; in tests, see
#> https://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html
#> Beginning SANN initialization ...
#> Beginning likelihood optimization ...





#> Use back arrow in plot pane to browse all plots