List `record' files from an AC/DC algorithm for PF

This function creates an ordered list of `record' files derived from the AC/DC/ACDC algorithm (ac, dc or acdc) for particle filtering (PF) via pf.

pf_setup_record(root, type = c("acs", "dc"), use_absolute_paths = FALSE, ...)

Arguments

root: A string that defines the directory in which files are loaded.
type: A character that defines the source of the files (type = "acs" refers to an AC* algorithm and type = "dc" refers to the DC algorithm).
use_absolute_paths: A logical variable that defines whether to return relative paths (FALSE) or absolute paths (TRUE) (see file_path_as_absolute).
...: Additional arguments passed to list.files (excluding full.names).

Value

The function returns an ordered list of file paths.

Details

This function requires the stringr package.

Author

Edward Lavender

Examples

#### Example (1): Example with the AC algorithm
# Define a directory in which to save files
root <- paste0(tempdir(), "/ac/")
dir.create(root)
# Implement the AC algorithm for some example time series
acc <- dat_acoustics[dat_acoustics$individual_id == 25, ][1:5, ]
out_ac <- ac(
  acoustics = acc,
  step = 120,
  bathy = dat_gebco,
  detection_containers = dat_containers,
  mobility = 250,
  write_record_spatial_for_pf = list(filename = root)
)
#> flapper::ac() called (@ 2023-08-29 15:45:47)...
#> flapper::.acs_pl() called (@ 2023-08-29 15:45:47)... 
#> ... Checking user inputs... 
#> ... Processing movement time series... 
#> ... Plotting movement time series (for each chunk)... 
#> ... Calling .acs() to implement ACDC algorithm on one chunk... 
#> flapper::.acs() called (@ 2023-08-29 15:45:47)... 
#> 
  |                                                                            
  |                                                                      |   0%... Initiating algorithm: moving over acoustic and internal ('archival') time steps... 
#> ... On acoustic time step ('timestep_detection') 1. 
#> ... ... On internal time step ('timestep_archival') 1. 
#> 
  |                                                                            
  |==================                                                    |  25%... On acoustic time step ('timestep_detection') 2. 
#> ... ... On internal time step ('timestep_archival') 1. 
#> 
  |                                                                            
  |===================================                                   |  50%... On acoustic time step ('timestep_detection') 3. 
#> ... ... On internal time step ('timestep_archival') 1. 
#> ... ... On internal time step ('timestep_archival') 2. 
#> ... ... ... Acoustic container is expanding... 
#> Warning: GEOS support is provided by the sf and terra packages among others
#> 
  |                                                                            
  |====================================================                  |  75%... On acoustic time step ('timestep_detection') 4. 
#> ... ... On internal time step ('timestep_archival') 1. 
#> 
  |                                                                            
  |======================================================================| 100%
#> ... Movement over acoustic and internal ('archival') time steps has been completed. 
#> ... flapper::.acs() call completed (@ 2023-08-29 15:45:47) after ~0.01 minutes. 
#> ... flapper::.acs_pl() call completed (@ 2023-08-29 15:45:47) after ~0.01 minutes. 
#> flapper::ac() finished (@ 2023-08-29 15:45:47)...

# List the files for pf()
files <- pf_setup_record(root, type = "acs", pattern = "*.grd")
utils::head(files)
#> [1] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/ac//chu_1_acc_1_arc_1.grd"
#> [2] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/ac//chu_1_acc_2_arc_1.grd"
#> [3] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/ac//chu_1_acc_3_arc_1.grd"
#> [4] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/ac//chu_1_acc_3_arc_2.grd"
#> [5] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/ac//chu_1_acc_4_arc_1.grd"
# Implement pf() using files (not shown).

#### Example (2): Example with the DC algorithm
# Define a directory in which to save files
root <- paste0(tempdir(), "/dc/")
dir.create(root)
# Implement the DC algorithm for some example time series
depth <- dat_archival[dat_archival$individual_id == 25, ][1:5, ]
out_dc <- dc(
  archival = depth,
  bathy = dat_gebco,
  write_record_spatial_for_pf = list(filename = root)
)
#> flapper::dc() called (@ 2023-08-29 15:45:47)... 
#> ... Setting up function... 
#> 'calc_depth_error' function taken to be independent of depth.
#> ... Implementing calc_depth_error()... 
#> ... Plotting movement time series (for each chunk)... 

#> ... Implementing algorithm over time steps... 
#> ... flapper::dc() call completed (@ 2023-08-29 15:45:47) after ~0 minutes. 
# List the files for pf()
files <- pf_setup_record(root, type = "dc", pattern = "*.grd")
utils::head(files)
#> [1] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/dc//arc_1.grd"
#> [2] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/dc//arc_2.grd"
#> [3] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/dc//arc_3.grd"
#> [4] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/dc//arc_4.grd"
#> [5] "/var/folders/nl/ygb3g6tj24z06jddbqqhj6hw0000gn/T//Rtmpwb5KFV/dc//arc_5.grd"
# Implement pf() using files (not shown).