Skip to contents

Get the file path for WATLAS or GIS data based on the user's name.

Source: R/fun_file_path.R
atl_file_path.Rd

This function returns a predefined file path based on the user's system username and the selected data type. Users must be predefined in the function.

Usage

atl_file_path(
  data_type = c("watlas_teams", "rasters", "shapefiles", "sqlite_db")
)

Arguments

data_type

A character string indicating the type of data. Options are:

  • "watlas_teams": Path to “WATLAS” SharePoint folder: Documents/data/

  • "rasters": Path to “Birds, fish ’n chips” SharePoint folder: Documents/data/GIS/rasters/

  • "shapefiles": Path to “Birds, fish ’n chips” SharePoint folder: Documents/data/GIS/shapefiles/

  • "sqlite_db": Path to ZEUS folder: ZEUS/cos/birds/bijleveld/fieldwork/WATLAS/localizations

Value

A character string representing the full file path to the selected data type for the current user.

Details

For local users with access to the NIOZ network, I would recommend to add a shortcut to your OneDrive of the “WATLAS” SharePoint folder: Documents/data/. The path in the function then refers to this copy on your OneDrive. Files in this folder (e.g. tags_watlas_all.xlsx and tide data) are often updated and changes are then automatically updated on your computer.

The second source of data is the “Birds, fish ’n chips” SharePoint folder: Documents/data/GIS/ which has the subfolders rasters and shapefiles. One can also create a OneDrive shortcut for this folder, however it contains many large files and files usually don't change. I would therefore recommend to only copy necessary data in a local folder on your computer and then link the path to this folder.

To build all articles for the package website, you need to specify your user paths here.

Examples

if (FALSE) { # \dontrun{
# test if all files can be accessed using atl_file_path() function

# packages
library(tools4watlas)

# file path to WATLAS teams data folder
fp <- atl_file_path("watlas_teams")
# check file path exists
file.exists(paste0(
  fp, "waterdata/allYears-tidalPattern-west_terschelling-UTC.csv"
))

# file path to Birds, fish 'n chips GIS/rasters folder
fp <- atl_file_path("rasters")
# check file path exists
file.exists(paste0(fp, "bathymetry/2024/bodemhoogte_20mtr_UTM31_int.tif"))


# file path to Birds, fish 'n chips GIS/shapefiles folder
fp <- atl_file_path("shapefiles")
# check file path exists
file.exists(
  paste0(fp, "open_street_map/land-polygons-complete-4326/land_polygons.shp")
)

# file path to sqlite databases
db_fp <- atl_file_path("sqlite_db")
# check file path exists
file.exists(
  paste0(db_fp, "watlas-2024.sqlite")
)
} # }