Set up global directory paths and create folders

This function sets up a directory for saving outputs (i.e. data, figures) generated through the use of the BeeBDC package, if the required folders do not already exist.

Usage

dirMaker(
  RootPath = RootPath,
  ScriptPath = NULL,
  DataPath = NULL,
  DataSubPath = "/Data_acquisition_workflow",
  DiscLifePath = NULL,
  OutPath = NULL,
  OutPathName = "Output",
  Report = TRUE,
  Check = TRUE,
  Figures = TRUE,
  Intermediate = TRUE,
  RDoc = NULL,
  useHere = TRUE
)

Arguments

RootPath: A character String. The RootPath is the base path for your project, and all other paths should ideally be located within the RootPath. However, users may specify paths not contained in the RootPath
ScriptPath: A character String. The ScriptPath is the path to any additional functions that you would like to read in for use with BeeBDC.
DataPath: A character string. The path to the folder containing bee occurrence data to be flagged and/or cleaned
DataSubPath: A character String. If a DataPath is not provided, this will be used as the DataPath folder name within the RootPath. Default is "/Data_acquisition_workflow"
DiscLifePath: A character String. The path to the folder which contains data from Ascher and Pcikering's Discover Life website.
OutPath: A character String. The path to the folder where output data will be saved.
OutPathName: A character String. The name of the OutPath subfolder located within the RootPath. Default is "Output".
Report: Logical. If TRUE, function creates a "Report" folder within the OutPath-defined folder. Default = TRUE.
Check: Logical. If TRUE, function creates a "Check" folder within the OutPath-defined folder. Default = TRUE.
Figures: Logical. If TRUE, function creates a "Figures" folder within the OutPath-defined folder. Default = TRUE.
Intermediate: Logical. If TRUE, function creates a "Intermediate" folder within the OutPath-defined folder in which to save intermediate datasets. Default = TRUE.
RDoc: A character String. The path to the current script or report, relative to the project root. Passing an absolute path raises an error. This argument is used by here::i_am() and incorrectly setting this may result in bdc figures being saved to your computer's root directory
useHere: Logical. If TRUE, dirMaker will use here::i_am() to declare the relative path to 'RDoc'. This is aimed at preserving some functionality with where bdc saves summary figures and tables. Default = TRUE.

Value

Results in the generation of a list containing the BeeBDC-required directories in your global environment. This function should be run at the start of each session. Additionally, this function will create the BeeBDC-required folders if they do not already exist in the supplied directory

Examples

  # load dplyr
  library(dplyr)
# Standard/basic usage:
RootPath <- tempdir()
dirMaker(
RootPath = RootPath,
# Input the location of the workflow script RELATIVE to the RootPath
RDoc = NULL,
useHere = FALSE) %>%
  # Add paths created by this function to the environment()
  list2env(envir = environment())  
#>  - We created the /tmp/RtmpGVhMj8/BDC_repo/BeeBDC/Rfile. This file needs to have the NewFunctions added to it otherise things won't work. These can be added from our GitHub
#>  - We created the /tmp/RtmpGVhMj8/Data_acquisition_workflowfile. This file needs to have the occurrence data that you want to use added to it otherise things won't work. Please choose this data or download it from the supp. materials of our paper
#> Warning: '/tmp/RtmpGVhMj8/BDC_repo/DiscoverLife_Data' already exists
#>  - We created the /tmp/RtmpGVhMj8/BDC_repo/DiscoverLife_Datafile. This file needs to have the DiscoverLife_Data added to it otherise things won't work. These can be added from our GitHub
#> Warning: '/tmp/RtmpGVhMj8/Data_acquisition_workflow/Output' already exists
#>  - We created the /tmp/RtmpGVhMj8/Data_acquisition_workflow/Outputfile.
#> <environment: 0x5652a6166d48>

# Custom OutPathName provided
  dirMaker(
 RootPath = RootPath,
 # Set some custom OutPath info
 OutPath = NULL,
 OutPathName = "T2T_Output",
 # Input the location of the workflow script RELATIVE to the RootPath
 RDoc = NULL,
 useHere = FALSE) %>%
   # Add paths created by this function to the environment()
   list2env(envir = environment())  
#> Warning: '/tmp/RtmpGVhMj8/Data_acquisition_workflow/T2T_Output' already exists
#>  - We created the /tmp/RtmpGVhMj8/Data_acquisition_workflow/T2T_Outputfile.
#> <environment: 0x5652ab6e1da0>
 # Set the working directory

# Further customisations are also possible
dirMaker(
  RootPath = RootPath,
  ScriptPath = "...path/Bee_SDM_paper/BDC_repo/BeeBDC/R",
  DiscLifePath = "...path/BDC_repo/DiscoverLife_Data",
  OutPathName = "AsianPerspective_Output",
  # Input the location of the workflow script RELATIVE to the RootPath
  RDoc = NULL,
  useHere = FALSE) %>%
  # Add paths created by this function to the environment()
  list2env(envir = environment())  
#>  - We created the ...path/Bee_SDM_paper/BDC_repo/BeeBDC/Rfile. This file needs to have the NewFunctions added to it otherise things won't work. These can be added from our GitHub
#> Warning: '...path/BDC_repo/DiscoverLife_Data' already exists
#>  - We created the ...path/BDC_repo/DiscoverLife_Datafile. This file needs to have the DiscoverLife_Data added to it otherise things won't work. These can be added from our GitHub
#> Warning: '/tmp/RtmpGVhMj8/Data_acquisition_workflow/AsianPerspective_Output' already exists
#>  - We created the /tmp/RtmpGVhMj8/Data_acquisition_workflow/AsianPerspective_Outputfile.
#> <environment: 0x5652ab874f50>