mtreg · December 11, 2020 21:13
diff --git a/gdbs_compile_layers.R b/gdbs_compile_layers.R
 ############################################################
 #' Compile layers from different gdb files with same, specified prefix, and desired coordinate system
 #'
 #' Compiles layers with standard prefix from multiple gdb files (specified by user) into single sf object. 
 #' This was originally developed to get respective layers from separate geodatabases that resulted from running the ACPF toolbox
 #' into single layers (e.g., all stream reach datasets into one layer, rather than spread across many gdb files) but may have broader applicability.
 #' (ACPF stands for Agricultural Conservaton Planning Framework; see https://acpf4watersheds.org/toolbox/)
 #'
 #' The handling of different projections is currently fairly crude - it just automatically reprojects files to the desired projection
 #' (even if already in that projection), though that step is generally fairly quick.
 #'
 #'   
 #' @param folder Folder with gdb files of interest
 #' @param prefix Common prefix for layers to combine.
 #' @param CRS Coordinate Reference System to project data to. If EPSG code, integer without quotes will work, but if proj4 code, use quotes.
 #' @return sf object
 #' @author Mike Treglia \email{michael.treglia@@tnc.org}
 #' #' @example 
 #'    ## Example assuming multiple gdb files are in D:/gdb_testing, and StreamReach layers are desired
 #'    sr <- gdbs_compile_layers(folder="D:/gdb_testing/", prefix="StreamReach", CRS=2263)
 #'    
 #'    # Users can easily explore results using the mapview package (not recommended for huge datasets)
 #'    # mapview::mapview(sr)
 #'    
 #'    ## Users can write out results to file - e.g., using st_write
 #'    # st_write(sr, dsn="D:/gdb_testing/StreamReach_Layers_Compiled.gpkg", layer="StreamReach_Layers_Compiled")
 #'    
 #'    

 gdbs_compile_layers <- function(folder, prefix, CRS) {
  ## Create a vector with the names of the gdb files
  require(sf) 
  
  lf <-
    list.files(path = folder,
               pattern = "*.gdb",
               full.names = TRUE)
  
  ## Create a list that is the same length (# of elements) as number of gdb folders
  l1 <- vector(mode = "list", length = length(lf))
  
  ## Fill in the list with a for loop
  ## Each element of the list is a data frame with a column of gdb name ('gdb') and column of layer name ('layer')
  for (i in 1:length(lf)) {
    l1[[i]] <-
      data.frame(
        gdb = rep(lf[i], length(sf::st_layers(lf[i])$name)),
        layer = sf::st_layers(lf[i])$name,
        stringsAsFactors = FALSE
      )
  }
  
  ## Create one dataframe of all gdb file names and layers
  gdb.layers <- do.call("rbind", l1)
  
  ## Select only rows that match have the desired prefix (StreamReach in this case)
  newdata <- gdb.layers[grepl(prefix, gdb.layers$layer),]
  
  
  ## Create new vector, l2, which will become a list of the respective sf objects
  l2 <- vector(mode = "list", length = nrow(newdata))
  
  ## Read in the sf objects
  for (i in 1:length(lf)) {
    l2[[i]] <-
      sf::st_read(
        dsn = newdata$gdb[i],
        layer = newdata$layer[i],
        stringsAsFactors = FALSE,
        quiet=TRUE
      )
 	 l2[[i]] <-
 		sf::st_transform(l2[[i]], crs=CRS)
      
  }
  
  ## Put together full dataset
  newdata_full <- do.call(rbind, l2)
  print(paste("layers beginning with '", prefix, "' were compiled with the following CRS: '", 
             CRS, "'.", sep="" ))
  
  return(newdata_full)
  
  
 }
	############################################################
	#' Compile layers from different gdb files with same, specified prefix, and desired coordinate system
	#'
	#' Compiles layers with standard prefix from multiple gdb files (specified by user) into single sf object.
	#' This was originally developed to get respective layers from separate geodatabases that resulted from running the ACPF toolbox
	#' into single layers (e.g., all stream reach datasets into one layer, rather than spread across many gdb files) but may have broader applicability.
	#' (ACPF stands for Agricultural Conservaton Planning Framework; see https://acpf4watersheds.org/toolbox/)
	#'
	#' The handling of different projections is currently fairly crude - it just automatically reprojects files to the desired projection
	#' (even if already in that projection), though that step is generally fairly quick.
	#'
	#'
	#' @param folder Folder with gdb files of interest
	#' @param prefix Common prefix for layers to combine.
	#' @param CRS Coordinate Reference System to project data to. If EPSG code, integer without quotes will work, but if proj4 code, use quotes.
	#' @return sf object
	#' @author Mike Treglia \email{michael.treglia@@tnc.org}
	#' #' @example
	#' ## Example assuming multiple gdb files are in D:/gdb_testing, and StreamReach layers are desired
	#' sr <- gdbs_compile_layers(folder="D:/gdb_testing/", prefix="StreamReach", CRS=2263)
	#'
	#' # Users can easily explore results using the mapview package (not recommended for huge datasets)
	#' # mapview::mapview(sr)
	#'
	#' ## Users can write out results to file - e.g., using st_write
	#' # st_write(sr, dsn="D:/gdb_testing/StreamReach_Layers_Compiled.gpkg", layer="StreamReach_Layers_Compiled")
	#'
	#'

	gdbs_compile_layers <- function(folder, prefix, CRS) {
	## Create a vector with the names of the gdb files
	require(sf)

	lf <-
	list.files(path = folder,
	pattern = "*.gdb",
	full.names = TRUE)

	## Create a list that is the same length (# of elements) as number of gdb folders
	l1 <- vector(mode = "list", length = length(lf))

	## Fill in the list with a for loop
	## Each element of the list is a data frame with a column of gdb name ('gdb') and column of layer name ('layer')
	for (i in 1:length(lf)) {
	l1[[i]] <-
	data.frame(
	gdb = rep(lf[i], length(sf::st_layers(lf[i])$name)),
	layer = sf::st_layers(lf[i])$name,
	stringsAsFactors = FALSE
	)
	}

	## Create one dataframe of all gdb file names and layers
	gdb.layers <- do.call("rbind", l1)

	## Select only rows that match have the desired prefix (StreamReach in this case)
	newdata <- gdb.layers[grepl(prefix, gdb.layers$layer),]


	## Create new vector, l2, which will become a list of the respective sf objects
	l2 <- vector(mode = "list", length = nrow(newdata))

	## Read in the sf objects
	for (i in 1:length(lf)) {
	l2[[i]] <-
	sf::st_read(
	dsn = newdata$gdb[i],
	layer = newdata$layer[i],
	stringsAsFactors = FALSE,
	quiet=TRUE
	)
	l2[[i]] <-
	sf::st_transform(l2[[i]], crs=CRS)

	}

	## Put together full dataset
	newdata_full <- do.call(rbind, l2)
	print(paste("layers beginning with '", prefix, "' were compiled with the following CRS: '",
	CRS, "'.", sep="" ))

	return(newdata_full)


	}