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#'@name lagos_ingest
#'@title Ingest LAGOSNE flat files
#'@description Ingest LAGOSNE data from component flat files
#'@param version character LAGOSNE database version string
#'@param limno_folder file.path to limno export folder. optional.
#'@param geo_folder file.path to geo export folder. optional.
#'@param locus_folder file.path to locus export folder. optional.
#'@importFrom utils read.table
#'@importFrom progress progress_bar
#'@examples \dontrun{
#' lagos_ingest("1.087.3",
#' limno_folder = "~/Downloads/LAGOS-NE-LIMNO-EXPORT",
#' geo_folder = "~/Downloads/LAGOS-NE-GEO-EXPORT",
#' locus_folder = "~/Downloads/LAGOS-NE-LOCUS-EXPORT")
#'}
lagos_ingest <- function(version, limno_folder = NA, geo_folder = NA,
locus_folder = NA){
pb <- progress::progress_bar$new(format = " Reading :type [:bar]",
total = 9,
clear = FALSE)
folder_version <- gsub("\\.", "", version)
# Set-up paths ####
limno_prefix <- paste0(limno_folder, "/")
limno_path <- function(fname){
paste0(limno_prefix,
fname, folder_version, ".csv")
}
geo_prefix <- paste0(geo_folder, "/", "LAGOSNE_")
geo_path <- function(fname, geo_prefix){
paste0(geo_prefix,
fname, "105.csv")
}
locus_prefix <- paste0(locus_folder, "/", "LAGOSNE_")
locus_path <- function(fname){
paste0(locus_prefix,
fname, "101.csv")
}
# Importing LAGOS limno data ####
pb$tick(tokens = list(type = "limno data"))
epi_nutr <- load_lagos_txt(limno_path("epi_waterquality"),
sep = ",")
epi_nutr$sampledate <- as.Date(strptime(epi_nutr$sampledate,
format = "%Y-%m-%d"))
lakes_limno <- read.csv(limno_path("lakeslimno"),
stringsAsFactors = FALSE)
lakes_limno$legacyid <-
suppressWarnings(sapply(lakes_limno$legacyid, format_nonscientific))
lagos_source_program <- load_lagos_txt(limno_path("sourceprogram"),
sep = ",")
limno <- list(epi_nutr = epi_nutr,
lakes_limno = lakes_limno,
lagos_source_program = lagos_source_program)
# Importing Lagos Geo data ####
lakes.geo <- load_lagos_txt(
geo_path("lakesgeo", paste0(geo_folder, "/", "LAGOSNE_")),
sep = ",")
# Importing Lagos Geo county data
pb$tick(tokens = list(type = "geo county data"))
county <- load_lagos_txt(geo_path("county_", geo_prefix),
sep = ",")
county.chag <- load_lagos_txt(geo_path("county_chag", geo_prefix),
sep = ",")
county.conn <- load_lagos_txt(geo_path("county_conn", geo_prefix),
sep = ",")
county.lulc <- load_lagos_txt(geo_path("county_lulc", geo_prefix),
sep = ",")
# Importing Lagos Geo edu data
pb$tick(tokens = list(type = "geo edu data"))
edu <- load_lagos_txt(geo_path("edu_", geo_prefix),
sep = ",")
edu.chag <- load_lagos_txt(geo_path("edu_chag", geo_prefix),
sep = ",")
edu.conn <- load_lagos_txt(geo_path("edu_conn", geo_prefix),
sep = ",")
edu.lulc <- load_lagos_txt(geo_path("edu_lulc", geo_prefix),
sep = ",")
# Importing Lagos Geo huc4 data
pb$tick(tokens = list(type = "geo huc4 data"))
hu4 <- load_lagos_txt(geo_path("hu4_", geo_prefix),
colClasses = c("hu4" = "factor"),
sep = ",")
hu4 <- pad_huc_ids(hu4, "hu4", 4)
hu4.chag <- load_lagos_txt(geo_path("hu4_chag", geo_prefix),
sep = ",")
hu4.conn <- load_lagos_txt(geo_path("hu4_conn", geo_prefix), as.is = TRUE,
sep = ",")
hu4.lulc <- load_lagos_txt(geo_path("hu4_lulc", geo_prefix), as.is = TRUE,
sep = ",")
# Importing Lagos Geo huc8 data
pb$tick(tokens = list(type = "geo huc8 data"))
hu8 <- load_lagos_txt(geo_path("hu8_", geo_prefix),
colClasses = c("hu8" = "factor"),
sep = ",")
hu8 <- pad_huc_ids(hu8, "hu8", 8)
hu8.chag <- load_lagos_txt(geo_path("hu8_chag", geo_prefix), as.is = TRUE,
sep = ",")
hu8.conn <- load_lagos_txt(geo_path("hu8_conn", geo_prefix), as.is = TRUE,
sep = ",")
hu8.lulc <- load_lagos_txt(geo_path("hu8_lulc", geo_prefix), as.is = TRUE,
sep = ",")
# Importing Lagos Geo huc12 data
pb$tick(tokens = list(type = "geo huc12 data"))
hu12 <- load_lagos_txt(geo_path("hu12_", geo_prefix),
colClasses = c("hu12" = "factor"),
sep = ",")
hu12 <- pad_huc_ids(hu12, "hu12", 12)
hu12.chag <- load_lagos_txt(geo_path("hu12_chag", geo_prefix),
as.is = TRUE, sep = ",")
hu12.conn <- load_lagos_txt(geo_path("hu12_conn", geo_prefix),
as.is = TRUE, sep = ",")
hu12.lulc <- load_lagos_txt(geo_path("hu12_lulc", geo_prefix),
as.is = TRUE, sep = ",")
# Importing Lagos Geo iws data
pb$tick(tokens = list(type = "geo iws data"))
iws <- load_lagos_txt(geo_path("iws_", geo_prefix),
sep = ",")
iws.conn <- load_lagos_txt(geo_path("iws_conn", geo_prefix),
sep = ",")
iws.lulc <- load_lagos_txt(geo_path("iws_lulc", geo_prefix),
sep = ",")
# Importing Lagos Geo state data
state <- load_lagos_txt(geo_path("state_", geo_prefix),
sep = ",")
state.chag <- load_lagos_txt(geo_path("state_chag", geo_prefix),
sep = ",")
state.conn <- load_lagos_txt(geo_path("state_conn", geo_prefix),
sep = ",")
state.lulc <- load_lagos_txt(geo_path("state_lulc", geo_prefix),
sep = ",")
# Importing lake buffer data ####
pb$tick(tokens = list(type = "geo buffer data"))
buffer100m <- load_lagos_txt(geo_path("buffer100m_", geo_prefix),
sep = ",")
buffer100m.lulc <- load_lagos_txt(geo_path("buffer100m_lulc", geo_prefix),
sep = ",")
buffer500m <- load_lagos_txt(geo_path("buffer500m_", geo_prefix),
sep = ",")
buffer500m.conn <- load_lagos_txt(geo_path("buffer500m_conn", geo_prefix),
sep = ",")
buffer500m.lulc <- load_lagos_txt(geo_path("buffer500m_lulc", geo_prefix),
sep = ",")
geo <- list(county = county,
county.chag = county.chag,
county.conn = county.conn,
county.lulc = county.lulc,
edu = edu,
edu.chag = edu.chag,
edu.conn = edu.conn,
edu.lulc = edu.lulc,
hu4 = hu4,
hu4.chag = hu4.chag,
hu4.conn = hu4.conn,
hu4.lulc = hu4.lulc,
hu8 = hu8,
hu8.chag = hu8.chag,
hu8.conn = hu8.conn,
hu8.lulc = hu8.lulc,
hu12 = hu12,
hu12.chag = hu12.chag,
hu12.conn = hu12.conn,
hu12.lulc = hu12.lulc,
iws = iws,
iws.conn = iws.conn,
iws.lulc = iws.lulc,
state = state,
state.chag = state.chag,
state.conn = state.conn,
state.lulc = state.lulc,
buffer100m = buffer100m,
buffer100m.lulc = buffer100m.lulc,
buffer500m = buffer500m,
buffer500m.conn = buffer500m.conn,
buffer500m.lulc = buffer500m.lulc,
lakes.geo = lakes.geo)
# Importing Lagos Locus data ####
pb$tick(tokens = list(type = "lake locus data"))
locus <- load_lagos_txt(locus_path("lakeslocus"), sep = ",")
list("limno" = limno, "geo" = geo, "locus" = locus)
}
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