R-in-dev/create_whole_database.R

In HopkinsIDD/globaltoolbox: Identify Location Names and Link with Other Data

devtools::install_github("HopkinsIDD/globaltoolbox")


# install.packages('/home/jkaminsky/git/globaltoolbox',type='source',repos=NULL)
options(warn=1,error=recover)

library(sf)
library(globaltoolbox)

reset_database("/home/jkaminsky/GAUL.sqlite")
create_database("/home/jkaminsky/GAUL.sqlite")

## Load alt_country_names
load_country_aliases('/home/jkaminsky/GAUL.sqlite')

dirname <- "/home/jkaminsky/GAUL_shp"
all_files <- list.files(dirname)
all_files <- all_files[!grepl(".zip",all_files)]
##for(file in all_files){
##  filename <- paste0(dirname,"/",file,"/",file,".shp")
##  print(filename)
##  year <- as.numeric(gsub('.*2015_([1234567890]*).*','\\1',filename))
##  print(paste("File: ",filename))
##  shp <- st_read(filename)
##  levels <- max(as.numeric(unique(gsub("_.*","",gsub("ADM","",names(shp))))),na.rm=TRUE)
##  hierarchy_column_names <- paste0("ADM",0:levels,"_NAME")
##  hierarchy_column_names <- hierarchy_column_names[hierarchy_column_names %in% names(shp)]
##  alias_column_names = rep(c(),times=length(hierarchy_column_names))
##  # alias_column_names = lapply(0:levels,function(x){
##  #   x <- paste0("ADM", x, "_CODE")
##  #   x <- x[x %in% names(shp)]
##  # })
##  load_hierarchical_sf(
##    filename = filename,
##    time_left = paste(year,"01","01",sep='-'),
##    time_right = paste(year,"12","31",sep='-'),
##    hierarchy_column_names = hierarchy_column_names,
##    alias_column_names = alias_column_names,
##    source_name = "GAUL",
##    geometry = TRUE,
##    max_depth = 3,
##    dbname = "/home/jkaminsky/GAUL.sqlite"
##  )
##  print(paste("File: ",filename,"finished"))
##}

shp <- st_read('/home/jkaminsky/gadm36.shp')
alias_column_names <- lapply(0:5,function(x){
  x = paste(c("GID","HASC","VARNAME","NLAME","VARNAME"),x,sep="_")
  return(x[x %in% names(shp)])
})
load_hierarchical_sf(
  filename = '/home/jkaminsky/gadm36.shp',
  time_left = '1800-01-01',
  time_right = '2019-12-31',
  hierarchy_column_names = paste("NAME",0:5,sep="_"),
  alias_column_names = alias_column_names,
  source_name = "GADM",
  max_depth =  3,
  geometry = TRUE,
  geometry_union = TRUE,
  dbname = "/home/jkaminsky/GAUL.sqlite"
)