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brazil_1950_2022.R
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# Packages and options ----------------------------------------------------
### Load packages required to define the pipeline:
library(targets)
library(tarchetypes)
library(qs)
### Set target options:
tar_option_set(
packages = c("zonalclim", "DBI", "RSQLite", "duckdb", "glue"),
format = "qs",
controller = crew::crew_controller_local(workers = 1)
)
### Run the R scripts in the R/ folder with your custom functions:
tar_source()
# Definitions -------------------------------------------------------------
# Zonal statistics sets
z1 <- c("mean", "max", "min", "stdev", "count")
z2 <- c("mean", "max", "min", "stdev", "sum", "count")
# Municipalities geom
mun_geom <- qread(file = "input_data/mun_geom.qs")
# Climate NetCDF file paths
files_2m_temperature_max <- list.files(
path = "/media/raphael/lacie/era5land_daily_latin_america/2m_temperature_max/",
pattern = ".nc$",
full.names = TRUE
)
files_2m_temperature_min <- list.files(
path = "/media/raphael/lacie/era5land_daily_latin_america/2m_temperature_min/",
pattern = ".nc$",
full.names = TRUE
)
files_2m_temperature_mean <- list.files(
path = "/media/raphael/lacie/era5land_daily_latin_america/2m_temperature_mean/",
pattern = ".nc$",
full.names = TRUE
)
files_2m_dewpoint_temperature <- list.files(
path = "/media/raphael/lacie/era5land_daily_latin_america/2m_dewpoint_temperature/",
pattern = ".nc$",
full.names = TRUE
)
files_10m_u_component_of_wind <- list.files(
path = "/media/raphael/lacie/era5land_daily_latin_america/10m_u_component_of_wind/",
pattern = ".nc$",
full.names = TRUE
)
files_10m_v_component_of_wind <- list.files(
path = "/media/raphael/lacie/era5land_daily_latin_america/10m_v_component_of_wind/",
pattern = ".nc$",
full.names = TRUE
)
files_surface_pressure <- list.files(
path = "/media/raphael/lacie/era5land_daily_latin_america/surface_pressure/",
pattern = ".nc$",
full.names = TRUE
)
files_total_precipitation <- list.files(
path = "/media/raphael/lacie/era5land_daily_latin_america/total_precipitation/",
pattern = ".nc$",
full.names = TRUE
)
# Targets -----------------------------------------------------------------
# Replace the target list below with your own:
list(
### Max temp
tar_target(
name = max_temperature_data_sqlite,
command = compute_zonal_statistics(
files_list = files_2m_temperature_max,
sf_geom = mun_geom,
zonal_list <- z1,
db_file = "output_data/max_temperature_data.sqlite"
),
format = "file",
cue = tar_cue(file = FALSE)
),
tar_target(
name = max_temperature_data_duckdb,
command = sqlite2duckdb(
sqlite_db = max_temperature_data_sqlite,
duckdb_db = "output_data/max_temperature_data.duckdb"
),
format = "file"
),
tar_target(
name = max_temperature_data_parquet,
command = duckdb2parquet(
duckdb_db = max_temperature_data_duckdb,
parquet_path = "output_data/parquet/"
),
format = "file"
),
### Min temp
tar_target(
name = min_temperature_data_sqlite,
command = compute_zonal_statistics(
files_list = files_2m_temperature_min,
sf_geom = mun_geom,
zonal_list <- z1,
db_file = "output_data/min_temperature_data.sqlite"
),
format = "file",
cue = tar_cue(file = FALSE)
),
tar_target(
name = min_temperature_data_duckdb,
command = sqlite2duckdb(
sqlite_db = min_temperature_data_sqlite,
duckdb_db = "output_data/min_temperature_data.duckdb"
),
format = "file"
),
tar_target(
name = min_temperature_data_parquet,
command = duckdb2parquet(
duckdb_db = min_temperature_data_duckdb,
parquet_path = "output_data/parquet/"
),
format = "file"
),
### Mean temp
tar_target(
name = mean_temperature_data_sqlite,
command = compute_zonal_statistics(
files_list = files_2m_temperature_mean,
sf_geom = mun_geom,
zonal_list <- z1,
db_file = "output_data/mean_temperature_data.sqlite"
),
format = "file",
cue = tar_cue(file = FALSE)
),
tar_target(
name = mean_temperature_data_duckdb,
command = sqlite2duckdb(
sqlite_db = mean_temperature_data_sqlite,
duckdb_db = "output_data/mean_temperature_data.duckdb"
),
format = "file"
),
tar_target(
name = mean_temperature_data_parquet,
command = duckdb2parquet(
duckdb_db = mean_temperature_data_duckdb,
parquet_path = "output_data/parquet/"
),
format = "file"
),
### Dewpoint temp
tar_target(
name = dewpoint_temperature_data_sqlite,
command = compute_zonal_statistics(
files_list = files_2m_dewpoint_temperature,
sf_geom = mun_geom,
zonal_list <- z1,
db_file = "output_data/dewpoint_temperature_data.sqlite"
),
format = "file",
cue = tar_cue(file = FALSE)
),
tar_target(
name = dewpoint_temperature_data_duckdb,
command = sqlite2duckdb(
sqlite_db = dewpoint_temperature_data_sqlite,
duckdb_db = "output_data/dewpoint_temperature_data.duckdb"
),
format = "file"
),
tar_target(
name = dewpoint_temperature_data_parquet,
command = duckdb2parquet(
duckdb_db = dewpoint_temperature_data_duckdb,
parquet_path = "output_data/parquet/"
),
format = "file"
),
### u component of wind temp
tar_target(
name = u_component_of_wind_data_sqlite,
command = compute_zonal_statistics(
files_list = files_10m_u_component_of_wind,
sf_geom = mun_geom,
zonal_list <- z1,
db_file = "output_data/u_component_of_wind_data.sqlite"
),
format = "file",
cue = tar_cue(file = FALSE)
),
tar_target(
name = u_component_of_wind_data_duckdb,
command = sqlite2duckdb(
sqlite_db = u_component_of_wind_data_sqlite,
duckdb_db = "output_data/u_component_of_wind_data.duckdb"
),
format = "file"
),
tar_target(
name = u_component_of_wind_data_parquet,
command = duckdb2parquet(
duckdb_db = u_component_of_wind_data_duckdb,
parquet_path = "output_data/parquet/"
),
format = "file"
),
### v component of wind temp
tar_target(
name = v_component_of_wind_data_sqlite,
command = compute_zonal_statistics(
files_list = files_10m_v_component_of_wind,
sf_geom = mun_geom,
zonal_list <- z1,
db_file = "output_data/v_component_of_wind_data.sqlite"
),
format = "file",
cue = tar_cue(file = FALSE)
),
tar_target(
name = v_component_of_wind_data_duckdb,
command = sqlite2duckdb(
sqlite_db = v_component_of_wind_data_sqlite,
duckdb_db = "output_data/v_component_of_wind_data.duckdb"
),
format = "file"
),
tar_target(
name = v_component_of_wind_data_parquet,
command = duckdb2parquet(
duckdb_db = v_component_of_wind_data_duckdb,
parquet_path = "output_data/parquet/"
),
format = "file"
),
### surface pressure
tar_target(
name = surface_pressure_data_sqlite,
command = compute_zonal_statistics(
files_list = files_surface_pressure,
sf_geom = mun_geom,
zonal_list <- z1,
db_file = "output_data/surface_pressure_data.sqlite"
),
format = "file",
cue = tar_cue(file = FALSE)
),
tar_target(
name = surface_pressure_data_duckdb,
command = sqlite2duckdb(
sqlite_db = surface_pressure_data_sqlite,
duckdb_db = "output_data/surface_pressure_data.duckdb"
),
format = "file"
),
tar_target(
name = surface_pressure_data_parquet,
command = duckdb2parquet(
duckdb_db = surface_pressure_data_duckdb,
parquet_path = "output_data/parquet/"
),
format = "file"
),
### total precipitation
tar_target(
name = total_precipitation_data_sqlite,
command = compute_zonal_statistics(
files_list = files_total_precipitation,
sf_geom = mun_geom,
zonal_list <- z2,
db_file = "output_data/total_precipitation_data.sqlite"
),
format = "file",
cue = tar_cue(file = FALSE)
),
tar_target(
name = total_precipitation_data_duckdb,
command = sqlite2duckdb(
sqlite_db = total_precipitation_data_sqlite,
duckdb_db = "output_data/total_precipitation_data.duckdb"
),
format = "file"
),
tar_target(
name = total_precipitation_data_parquet,
command = duckdb2parquet(
duckdb_db = total_precipitation_data_duckdb,
parquet_path = "output_data/parquet/"
),
format = "file"
)
)