Extract time series of wrf file list of lat/lon

Read and extract data from a list of wrf output files and a table of lat/lon points based on the distance of the points and the center of model grid points, points outside the domain (and points on domain boundary) are not extracted.

Usage

extract_serie(
  filelist,
  point,
  variable = "o3",
  field = "4d",
  level = 1,
  prefix = "serie",
  new = "check",
  return.nearest = FALSE,
  fast = FALSE,
  use_ij = FALSE,
  model = "WRF",
  id = "id",
  remove_ch = FALSE,
  verbose = TRUE
)

Arguments

filelist

list of files to be read

point

data.frame with lat/lon

variable

variable name

field

dimension of the variable, '4d' (default), '2dz', '2dz', '2d' or 'xyzt', 'xyz', 'xyz', and 'xy' see notes

Field	Dimensions	Example
3dt	xyzt	WRF dimensions for 3D array with multiple times
2dt	xyt	WRF dimensions for 2D array with multiple times
2dz	xyz	WRF dimensions for 3D array with single time
2d	xy	WRF dimensions for 2D array with single time

level

model level (index) to be extracted

prefix

to output file, default is serie

new

TRUE, FALSE of 'check' see notes

return.nearest

return the data.frame of nearest points instead of extract the serie

fast

faster calculation of grid distances but less precise

use_ij

logical, use i and j from input instead of calculate

model

"WRF" (default), "CAMx" (CAMx, CMAQ and smoke files), and "WACCM" (WACCM and CAM-Chem)

id

name of the column with station names, if point is a SpatVector (points) from terra package

remove_ch

remove special characters on row.names

verbose

display additional information

Value

No return value

Note

The field argument '4d' or '2dz' is used to read a 4d/3d variable droping the 3rd dimension (z), this should be based how ncdf4 R-package reads the model output.

new = TRUE create a new file, new = FALSE append the data in a old file, and new = 'check' check if the file exist and append if the file exist and create if the file doesnt exist

The option field '3d' was removed, a new option should be used instead (2dt or 2dz).

The site-list of two global data-sets (METAR/ISD and AERONET) are provided on examples and site-list for stations on Brazil (INMET and Air Quality stations). Site-lists for other regions (US, Canada, Europa, etc) are provided as additional examples.

Examples

cat('Example 1: METAR site list\n')
#> Example 1: METAR site list
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_METAR.Rds"))

cat('Example 2: Integrated Surface Dataset (ISD) site list\n')
#> Example 2: Integrated Surface Dataset (ISD) site list
# row.names are a combination of State Code,  County Code  and Site Number (2,3 and 4 digits)
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_ISD.Rds"))

cat('Example 4: AERONET site list\n')
#> Example 4: AERONET site list
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_AERONET.Rds"))

cat('Example 5: list of INMET stations in Brazil\n')
#> Example 5: list of INMET stations in Brazil
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_INMET.Rds"))

cat('Example 6: list of Air Quality stations in Brazil\n')
#> Example 6: list of Air Quality stations in Brazil
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_AQ_BR.Rds"))

cat('Example 7: list of AQM stations in US\n')
#> Example 7: list of AQM stations in US
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_AQS.Rds"))

cat('Example 8: list of CASTNET stations in rural areas of US/Canada\n')
#> Example 8: list of CASTNET stations in rural areas of US/Canada
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_CASTNET.Rds"))

cat('Example 9: list of Longterm European Program (EMEP) stations\n')
#> Example 9: list of Longterm European Program (EMEP) stations
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_EMEP.Rds"))

cat('Example 10: list of FLUXNET stations\n')
#> Example 10: list of FLUXNET stations
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_FLUXNET.Rds"))

cat('Example 11: list of IMPROVE stations\n')
#> Example 11: list of IMPROVE stations
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_IMPROVE.Rds"))

cat('Example 12: list of TOAR stations\n')
#> Example 12: list of TOAR stations
sites <- readRDS(paste0(system.file("extdata",package="eva3dm"),"/sites_TOAR.Rds"))

files    <- dir(path = system.file("extdata",package="eva3dm"),
                pattern = 'wrf.day',
                full.names = TRUE)
dir.create(file.path(tempdir(),"SERIE"))
folder <- file.path(tempdir(),"SERIE")

# extract data for 3 locations
extract_serie(filelist = files, point = sites[1:3,],prefix = paste0(folder,'/serie'))
#> extracting series of o3 field 4d for 3 points
#> dim of lat/lon: 125 125 
#> used dim of lat/lon: 125 125 
#> inside lat / lon range: 0 points
#> [1] "no data to extract!"