extract_ts_wald: Extact Timeseries of Values for Spatial Points

In sustainablefarms/sflddata: Data Extraction Methods for the Linking Data Project

Extact Timeseries of Values for Spatial Points

Description

For every spatial point provided the function extracts a time series values from the given netcdf4 file.

Some ndcf files in the WALD database appear to have dimensions ordered by (latitude, longitude, time), Furthermore raster reads the pixels of array data in the reverse order of the latitude values. This function applies these conversions to an sp object so that the data extract through raster will match up perfectly. The following takes a sp object as one would normally experience it.

Usage

extract_ts_wald(
  points,
  filelocation,
  varname,
  crs = CRS("+proj=longlat +datum=WGS84"),
  nl = NULL
)

sp_2_waldncdfcoords(spobj, nc, crs = CRS("+proj=longlat +datum=WGS84"))

extract_point_wald_manual(long, lat, nc, varname, nl = NULL)

Arguments

points	A Spatial Points Data Frame
filelocation	A string specifying the location of the netcdf4 file
varname	The name of the variable in the netcdf4 file to be converted into the values of the time series.
crs	The spatial coordinate system (in PROJ.4 format) of the ncdf file (ignoring the order of the dimensions and reversed latitudes).
nl	Integer. Number of layers to extract from the ncdf file.
spobj	a SpatialPolygons, SpatialPoints, SpatialLine, or SpatialGrid etc object
nc	Open netcdf file or the location of netcdf file
long	Longitude of point
lat	Latitude of point

Details

Some netcdf4 files have dimensions ordered as 'latitude, longitude, time'. The package raster currently has a bug and cannot extract these correctly so the function involves a work around. Each extraction is checked using custom built extraction function.

The transform assumes that the way raster reads the ncdf values is such that: (1) the latlong coordinates assigned to each pixel in the netcdf file are switched in order. (2) the latitude in the netcdf file is reversed by the function f(x) = -x - 54 where '-54' is the sum of the end points of the range in latitudes.

Following the CF conventions for netCDF file, it is assumed that the list of longitude and latitude represents the centres of pixels. The pixel that contains the point can then be found using the closest longitude and latitude, when the point is within the grid.

Value

A matrix. Each row corresponds to the same row in the points SPDF. Each column corresponds to a layer in the ncdf file, typically a time point..

Functions

• sp_2_waldncdfcoords: Transform an sp object to the spatial coordinates of a (latitude, longitude, time) ncdf file as interpreted by the package raster

• extract_point_wald_manual: Extract values at a single point from a netCDF file in WGS84 longlat coordinates without using the raster package.

WARNING

this function should be checked with a person knowledgable of the WALD data and its projection.

Examples

source("./R/sites_2_sp_points.R")
sws_sites <- readRDS("./private/data/sws_sites.rds")
points <- sws_sites_2_spdf(sws_sites)
filelocation <- "http://dapds00.nci.org.au/thredds/dodsC/ub8/au/OzWALD/annual/OzWALD.annual.Pg.AnnualSums.nc"
varname = "AnnualSums"
crs = CRS("+proj=longlat +datum=WGS84")
tseries <- extract_ts_wald(points,
       filelocation,
       varname = varname,
       crs = crs)
countries <- rworldmap::getMap(resolution = "high") #do this for a world map polygon
row.names(countries) <- unlist(lapply(countries@polygons, function(x) attr(x, 'ID'))) #a polishing fix required of this data frame
auspoly <- countries[16, ] #Australia outline
sp_2_waldncdfcoords(auspoly)
long <- 148.0779
lat <- -35.13167
nc <- "http://dapds00.nci.org.au/thredds/dodsC/ub8/au/OzWALD/annual/OzWALD.annual.Pg.AnnualSums.nc"
extract_point_wald_manual(long, lat, nc)

sustainablefarms/sflddata documentation built on April 19, 2022, 11:19 a.m.