wiki:udg/ecoms/RPackage/examples

Version 15 (modified by juaco, 9 years ago) (diff)

--

In the next lines we describe an illustrative example of the loadSystem4 function. We will retrieve System4 simulation data for the Iberian Peninsula, considering mean surface temperature for January and the first simulation member, for the 10-year period 1990-1999. This simple example has been chosen because of the fast data access (note that this also depends on the connection speed). Using a standard broadband connection, loading the following dataset took approximately 19 seconds:

> openDAP.query <- loadSystem4(dataset = "http://www.meteo.unican.es/tds5/dodsC/system4/System4_Seasonal_15Members.ncml", 
+                             var = "tas", members = 1,
+                             lonLim = c(-10,5), latLim = c(35,45),
+                             season = 1, years = 1990:1999, leadMonth = 1)

Data are now ready for analysis into our R session:

> str(openDAP.query)
List of 7
 $ VarName      : chr "Mean_temperature_at_2_metres"
 $ VarUnits     : chr "degC"
 $ TimeStep     :Class 'difftime'  atomic [1:1] 1
  .. ..- attr(*, "tzone")= chr ""
  .. ..- attr(*, "units")= chr "days"
 $ MemberData   :List of 1
  ..$ : num [1:310, 1:280] 13.3 13.9 12.5 13 13 ...
 $ LatLonCoords : num [1:280, 1:2] 45 44.2 43.5 42.7 42 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:2] "lat" "lon"
 $ RunDates     : POSIXlt[1:310], format: "1989-12-01" "1989-12-01" "1989-12-01" ...
 $ ForecastDates:List of 2
  ..$ Start: POSIXlt[1:310], format: "1990-01-01" "1990-01-02" "1990-01-03" ...
  ..$ End  : POSIXct[1:310], format: "1990-01-02" "1990-01-03" "1990-01-04" ...

A common task consists of the representation of data, e.g. by mapping the spatial mean for the period considered. Another common task is the representation of time series for selected point locations/grid cells. In this example, we will map the mean temperature field for the period selected (1990-99) preserving the original spatial resolution of the model. Furthermore, we will display time series of the requested dataset at four grid points coincident with the locations of four Spanish cities. To this aim, we will make use of some base R functions and also from some contributed packages that can be very useful for climate data handling and representation.

> # Calculation of the mean values of the period for each grid cell:
> mean.field <- colMeans(openDAP.query$MemberData[[1]])
> # Creation of a matrix with selected point locations:
> city.names <- c("Sevilla", "Madrid", "Santander", "Zaragoza")
> locations <- matrix(c(-5.9, 37.4167, -3.68, 40.4, -3.817, 43.43, -0.8167, 41.667), ncol=2, byrow = TRUE)
> dimnames(locations) <- list(city.names, c("lon","lat"))
> print(locations)
             lon     lat
Sevilla   -5.9000 37.4167
Madrid    -3.6800 40.4000
Santander -3.8170 43.4300
Zaragoza  -0.8167 41.6670

Note that the geographical coordinates of the requested spatial domain are nor perfectly uniform, and as a result it is not possible to represent the data as a regular grid. To overcome this problem, we perform an interpolation, although we preserve the native grid cell size of the model (0.75deg) for data representation. The R package akima provides a extremely fast interpolation algorithm by means of the interp function.

> lat <- openDAP.query$LatLonCoords[ ,1]
> lon <- openDAP.query$LatLonCoords[ ,2]
# Requires "akima::interp" for regular grid (bilinear) interpolation 
> library(akima)
> grid.075 <- interp(lon, lat, mean.field, xo = seq(min(lon), max(lon), .75), yo = seq(min(lat), max(lat), .75))

After the interpolation, data are now in a regular grid. Note that the object grid.075 is a list with the usual x,y,z components as required by many R functions for gridded data representation (e.g. image, contour, persp...)

> str(grid.075)
List of 3
 $ x: num [1:19] -9.75 -9 -8.25 -7.5 -6.75 ...
 $ y: num [1:14] 35.2 36 36.7 37.5 38.2 ...
 $ z: num [1:19, 1:14] 15.1 15.1 15 15 14.3 ...

In the following lines of code we plot the mean temperature field. In addition, we will also add to the map the point locations of the selected cities for which the time series will be represented. The R package fields provides many useful tools for spatial data handling and representation, including a world map that can be easily incorporated in our plots.

> # Representation of the mean temperature of the period
> library(fields)
> image.plot(grid.075, asp=1,ylab = "latitude", xlab = "longitude", col=topo.colors(36),
+           main = "Mean surface T January 1990-99", legend.args=list(text="degC", side=3, line=1))
# Adds selected locations to the plot and puts labels:
> points(locations, pch=15)
> text(locations, pos=3, city.names)
# Adds the world map to the current plot:
> world(add=TRUE)

No image "TmeanJan.png" attached to udg/ecoms/RPackage/examples

Next, we plot the time series for the selected locations. To this aim, we calculate the nearest grid points to the specified locations. This can be easily done using the function fields::rdist. Note that the output of loadSystem4 returns a matrix of Lat-Lon coordinates, as usually found in many climate datasets. However, the usual format of 2D coordinates matrix in R is Lon-Lat. As a result, note that we specify the coordinates by reversing the column order (i.e.: openDAP.query$LatLonCoords[ ,2:1] instead of openDAP.query$LatLonCoords):

> # Creation of a Euclidean distance matrix among all pairs of selected locations and grid points 
> dist.matrix <- rdist(openDAP.query$LatLonCoords[ ,2:1], locations)
> # Positions of the nearest grid points
> index <- rep(NA,ncol(dist.matrix))
> for (i in 1:ncol(dist.matrix)) {
+      index[i] <- which.min(dist.matrix[ ,i])
+ }
> # index contains the column positions in the `MemberData` matrices
> locations.data <- openDAP.query$MemberData[[1]][ ,index]
> colnames(locations.data) <- city.names
> str(locations.data)
 num [1:310, 1:4] 7.71 8.78 10.77 10.88 11.55 ...
 - attr(*, "dimnames")=List of 2
  ..$ : NULL
  ..$ : chr [1:4] "Sevilla" "Madrid" "Santander" "Zaragoza"

The object locations.data is a matrix in which time series are arranged in columns for each of the four locations selected.

> ylimits <- c(floor(min(locations.data)), ceiling(max(locations.data)))
> plot(locations.data[ ,1], ty='n', ylim = ylimits, axes=FALSE, ylab="degC", xlab="Year")
> axis(1,at = seq(1,31*11,31), labels=c(1990:1999,""))
> axis(2, ylim=ylimits)
> abline(v=seq(1,31*10,31), lty=2)
> for (i in 1:ncol(locations.data)) {
+      lines(locations.data[ ,i], col=i)
+ }
> legend("bottomleft", city.names, lty=1, col=1:4)
> title(main = "Mean surface Temperature January")

No image "timeSeries.png" attached to udg/ecoms/RPackage/examples