Download, Edit and Include Wind and Sea Currents Data in Ecological and Evolutionary Analysis

Downloads and processes surface wind data from the Global Forecast System < https://www.ncei.noaa.gov/products/weather-climate-models/global-forecast> and sea-current data from Ocean Surface Current Analyses Real-time (OSCAR). Converts flow speed and direction into spatial rasters and directed movement costs and conductances for connectivity and least-cost path analyses.

rWind

Overview

rWind is a library in the R language for statistical computing and graphics (R Development Core Team), designed specifically to download and process wind and sea currents data from the Global Forecasting System. From these data, users can obtain wind/sea currents speed and direction layers in order to compute connectivity values between locations. There are other great R libraries that covers data download and data managing that could overlap with rWind, such us rnoaa, RNCEP or weatherr. However, rWind is specially focused to offer to the users a straightforward workflow from data download to cost analysis between locations. rWind fills the gap between wind/sea currents data accessibility and their inclusion in a general framework to be applied broadly in ecological or evolutionary studies.

It has been peer-reviewed published in: Fernández‐López, J. and Schliep, K. (2019), rWind: download, edit and include wind data in ecological and evolutionary analysis. Ecography, 42: 804-810. https://doi.org/10.1111/ecog.03730
https://onlinelibrary.wiley.com/doi/full/10.1111/ecog.03730

For more information about data source, please check:

NOAA/NCEP Global Forecast System (GFS) Atmospheric Model colection (wind data)

• https://pae-paha.pacioos.hawaii.edu/erddap/griddap/ncep_global.html
• Historical GFS 0.5 degree data: https://www.ncei.noaa.gov/access/metadata/landing-page/bin/iso?id=gov.noaa.ncdc:C00634

Ocean Surface Current Analyses Real-time (OSCAR) (sea currents data)

• https://doi.org/10.5067/OSCAR-03D01
  

To install the latest released version of rWind on CRAN use install.packages("rWind")
To install the latest development version devtools::install_github("jabiologo/rWind")

Quick example: Computing anisotropic shortest paths across Strait of Gibraltar

First, load the packages used in this example.

# use install.packages() if some is not installed
# you can install the latest development version using the command 
# devtools::install_github("jabiologo/rWind")
library(rWind)
library(terra)
library(gdistance)

In this simple example, we introduce the most basic functionality of rWind, to get the shortest paths between two points across Strait of Gibraltar. Notice that, as wind connectivity is anisotropic (direction dependent), shortest path from A to B usually does not match with shortest path from B to A.

First, we download wind data of a selected date (e.g. 2015 February 12th).

w <- wind.dl(2015, 2, 12, 12, -7, -4, 34.5, 37.5)

Next we transform this data.frame into a two-layer SpatRaster, with wind direction and speed.

wind_layer <- wind2raster(w)

Then, we will use flow.dispersion function to obtain a transitionLayer object with conductance values, which will be used later to obtain the shortest paths.

Conductance <- flow.dispersion(wind_layer, type = "passive")

For a general active-movement index, use type = "active". The model projects flow speed onto movement direction: supportive flow lowers relative cost, opposing flow raises it, and perpendicular flow is neutral. speed.scale controls sensitivity and defaults to the median positive speed of the layer.

ActiveConductance <- flow.dispersion(
  wind_layer,
  type = "active",
  speed.scale = median(w$speed[w$speed > 0], na.rm = TRUE)
)

Transition costs average the origin and destination cells and diagonal steps are multiplied by sqrt(2). They remain relative grid costs: physical longitude/latitude distances are not corrected.

Now, we will use shortestPath function from gdistance package [@gdistance] to compute shortest path from our Conductance object between the two selected points.

AtoB<- shortestPath(Conductance, 
                    c(-5.5, 37), c(-5.5, 35), output="SpatialLines")
BtoA<- shortestPath(Conductance, 
                    c(-5.5, 35), c(-5.5, 37), output="SpatialLines")

Finally, we plot the map and we will add the shortest paths as lines and some other features.

plot(wind_layer[["speed"]],
  col = hcl.colors(20, "YlOrRd", rev = TRUE),
  main = "Wind-assisted paths across the Strait of Gibraltar",
  xlab = "Longitude", ylab = "Latitude"
)

points(-5.5, 37, pch=19, cex=3.4, col="red")
points(-5.5, 35, pch=19, cex=3.4, col="blue")

lines(vect(AtoB), col="red", lwd=4, lty=2)
lines(vect(BtoA), col="blue", lwd=4, lty=2)

arrow_scale <- 0.12 / max(w$speed, na.rm = TRUE)
arrows(w$lon, w$lat,
  w$lon + w$ugrd10m * arrow_scale,
  w$lat + w$vgrd10m * arrow_scale,
  length = 0.035
)

text(-5.75, 37.25,labels="Spain", cex= 2.5, col="red", font=2)
text(-5.25, 34.75,labels="Morocco", cex= 2.5, col="blue", font=2)
legend("topleft", legend = c("From Spain to Morocco", "From Morocco to Spain"),
    lwd=4, lty=1, col=c("red","blue"), cex=0.8, bg="white")

For more information and examples, you can check my blog