Minimum Dispersal Routes)
ecospat.mdr is a function that implement a minimum cost arborescence approach to analyse the invasion routes of a species from dates occurrence data.
ecospat.mdr (data, xcol, ycol, datecol, mode, rep, mean.date.error, fixed.sources.rows)
data |
dataframe with occurence data. Each row correspond to an occurrence. |
xcol |
The column in data containing x coordinates. |
ycol |
The column in data containing y coordinates. |
datecol |
The column in data containing dates. |
mode |
"observed", "min" or "random". "observed" calculate routes using real dates. "min" reorder dates so the the total length of the routes are minimal. "random" reatribute dates randomly. |
rep |
number of iteration of the analyse. if > 1, boostrap support for each route is provided. |
mean.date.error |
mean number of years to substract to observed dates. It is the mean of the truncated negative exponential distribution from which the time to be substracted is randomly sampled. |
fixed.sources.rows |
the rows in data (as a vector) corresponding to source occurrence(s) that initiated the invasion(s). No incoming routes are not calculated for sources. |
The function draws an incoming route to each occurence from the closest occurrence already occupied (with a previous date) and allows to substract a random number of time (years) to the observed dates from a truncated negative exponential distribution. It is possible to run several iterations and to get boostrap support for each route.
itexp and rtexp functions are small internal functions to set a truncated negative exponential distribution.
A list is returned by the function with in positon [[1]], a datafame with each row corresponding to a route (with new/old coordinates, new/old dates, length of the route, timespan, dispersal rate), in position [[2]] the total route length, in position [[3]] the median dispersal rate and in position [[4]] the number of outgoing nodes (index of clustering of the network)
Olivier Broennimann olivier.broennimann@unil.ch
Hordijk, W. and O. Broennimann. 2012. Dispersal routes reconstruction and the minimum cost arborescence problem. Journal of theoretical biology, 308, 115-122.
Broennimann, O., P. Mraz, B. Petitpierre, A. Guisan, and H. Muller-Scharer. 2014. Contrasting spatio-temporal climatic niche dynamics during the eastern and western invasions of spotted knapweed in North America.Journal of biogeography, 41, 1126-1136.
library(maps)
data(ecospat.testMdr)
data<- ecospat.testMdr
intros<-order(data$date)[1:2] # rows corresponding to first introductions
# plot observed situation
plot(data[,2:1],pch=15,cex=0.5)
points(data[intros,2:1],pch=19,col="red")
text(data[,2]+0.5,data[,1]+0.5,data[,3],cex=0.5)
map(add=TRUE)
# calculate minimum cost arborescence (MCA) of dispersal routes
obs<-ecospat.mdr(data=data,xcol=2,ycol=1,datecol=3,mode="min",rep=100,
mean.date.error=1,fixed.sources.rows=intros)
# plot MCA results
# arrows' thickness indicate support for the routes
mca<-obs[[1]]
plot(mca[,3:4],type="n",xlab="longitude",ylab="latitude")
arrows(mca[,1],mca[,2],mca[,3],mca[,4],length = 0.05,lwd=mca$bootstrap.value*2)
map(add=TRUE)
# plot intros
points(data[intros,2:1],pch=19,col="red")
text(data[intros,2]+0.5,data[intros,1]+0.5,data[intros,3],cex=1,col="red")
# dispersal routes statistics
obs[[2]] # total routes length in DD
obs[[3]] # median dispersal rate in DD/yr
obs[[4]] # number of outcoming nodesPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.