Finding overlapping polygons

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Finding overlapping polygons

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Dear everyone,

I am studying the potential spatial distribution between vertebrate
invasive species and native ones (threatened) in the souther cone of
South America. The invasive species' distribution was grossly
approximated using an ecoregional approach, which is not relevant here.
The analysis is based on shapefiles for all terrestrial mammals and
birds of the world obtained from BirdLife International
(http://www.biodiversityinfo.org/spcdownload/r5h8a1/) and IUCN
(http://www.iucnredlist.org/technical-documents/spatial-data) public
domains.

Our goal: using a two-step approach, identify native species (polygons)
whose distributionoverlap -totally or partially- with that of the invasive.

Our problem: Some species (with small distribution) which are known to
occur within the invasive distribution range are being left out of the
final selection (checkedin QGIS). I suspect the function "isin" in the
fastshp package (2nd loop) fails to select some of the overlapping
polygons in Step 2, or some other problem. If a reproducible example is
absolutely required, I can upload to dropbox.

For the sake of simplicity, I will present present a case example
including one invasive species (e.g. wild boar) and all terrestrial
mammals.

# Analysis of Wild Boar distributional overlap with IUCN mammal species
install.packages("rgdal") install.packages("sp")
install.packages("ggplot2") install.packages("rgeos")
install.packages("raster") install.packages("fastshp", repos =
"http://rforge.net", type = "source")install.packages("cleangeo")

mypath <- ("/Users/ ... /Terrestrial mammals") files <-
list.files(path=mypath, pattern = "\\.shp$", full.names=T)
length(files)  # 5,465 mammal species # Load study area

study_area <- read.shp("C:/Users/.../Study_area.shp", format="table",
close=FALSE) salon <- range(study_area$x, na.rm=T) salat <-
range(study_area$y, na.rm=T) bounding <- c(salon, salat) box <-
data.frame(salon, salat) colnames(box) <- c("Longitud","Latitude") box

# Step 1. Run all native IUCN species' distribution through a loop and
select those which overlap with the invasive's bounding box distribution

keep <- rep(NA, length(files)) length(keep)  # 5,465 for(i in
1:length(files)){   r <- read.shp(files[i], format="table")   rlon <-
range(r$x)   rlat <- range(r$y) ## Is out of the bounding box? test.lat
<- (min(rlat) > max(salat)) |     (max(rlat) < min(salat))   test.lon <-
(min(rlon) > max(salon)) |     (max(rlon) < min(salon)) keep[i] <-
!(test.lon | test.lat) } keep <- which(keep==1) # Index of shapefiles
that passed the first filter length(keep) # 773 species passed 1st
filter # Step 2. Load invasive species distribution area

study_area <- readOGR("/Users/.../Study area","Study_area") study_area
<- spTransform(study_area, CRS("+init=epsg:32721")) # To UTM # Get a
report of geometry validity & issues for a sp spatial object report <-
clgeo_CollectionReport(study_area) summary <-
clgeo_SummaryReport(report) summary # Remove holes and simplify geometry
of study area for computational efficiency outer <-
Filter(function(x){x@ringDir==1}, study_area@polygons[[1]]@Polygons) #
PREGUNTAR study_area <- SpatialPolygons(list(Polygons(outer, ID=1)))
study_area <- disaggregate(study_area) areas <- gArea(study_area,
byid=TRUE) #Remove polygons smaller than 3000 km2 study_area <-
study_area[which(areas > 3E9),] study_area <- gSimplify(study_area,
20000, topologyPreserve=TRUE) # Simplify geometry
proj4string(study_area) <- CRS("+init=epsg:32721") study_area <-
spTransform(study_area, CRS("+proj=longlat +datum=WGS84 +no_defs
+ellps=WGS84 +towgs84=0,0,0")) xy <- fortify(study_area) #
SpatialPolygons to data frame keep2 <- rep(NA,length(keep)) # 773 sp.
that passed first filter for(i in 1:length(keep)){   r <-
read.shp(files[keep[i]], format="polygon")   isin <- any(inside(r,
x=xy$long, y=xy$lat), na.rm=T)   keep2[i] <- isin } keep2 <-
which(keep2) # Index of shapefiles that passed the second sort
length(keep2)  # 532 species that passed the second filter species <-
list.files(path=mypath, pattern = "\\.shp$",full.names=F) species <-
sub(".shp", "", species) species <- species[keep[keep2]]



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