Extract shapefiles from longitude/latitude gridded data - r

Question

I have some gridded data of sea surface temperature values in the Mediterranean to which I've applied clustering. I have 420 files with three columns structure (long,lat,value). The data for a particular file looks like this map
Now I want to extract the cluster areas as shapefile for postprocessing. I have found this post (https://gis.stackexchange.com/a/187800/9227) and tried to use its code like this
# Packages
library(sp)
library(rgdal)
library(raster)
# Paths
ruta_datos<-"/home/meteo/PROJECTES/VERSUS/OUTPUT/DATA/CLUSTER_MED/"
setwd("~/PROJECTES/VERSUS/temp")
# File list
files <- list.files(path = ruta_datos, pattern = "SST-cluster-mitja-mensual")
for (i in 1:length(files)){
datos<-read.csv(paste0(ruta_datos,files[i],sep=""),header=TRUE)
nclusters<-max(datos$cluster)
for (j in 1:nclusters){
clust.dat<-subset(datos, cluster == j)
coordinates(clust.dat)=~longitud+latitud
proj4string(clust.dat)=CRS("+init=epsg:4326")
pts = spTransform(clust.dat,CRS("+init=epsg:4326"))
gridded(pts) = TRUE
r = raster(pts)
projection(r) = CRS("+init=epsg:4326")
# make all values the same. Either do
s <- r > -Inf
# convert to polygons
pp <- rasterToPolygons(s, dissolve=TRUE)
# save shapefile
shname<-paste("SST-shape-",substr(files[i],27,32),"-",j,sep="")
writeOGR(pp, dsn = '.', layer = shname, driver = "ESRI Shapefile")
}
}
But the code stops for with this error message
gridded(pts) = TRUE
suggested tolerance minimum: 1
Error in points2grid(points, tolerance, round) : dimension 2
: coordinate intervals are not constant
Warning message: In points2grid(points, tolerance, round) : grid has empty
column/rows in dimension 1
I don't understand that at a certain file it says that coordinate intervals are not constant while they indeed are, original SST data from which clustering was derived are on a regular grid over the whole globe. All cluster data files have the same size, 4248 points. A sample data file is available here
What does the tolerance suggestion means? I've been looking for a solution and found some suggestion to use SpatialPixelsDataFrame but couldn't find out how to apply.
Any help would be appreciated. Thanks.

Answer 1

I am not an expert of geospatial data but for me, if you filter on cluster, data are indeed not on a grid. So far as I understand, you start from a grid (convex set of regularly distant points).
I tried following modifications to your code and some files are generated but I can't test whether they are correct or not.
Principle is to build the grid on all data then only filter on cluster before calling raster.
This gives:
files <- list.files(path = ruta_datos, pattern = "SST-cluster-mitja-mensual")
for (i in 1:length(files)){
datos<-read.csv(paste0(ruta_datos,files[i],sep=""),header=TRUE)
nclusters<-max(datos$cluster)
for (j in 1:nclusters){
## clust.dat<-subset(datos, cluster == j)
clust.dat <- datos
coordinates(clust.dat)=~longitud+latitud
proj4string(clust.dat)=CRS("+init=epsg:4326")
pts = spTransform(clust.dat,CRS("+init=epsg:4326"))
gridded(pts) = TRUE
## r = raster(pts)
r= raster(pts[pts$cluster==j,])
projection(r) = CRS("+init=epsg:4326")
# make all values the same. Either do
s <- r > -Inf
# convert to polygons
pp <- rasterToPolygons(s, dissolve=TRUE)
# save shapefile
shname<-paste("SST-shape-",substr(files[i],27,32),"-",j,sep="")
writeOGR(pp, dsn = '.', layer = shname, driver = "ESRI Shapefile")
}
}
So, two lines in comment and update just the line below.