Sorry for cross-posting. I also posted this question at the R-SIG-GEO discussion list, but since I wanted to get as much feedback as possible I decided to post it here too.
I am trying to extract temperature values from a raster stack for about 400 municipalities in Brazil. My final goal is to create a data frame that is going to be used as a database for an interactive map server - probably using shiny and leaflet.
The final data frame would look like this:
> head(df)
Location Var Cut Year Month Freq
Campinas temperature 10 2010 1 11
Campinas temperature 10 2010 2 19
Campinas temperature 10 2010 3 30
Campinas temperature 10 2010 4 29
Campinas temperature 10 2010 5 31
Campinas temperature 10 2010 6 30
I have global raster stacks with daily data and I am counting, for each month in the raster, the number of days above certain temperature threshold. Please see below:
library(raster)
library(zoo)
library(maptools)
# Create a rasterStack similar to my data - same dimensions and layer names
r <- raster(ncol=360, nrow=180)
s <- stack(lapply(1:730, function(x) setValues(r, runif(ncell(r),min=0,max=30))))
idx <- seq(as.Date("2010/1/1"), by = "day", length.out = 730)
s <- setZ(s, idx)
s
# Define functions for 10, 15, 20 and 25 degrees
fun1 <- function(x, na.rm) {
sum(x > 10, na.rm)
}
fun2 <- function(x, na.rm) {
sum(x > 15, na.rm)
}
fun3 <- function(x, na.rm) {
sum(x > 20, na.rm)
}
fun4 <- function(x, na.rm) {
sum(x > 25, na.rm)
}
# Count number of days above the threshold temperature
days.above.10 <- zApply(s, by=as.yearmon, fun = fun1)
days.above.15 <- zApply(s, by=as.yearmon, fun = fun2)
days.above.20 <- zApply(s, by=as.yearmon, fun = fun3)
days.above.25 <- zApply(s, by=as.yearmon, fun = fun4)
Now, what I would like to do is to programmatically extract values for each location on my study area. The locations are defined as a shapefile with municipal contours of the Sao Paulo state in Brazil.
In this example, however, just for reproducibility's sake, I will be using a world polygon. But keep in mind that in my actual data the polygons will be much smaller.
# Import *sample* polygon data and subset only five "locations"
data(wrld_simpl)
locs <- subset(wrld_simpl, wrld_simpl@data$NAME %in% c("Argentina","Bolivia","Brazil","Paraguay","Uruguay"))
# Plot
plot(days.above.10,1)
plot(locs,add=T)
I feel like half of the work is done, but I am just grasping with the conversion to data frames.
Based on this self-contained example I provided, what would be the best strategy to come out with a data frame per location, like this?
> head(Argentina.df)
Location Var Cut Year Month Freq
Argentina temperature 10 2010 1 11
Argentina temperature 10 2010 2 19
Argentina temperature 10 2010 3 30
Argentina temperature 10 2010 4 12
Argentina temperature 10 2010 5 17
Argentina temperature 10 2010 6 14
> head(Bolivia.df)
Location Var Cut Year Month Freq
Bolivia temperature 10 2010 1 29
Bolivia temperature 10 2010 2 31
Bolivia temperature 10 2010 3 30
Bolivia temperature 10 2010 4 17
Bolivia temperature 10 2010 5 19
Bolivia temperature 10 2010 6 12
and so on.
Note that "cut" refers to the temperature thresholds defined in the functions above. Each cut should come from the equivalent raster stack: days.above.10, days.above.15 and so on.
