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:


# 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)

# 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"
locs <- subset(wrld_simpl, wrld_simpl@data$NAME %in% c("Argentina","Bolivia","Brazil","Paraguay","Uruguay"))

# Plot

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.


1 Answer 1


Since you are dealing with a rasterStack type of data you need to extract values using the extract function.The outcome therefore will be a vector.

As you see in the following line, the method for the extract function is:


in the position of x you will put the raster object and in the y the locations. Then use the as.data.frame function to turn the extracted object, into a dataframe.

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