bash-$ ncdump -h .nc
bash-$ R
R> library(ncdf4)
R> print(nc_open("test.nc")

my.nc <- nc_open("test.nc")

ncvar_get(my.nc, "lwdown", start = c(5, 1, 1), count = c(10, 1, 1))

my.nc$var$lwdown$dim[[1]]$name
[1] "time"
my.nc$var$lwdown$dim[[2]]$name
[1] "lon"
my.nc$var$lwdown$dim[[3]]$name
[1] "lat"

start <- c(lat = 1, lon = 1, time = 5)
count <- c(lat = 1, lon = 1, time = 10)
dim.order <- sapply(my.nc$var$lwdown$dim, function(x) x$name)

ncvar_get(my.nc, "lwdown", start = start[dim.order], count = count[dim.order])