ameriflux_demo.RmdThis is a demonstration of the PEcAn utilities for downloading met data, converting it to the PEcAn-CF format (which is based on the Climate Forecasting conventions and similar to MsTMIP). These variables are defined in the PEcAn documentation.
In this example we will download 12 years of met data from the Bondville Ameriflux site. It has an Ameriflux SITE_ID of US-Bo1
The PEcAn.data.atmosphere source code is in modules/data.atmosphere and the documentation can be found with either package?PEcAn.data.atmosphere or in the data.atmosphere package documentation.
library(knitr)
library(ggplot2)
library(ggthemes)
library(PEcAn.data.atmosphere)download.Ameriflux(sitename = "US-Bo1", outfolder = "/tmp/",
start_date = "1996-01-01", end_date = "2008-04-10")met2CF.Ameriflux(in.path = "/tmp/", in.prefix = "US-Bo1", outfolder = "/tmp/out/",
start_date = "1996-01-01", end_date = "2008-04-10")NB: this is not required within PEcAn; used here for convenience. See documentation for NCO ncrcat function.
system("ncrcat -O -h /tmp/out/US-Bo1.199[6789].nc /tmp/out/US-Bo1.200[12348678].nc /tmp/out/US-Bo11996-2008.nc")Using the load.cfmet convenience function. Ameriflux is provided at 30 min intervals. If needed at a finer resolution, see ?cfmet.downscale.time (which works with subdaily and daily data). There is no cfmet.upscale.time function, but would be straightforward to implement if needed.
bondville.nc <- nc_open("/tmp/out/US-Bo11996-2008.nc")
bondville.cfmet <- load.cfmet(bondville.nc, lat = 40.0061988830566, lon = -88.290397644043, start.date = "1996-08-25", end.date = "2008-04-10")[!is.na(air_pressure)]theme_set(theme_tufte())
p1 <- ggplot() + geom_line(data = bondville.cfmet, aes(x = date, y = surface_downwelling_shortwave_flux_in_air)) + ylab(paste(bondville.nc$var$surface_downwelling_shortwave_flux_in_air$longname, bondville.nc$var$surface_downwelling_shortwave_flux_in_air$units))
p2 <- ggplot() + geom_line(data = bondville.cfmet, aes(x = date, y = surface_downwelling_longwave_flux_in_air)) +
ylab(paste(bondville.nc$var$surface_downwelling_longwave_flux_in_air$longname, bondville.nc$var$surface_downwelling_longwave_flux_in_air$units))
p3 <- ggplot() + geom_line(data = bondville.cfmet, aes(x = date, y = surface_downwelling_photosynthetic_photon_flux_in_air)) + ylab("PAR umol/m2/s")
p4 <- ggplot() + geom_line(data = bondville.cfmet, aes(x = date, y = air_pressure)) +
ylab(paste(bondville.nc$var$air_pressure$longname, bondville.nc$var$air_pressure$units))
p5 <- ggplot() + geom_line(data = bondville.cfmet, aes(x = date, y = air_temperature )) +
ylab(paste(bondville.nc$var$air_temperature$longname, bondville.nc$var$air_temperature$units))
p6 <- ggplot(data = bondville.cfmet, aes(x = date)) +
geom_line(aes(y = wind_speed)) +
#geom_line(aes(y = northward_wind), color = 'blue', alpha = 0.3) +
#geom_line(aes(y = eastward_wind), color = 'red', alpha = 0.3) +
#ggtitle("wind speed: scalar (black) north vector (blue) and east vector (red) ") +
ylab(paste(bondville.nc$var$wind_speed$longname, bondville.nc$var$wind_speed$units))
p7 <- ggplot() + geom_line(data = bondville.cfmet, aes(x = date, y = relative_humidity )) +
ylab(paste(bondville.nc$var$relative_humidity$longname, bondville.nc$var$relative_humidity$units))
p8 <- ggplot() + geom_line(data = bondville.cfmet, aes(x = date, y = specific_humidity )) +
ylab(paste(bondville.nc$var$specific_humidity$longname, bondville.nc$var$specific_humidity$units))
p9 <- ggplot() + geom_line(data = bondville.cfmet, aes(x = date, y = precipitation_flux)) +
ylab(paste(bondville.nc$var$ precipitation_flux$longname, bondville.nc$var$precipitation_flux$units))
plots <- list(p1, p2, p3, p4, p5, p6, p7, p8, p9)To use the data, you can convert these to a model specific format
library(PEcAn.BIOCRO)
# met2model.BioCro uses the following
bondville.biocromet <- cf2biocro(bondville.cfmet, longitude = -88.0, zulu2solarnoon = TRUE)
# write as csv for sharing
write.csv(bondville.biocromet, "../soy/data/bondville_1996-2008.csv", row.names = FALSE)