In stineb/rbeni: Useful R functions for Beni.

library(rbeni)
knitr::opts_chunk$set(echo = TRUE)

Used for debugging

nc_out <- read_nc_onefile("~/sofun_outputs/output_nc_global_sofun/global_ORG.2001.d.fapar.nc")
nc_in <-  read_nc_onefile("~/sofun/input/global/fapar/fAPAR3g_v2_1982_2016_FILLED.nc")

nc_out$vars$fapar[706, 315, 212]
nc_in$vars$FAPAR_FILLED[706, 315, 235]

nc_out$vars$fapar[,,212] %>% image()
nc_in$vars$FAPAR_FILLED[,,235] %>% image()

NetCDF handling

Reading from NetCDF

nc <- read_nc_onefile("~/sofun/input/global/fapar/fpar_MODIS-C006-MOD15A2_SUBSET.nc")

# manipulate inside
nc$time <- c(nc$time[1] - lubridate::days(31), nc$time)
nc$vars$fpar <- abind::abind(nc$vars$fpar[,,1], nc$vars$fpar, along = 3)

# rasta <- raster::brick("~/sofun/input/global/fapar/tmp.nc")
# rasterVis::levelplot(rasta)

Manipulate nc object

nc_sub <- nc_selname(nc, "fpar")

Writing NetCDF

# raster::writeRaster(rasta, filename = "~/sofun/input/global/fapar/tmp2.nc", format = "CDF", overwrite = TRUE )
# nc2 <- read_nc_onefile("~/sofun/input/global/fapar/tmp2.nc")
# image(nc2$vars$Date[,,2])

write_nc2(
  nc_sub, 
  varnam = "fpar", 
  outfilnam = "~/sofun/input/global/fapar/fpar_MODIS-C006-MOD15A2_SUBSET_writtenbyR.nc", 
  units_time = "days since 2000-01-01"
  )
print(nc_sub$vars$fpar[720, 148, 13])
print(range(nc_sub$vars$fpar[,,13]))

nc_test <- read_nc_onefile("~/sofun/input/global/fapar/fpar_MODIS-C006-MOD15A2_SUBSET_writtenbyR.nc")
print(nc_test$vars$fpar[720,148,25])

nc_test2 <- read_nc_onefile("~/sofun/input/global/fapar/fAPAR3g_v2_1982_2016_FILLED.nc")
print(nc_test2$vars$fpar[717,105,241])


nc_ccov <- read_nc_onefile("~/data/cru/ts_4.01/cru_ts4.01.1901.2016.cld.dat.nc")
idx <- which(lubridate::year(nc_ccov$time)==2001 & lubridate::month(nc_ccov$time)==1)
print(nc_ccov$vars$cld[720, 148, idx])
print(range(nc_ccov$vars$cld[,,idx], na.rm=TRUE))

Test if it worked ok.

nc_written <- read_nc_onefile("~/sofun/input/global/fapar/fpar.nc")
image(nc_written$vars$fpar[,,2])

Plotting a map

image(nc$vars$fpar[,,2])

stineb/rbeni documentation built on Feb. 24, 2023, 5:40 a.m.