agriwater
Evapotranspiration and Energy Fluxes Spatial Analysis

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R/modis_single.R

R/modis_single.R
In agriwater: Evapotranspiration and Energy Fluxes Spatial Analysis

Defines functions albedo_modis radiation_modis evapo_modis kc_modis

Documented in albedo_modis evapo_modis kc_modis radiation_modis 

#SINGLE VALUES OF AGROMETEOROLOGICAL DATA
#MODIS

#'Crop coefficient (ETa / ET0) using MODIS with single agrometeorological data.
#'
#' @param doy   is the Day of Year (DOY)
#' @param RG  is the global solar radiation
#' @param Ta  is the average air temperature
#' @param a  is one of the regression coefficients of SAFER algorithm
#' @param b  is one of the regression coefficients of SAFER algorithm
#' @export
#' @import raster
#' @import sp
#' @import rgdal
#' @importFrom utils read.csv
#'
#' @return It returns in raster format (.tif) the Surface Albedo at 24h scale ("Alb_24"), NDVI, Surface Temperature ("LST"), Crop Coefficient ("kc") and net radiation ("Rn_MJ").
#' @examples
#' library(agriwater)
#'
#' # dependencies of package 'agriwater'
#' library(sp)
#' library(raster)
#' library(rgdal)
#' rgdal_show_exportToProj4_warnings"="none"
#'
#'
#' # Using a temporary folder to run example
#' wd <- tempdir()
#' initial = getwd()
#' setwd(wd)
#'
#' # creating raster which simulate MODIS reflectances - for using
#' # real data, please download:
#' # https://drive.google.com/open?id=14E1wHNLxG7_Dh4I-GqNYakj8YJDgKLzk
#'
#' xy <- matrix(rnorm(4, mean = 0.07, sd = 0.01), 2, 2)
#' rast <- raster(xy)
#' extent(rast) <- c(-40.5,-40.45,-9.5,-9.45)
#' projection(rast) <- CRS("+proj=longlat +datum=WGS84")
#' writeRaster(rast, file.path(wd, "B2"),format = "GTiff", overwrite=TRUE)
#' xy <- matrix(rnorm(4, mean = 0.05, sd = 0.015),2, 2)
#' rast <- raster(xy)
#' extent(rast) <- c(-40.5,-40.45,-9.5,-9.45)
#' projection(rast) <- CRS("+proj=longlat +datum=WGS84")
#' writeRaster(rast, file.path(wd, "B1"),format = "GTiff", overwrite=TRUE)
#'
#  # creating mask of study area
#' mask <- as(extent(rast), 'SpatialPolygons')
#' projection(mask) <- CRS("+proj=longlat +datum=WGS84")
#' shapefile(mask, file.path(wd,"mask.shp"), overwrite=TRUE)
#'
#' # using "agriwater"
#' DOY = 134
#' a = 1.8
#' b = -0.008
#' RG = 17.6
#' Ta = 27.9
#' kc_modis(DOY, RG, Ta, a, b)
#'
#' #Exiting temporary folder and returning to previous workspace
#' setwd(initial)

kc_modis = function(doy, RG, Ta, a, b){

  b1 <- raster("B1.tif")
  b2 <- raster("B2.tif")

  mask <- readOGR("mask.shp")

  b1_crop <- crop(b1, extent(mask))
  b1_mascara <- mask(b1_crop, mask)
  b2_crop <- crop(b2, extent(mask))
  b2_mascara <- mask(b2_crop, mask)


  Alb_inst=b1_mascara*0.41*0.0001+b2_mascara*0.14*0.0001+0.08

  Alb_24=1.0223*Alb_inst+ 0.0149


  writeRaster(Alb_24, "Alb_24", format = "GTiff", overwrite=TRUE)

  NDVI =(b2_mascara-b1_mascara)/(b2_mascara+b1_mascara)

  writeRaster(NDVI, "NDVI", format = "GTiff", overwrite=TRUE)

  lati <- long <- b2_mascara
  xy <- coordinates(b2_mascara)
  long[] <- xy[, 1]
  long <- crop(long, extent(mask))
  lati[] <- xy[, 2]
  lati <- crop(lati, extent(mask))


  map1 <- (long/long)*((2*pi)/365)*(doy-1)

  Et <- (0.000075+0.001868*cos(map1)-0.032077*sin(map1)-0.014615*cos(2*map1)-0.04089*sin(2*map1))

  LAT <- (13+(4*long/60)+(Et/60))

  Dec <- 0.006918-0.399912*cos(map1)+0.070257*sin(map1)+0.006758*cos(2*map1)+0.000907*sin(2*map1)-0.002697*cos(3*map1)+0.00148*sin(3*map1)

  W <- 15*(LAT-12)*(pi/180)

  cos_zwn <- sin(lati*pi/180)*sin(Dec)+cos(lati*pi/180)*cos(Dec)*cos(W)

  E0 <- (1.00011+0.034221*cos(map1)+0.00128*sin(map1)+0.000719*cos(2*map1)+0.000077*sin(2*map1))

  Ws = acos(((-1)*tan(lati*pi/180))*tan(Dec))

  R =(Ws*sin(lati*pi/180)*sin(Dec))+(cos(lati*pi/180)*cos(Dec)*sin(Ws))

  RsTOP_aux =(1367/pi)*E0*R

  RsTOP = resample(RsTOP_aux, b1_mascara, method="bilinear")

  Transm =(RG*11.6)/RsTOP

  Rn_coeff =6.99*Ta-39.99

  Rn =((1-Alb_24)*(RG*11.6))-(Rn_coeff*Transm)

  Rn_MJ =Rn/11.6

  writeRaster(Rn_MJ, "Rn_MJ", format = "GTiff", overwrite=TRUE)

  slope =(4098*(0.6108*exp((17.27*(Ta))/((Ta)+237.3)))/((Ta)+237.3)^2)

  LEeq = (slope*Rn)/(slope+0.066)

  rm(b1, b2, b1_mascara, b2_mascara, mask, slope, Rn_coeff, RsTOP, RsTOP_aux, R, Ws, E0, cos_zwn, W, Dec, LAT, Et, map1, lati, long)

  RR =Alb_24*RG

  Emiss_atm = 0.9364*(((-1)*log(Transm))^0.1135)

  Emiss_atm[Emiss_atm > 1] <- 1

  RLdown_wm2 =(Emiss_atm*5.67*(10^(-8))*((Ta +273.15)^4))

  RL_down =RLdown_wm2/11.6

  RL_up =(RG-RR+RL_down-Rn_MJ)

  Esurf_r1 <- NDVI

  Esurf_r1[NDVI < 0] <- 1

  Esurf_r1[NDVI >= 0] <- NA

  Esurf_r2 <- 1.0035+0.0589*log(NDVI)

  Esurf <- merge(Esurf_r1, Esurf_r2)

  TS24 =((RL_up*11.6)/((Esurf*5.67)*(10^(-8))))^(0.25)

  TS24[TS24 < 273.15] = NA

  writeRaster(TS24, "LST", format = "GTiff", overwrite=TRUE)

  NDVI[NDVI <= 0] = NA

  kc=exp((a)+(b*((TS24-273.15)/(Alb_24*NDVI))))

  writeRaster(kc, "kc", format = "GTiff", overwrite=TRUE)
}

#' Actual evapotranspiration (ETa) using MODIS with single agrometeorological data.
#' @param doy  is the Day of Year (DOY)
#' @param RG is the global solar radiation
#' @param Ta is the average air temperature
#' @param ET0 is the reference evapotranspiration
#' @param a  is one of the regression coefficients of SAFER algorithm
#' @param b is one of the regression coefficients of SAFER algorithm
#' @export
#' @import raster
#' @import sp
#' @import rgdal
#' @importFrom utils read.csv
#'
#' @return It returns in raster format (.tif) the Surface Albedo at 24h scale ("Alb_24"), NDVI, Surface Temperature ("LST"), net radiation ("Rn_MJ"), Crop Coefficient ("kc") and Actual Evapotranspiration (evapo).
#' @examples
#' library(agriwater)
#'
#' # dependencies of package 'agriwater'
#' library(sp)
#' library(raster)
#' library(rgdal)
#' rgdal_show_exportToProj4_warnings"="none"
#'
#' # Using a temporary folder to run example
#' wd <- tempdir()
#' initial = getwd()
#' setwd(wd)
#'
#'
#' # creating raster which simulate Sentinel-2 reflectances - for using
#' # real data, please download:
#' # https://drive.google.com/open?id=14E1wHNLxG7_Dh4I-GqNYakj8YJDgKLzk
#'
#' wd <- tempdir()
#' xy <- matrix(rnorm(4, mean = 0.05, sd = 0.015),2, 2)
#' rast <- raster(xy)
#' extent(rast) <- c(-40.5,-40.45,-9.5,-9.45)
#' projection(rast) <- CRS("+proj=longlat +datum=WGS84")
#' writeRaster(rast, file.path(wd, "B2"),format = "GTiff", overwrite=TRUE)
#' xy <- matrix(rnorm(4, mean = 0.05, sd = 0.015),2, 2)
#' rast <- raster(xy)
#' extent(rast) <- c(-40.5,-40.45,-9.5,-9.45)
#' projection(rast) <- CRS("+proj=longlat +datum=WGS84")
#' writeRaster(rast, file.path(wd, "B1"),format = "GTiff", overwrite=TRUE)
#'
#  # creating mask of study area
#' mask <- as(extent(rast), 'SpatialPolygons')
#' projection(mask) <- CRS("+proj=longlat +datum=WGS84")
#' shapefile(mask, file.path(wd,"mask.shp"), overwrite=TRUE)
#'
#' # using "agriwater" - it's the same procedure as the used for
#' # evapo_l8(), evapo_l8t(), evapo_modis_grid(), evapo_l8_grid(),
#' # evapo_l8t_grid(), evapo_s2() and evapo_s2_grid()
#' DOY = 134
#' a = 1.8
#' b = -0.008
#' RG = 17.6
#' Ta = 27.9
#' ET0 = 3.8
#' evapo_modis(DOY, RG, Ta, ET0, a, b)
#'
#' #Exiting temporary folder and returning to previous workspace
#' setwd(initial)

evapo_modis = function(doy, RG, Ta, ET0, a, b){

  b1 <- raster("B1.tif")
  b2 <- raster("B2.tif")

  mask <- readOGR("mask.shp")

  b1_crop <- crop(b1, extent(mask))
  b1_mascara <- mask(b1_crop, mask)
  b2_crop <- crop(b2, extent(mask))
  b2_mascara <- mask(b2_crop, mask)


  Alb_inst=b1_mascara*0.41*0.0001+b2_mascara*0.14*0.0001+0.08

  Alb_24=1.0223*Alb_inst+ 0.0149

  writeRaster(Alb_24, "Alb_24", format = "GTiff", overwrite=TRUE)

  NDVI =(b2_mascara-b1_mascara)/(b2_mascara+b1_mascara)

  writeRaster(NDVI, "NDVI", format = "GTiff", overwrite=TRUE)


  lati <- long <- b2_mascara
  xy <- coordinates(b2_mascara)
  long[] <- xy[, 1]
  long <- crop(long, extent(mask))
  lati[] <- xy[, 2]
  lati <- crop(lati, extent(mask))


  map1 <- (long/long)*((2*pi)/365)*(doy-1)

  Et <- (0.000075+0.001868*cos(map1)-0.032077*sin(map1)-0.014615*cos(2*map1)-0.04089*sin(2*map1))

  LAT <- (13+(4*long/60)+(Et/60))

  Dec <- 0.006918-0.399912*cos(map1)+0.070257*sin(map1)+0.006758*cos(2*map1)+0.000907*sin(2*map1)-0.002697*cos(3*map1)+0.00148*sin(3*map1)

  W <- 15*(LAT-12)*(pi/180)

  cos_zwn <- sin(lati*pi/180)*sin(Dec)+cos(lati*pi/180)*cos(Dec)*cos(W)

  E0 <- (1.00011+0.034221*cos(map1)+0.00128*sin(map1)+0.000719*cos(2*map1)+0.000077*sin(2*map1))

  Ws = acos(((-1)*tan(lati*pi/180))*tan(Dec))

  R =(Ws*sin(lati*pi/180)*sin(Dec))+(cos(lati*pi/180)*cos(Dec)*sin(Ws))

  RsTOP_aux =(1367/pi)*E0*R

  RsTOP = resample(RsTOP_aux, b1_mascara, method="bilinear")

  Transm =(RG*11.6)/RsTOP

  Rn_coeff =6.99*Ta-39.99

  Rn =((1-Alb_24)*(RG*11.6))-(Rn_coeff*Transm)

  Rn_MJ =Rn/11.6

  writeRaster(Rn_MJ, "Rn_MJ", format = "GTiff", overwrite=TRUE)

  slope =(4098*(0.6108*exp((17.27*(Ta))/((Ta)+237.3)))/((Ta)+237.3)^2)

  LEeq = (slope*Rn)/(slope+0.066)

  rm(b1, b2, b1_mascara, b2_mascara, mask, slope, Rn_coeff, RsTOP, RsTOP_aux, R, Ws, E0, cos_zwn, W, Dec, LAT, Et, map1, lati, long)

  RR =Alb_24*RG

  Emiss_atm = 0.9364*(((-1)*log(Transm))^0.1135)

  Emiss_atm[Emiss_atm > 1] <- 1

  RLdown_wm2 =(Emiss_atm*5.67*(10^(-8))*((Ta +273.15)^4))

  RL_down =RLdown_wm2/11.6

  RL_up =(RG-RR+RL_down-Rn_MJ)

  Esurf_r1 <- NDVI

  Esurf_r1[NDVI < 0] <- 1

  Esurf_r1[NDVI >= 0] <- NA

  Esurf_r2 <- 1.0035+0.0589*log(NDVI)

  Esurf <- merge(Esurf_r1, Esurf_r2)

  TS24 =((RL_up*11.6)/((Esurf*5.67)*(10^(-8))))^(0.25)

  TS24[TS24 < 273.15] = NA

  writeRaster(TS24, "LST", format = "GTiff", overwrite=TRUE)

  NDVI[NDVI <= 0] = NA

  kc=exp((a)+(b*((TS24-273.15)/(Alb_24*NDVI))))

  writeRaster(kc, "kc", format = "GTiff", overwrite=TRUE)

  ET=kc*ET0

  writeRaster(ET, "evapo", format = "GTiff", overwrite=TRUE)
}

#'Energy balance using Landsat-8 images with single agrometeorological data.
#'@param doy is the Day of Year (DOY)
#'@param RG is the global solar radiation
#'@param Ta is the average air temperature
#'@param ET0  is the reference evapotranspiration
#'@param a is one of the regression coefficients of SAFER algorithm
#'@param b is one of the regression coefficients of SAFER algorithm
#'@export
#'@import raster
#' @import sp
#' @import rgdal
#' @importFrom utils read.csv
#'
#'@return It returns in raster format (.tif) the Surface Albedo at 24h scale ("Alb_24"), NDVI, Surface Temperature ("LST"), Crop Coefficient ("kc"), Actual Evapotranspiration (evapo), latent heat flux "LE_MJ"), net radiation ("Rn_MJ"), ground heat flux ("G_MJ") and the sensible heat flux ("H_MJ").
#' @examples
#' library(agriwater)
#'
#' # dependencies of package 'agriwater'
#' library(sp)
#' library(raster)
#' library(rgdal)
#' rgdal_show_exportToProj4_warnings"="none"
#'
#' # Using a temporary folder to run example
#' wd <- tempdir()
#' initial = getwd()
#' setwd(wd)
#'
#' # creating raster which simulate Sentinel-2 reflectances - for using
#' # real data, please download:
#' # https://drive.google.com/open?id=14E1wHNLxG7_Dh4I-GqNYakj8YJDgKLzk
#'
#' wd <- tempdir()
#' setwd <- tempdir()
#' xy <- matrix(rnorm(4, mean = 0.05, sd = 0.015),2, 2)
#' rast <- raster(xy)
#' extent(rast) <- c(-40.5,-40.45,-9.5,-9.45)
#' projection(rast) <- CRS("+proj=longlat +datum=WGS84")
#' writeRaster(rast, file.path(wd, "B2"),format = "GTiff", overwrite=TRUE)
#' xy <- matrix(rnorm(4, mean = 0.05, sd = 0.015),2, 2)
#' rast <- raster(xy)
#' extent(rast) <- c(-40.5,-40.45,-9.5,-9.45)
#' projection(rast) <- CRS("+proj=longlat +datum=WGS84")
#' writeRaster(rast, file.path(wd, "B1"),format = "GTiff", overwrite=TRUE)
#'
#' # creating mask of study area
#' mask <- as(extent(rast), 'SpatialPolygons')
#' projection(mask) <- CRS("+proj=longlat +datum=WGS84")
#' shapefile(mask, file.path(wd,"mask.shp"), overwrite=TRUE)
#'
#' # using "agriwater" - it's the same procedure as the used for
#' # radiation_l8(), radiation_l8t(), radiation_s2(),
#' # radiation_l8_grid(), radiation_l8t_grid(),
#' # radiation_s2_grid(), radiation_s2() and radiation_modis_grid()
#' DOY = 134
#' a = 1.8
#' b = -0.008
#' RG = 17.6
#' Ta = 27.9
#' ET0 = 3.8
#' radiation_modis(DOY, RG, Ta, ET0, a, b)
#'
#' #Exiting temporary folder and returning to previous workspace
#' setwd(initial)

radiation_modis =  function(doy, RG, Ta, ET0, a, b){


  b1 <- raster("B1.tif")
  b2 <- raster("B2.tif")

  mask <- readOGR("mask.shp")

  b1_crop <- crop(b1, extent(mask))
  b1_mascara <- mask(b1_crop, mask)
  b2_crop <- crop(b2, extent(mask))
  b2_mascara <- mask(b2_crop, mask)


  Alb_inst=b1_mascara*0.41*0.0001+b2_mascara*0.14*0.0001+0.08

  Alb_24=1.0223*Alb_inst+ 0.0149

  writeRaster(Alb_24, "Alb_24", format = "GTiff", overwrite=TRUE)

  NDVI =(b2_mascara-b1_mascara)/(b2_mascara+b1_mascara)

  writeRaster(NDVI, "NDVI", format = "GTiff", overwrite=TRUE)


  lati <- long <- b2_mascara
  xy <- coordinates(b2_mascara)
  long[] <- xy[, 1]
  long <- crop(long, extent(mask))
  lati[] <- xy[, 2]
  lati <- crop(lati, extent(mask))


  map1 <- (long/long)*((2*pi)/365)*(doy-1)

  Et <- (0.000075+0.001868*cos(map1)-0.032077*sin(map1)-0.014615*cos(2*map1)-0.04089*sin(2*map1))

  LAT <- (13+(4*long/60)+(Et/60))

  Dec <- 0.006918-0.399912*cos(map1)+0.070257*sin(map1)+0.006758*cos(2*map1)+0.000907*sin(2*map1)-0.002697*cos(3*map1)+0.00148*sin(3*map1)

  W <- 15*(LAT-12)*(pi/180)

  cos_zwn <- sin(lati*pi/180)*sin(Dec)+cos(lati*pi/180)*cos(Dec)*cos(W)

  E0 <- (1.00011+0.034221*cos(map1)+0.00128*sin(map1)+0.000719*cos(2*map1)+0.000077*sin(2*map1))

  Ws = acos(((-1)*tan(lati*pi/180))*tan(Dec))

  R =(Ws*sin(lati*pi/180)*sin(Dec))+(cos(lati*pi/180)*cos(Dec)*sin(Ws))

  RsTOP_aux =(1367/pi)*E0*R

  RsTOP = resample(RsTOP_aux, b1_mascara, method="bilinear")

  Transm =(RG*11.6)/RsTOP

  Rn_coeff =6.99*Ta-39.99

  Rn =((1-Alb_24)*(RG*11.6))-(Rn_coeff*Transm)

  Rn_MJ =Rn/11.6

  writeRaster(Rn_MJ, "Rn_MJ", format = "GTiff", overwrite=TRUE)

  slope =(4098*(0.6108*exp((17.27*(Ta))/((Ta)+237.3)))/((Ta)+237.3)^2)

  LEeq = (slope*Rn)/(slope+0.066)

  rm(b1, b2, b1_mascara, b2_mascara, mask, slope, Rn_coeff, RsTOP, RsTOP_aux, R, Ws, E0, cos_zwn, W, Dec, LAT, Et, map1, lati, long)

  RR =Alb_24*RG

  Emiss_atm = 0.9364*(((-1)*log(Transm))^0.1135)

  Emiss_atm[Emiss_atm > 1] <- 1

  RLdown_wm2 =(Emiss_atm*5.67*(10^(-8))*((Ta +273.15)^4))

  RL_down =RLdown_wm2/11.6

  RL_up =(RG-RR+RL_down-Rn_MJ)

  Esurf_r1 <- NDVI

  Esurf_r1[NDVI < 0] <- 1

  Esurf_r1[NDVI >= 0] <- NA

  Esurf_r2 <- 1.0035+0.0589*log(NDVI)

  Esurf <- merge(Esurf_r1, Esurf_r2)

  TS24 =((RL_up*11.6)/((Esurf*5.67)*(10^(-8))))^(0.25)

  TS24[TS24 < 273.15] = NA

  writeRaster(TS24, "LST", format = "GTiff", overwrite=TRUE)

  NDVI[NDVI <= 0] = NA

  kc=exp((a)+(b*((TS24-273.15)/(Alb_24*NDVI))))

  ET=kc*ET0

  LE_MJ =ET*2.45

  writeRaster(LE_MJ, "LE_MJ", format = "GTiff", overwrite=TRUE)

  G_Rn =3.98*exp(-25.47*Alb_24)

  G_MJ =G_Rn*Rn_MJ

  writeRaster(G_MJ, "G_MJ", format = "GTiff", overwrite=TRUE)

  H_MJ =Rn_MJ-LE_MJ-G_MJ

  writeRaster(H_MJ, "H_MJ", format = "GTiff", overwrite=TRUE)

}

#' Surface Albedo using MODIS images.
#'
#' @export
#' @import raster
#' @import sp
#' @import rgdal
#' @importFrom utils read.csv
#'
#' @return It returns in raster format (.tif) the Surface Albedo at 24h scale ("Alb_24").
#' @examples
#' library(agriwater)
#'
#' # dependencies of package 'agriwater'
#' library(sp)
#' library(raster)
#' library(rgdal)
#' rgdal_show_exportToProj4_warnings"="none"
#'
#' # Using a temporary folder to run example
#' wd <- tempdir()
#' initial = getwd()
#' setwd(wd)
#'
#' # creating raster which simulate Sentinel-2 reflectances - for using
#' # real data, please download:
#' # https://drive.google.com/open?id=14E1wHNLxG7_Dh4I-GqNYakj8YJDgKLzk
#'
#' wd <- tempdir()
#' setwd <- tempdir()
#' xy <- matrix(rnorm(4, mean = 0.05, sd = 0.015),2, 2)
#' rast <- raster(xy)
#' extent(rast) <- c(-40.5,-40.45,-9.5,-9.45)
#' projection(rast) <- CRS("+proj=longlat +datum=WGS84")
#' writeRaster(rast, file.path(wd, "B2"),format = "GTiff", overwrite=TRUE)
#' xy <- matrix(rnorm(4, mean = 0.05, sd = 0.015),2, 2)
#' rast <- raster(xy)
#' extent(rast) <- c(-40.5,-40.45,-9.5,-9.45)
#' projection(rast) <- CRS("+proj=longlat +datum=WGS84")
#' writeRaster(rast, file.path(wd, "B1"),format = "GTiff", overwrite=TRUE)
#'
#' # creating mask of study area
#' mask <- as(extent(rast), 'SpatialPolygons')
#' projection(mask) <- CRS("+proj=longlat +datum=WGS84")
#' shapefile(mask, file.path(wd,"mask.shp"), overwrite=TRUE)
#'
#' # using "agriwater"
#' albedo_modis()
#'
#' #Exiting temporary folder and returning to previous workspace
#' setwd(initial)

albedo_modis = function(){

  b1 <- raster("B1.tif")
  b2 <- raster("B2.tif")

  mask <- readOGR("mask.shp")

  b1_crop <- crop(b1, extent(mask))
  b1_mascara <- mask(b1_crop, mask)
  b2_crop <- crop(b2, extent(mask))
  b2_mascara <- mask(b2_crop, mask)


  Alb_inst=b1_mascara*0.41*0.0001+b2_mascara*0.14*0.0001+0.08

  Alb_24=1.0223*Alb_inst+ 0.0149

  writeRaster(Alb_24, "Alb_24", format = "GTiff", overwrite=TRUE)
}

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agriwater documentation built on Feb. 2, 2021, 9:07 a.m.

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