R Notebook

#======================================================================================================= # Authors: Mohau Mateyisi $ Lerato Mpheshea # # Email: MMateyisi@csir.co.za # # Date: 03rd March, 2019 # # Vesion 02 (trial) # # Property of CSIR NRE # # Disclaimer: Neither the Authers nor and the host # # institution CSIR should be held liabile to any # # loss or damage that may be incured due to # # the use of this script. # # . # #=======================================================================================================

library("raster")

## Loading required package: sp

library("ncdf4")

location.of.ncdfFIles<-"E:\\CCAM-CABLE"
filesIN<-list.files(location.of.ncdfFIles)
fileIN<- filesIN[1]



Get.aggregated.layer <- function(fileIN,dirW){
  
  # Extract data feature from file name
  FILEIN.FEATURES <-unlist(strsplit(fileIN,"-"))
  PARAMETER <-FILEIN.FEATURES[3]
  MODEL <- FILEIN.FEATURES[1]
  
  
  # upload netcdf file as a data brick
  In.data  <- brick(paste(dirW,fileIN,sep="\\"),varname = PARAMETER)
  
  # combine input data bricks
  T12 <- stack(In.data) 
  rnlayers=nlayers(T12)
  
  # output template
  Out.temp <- raster(In.data)
  
 
 
  # The output vector of the three term mean anomaly matrices
  Out.vec<-vector("list",1)
  
  stack.seq.aggregate <- function(myvec,na.rm=T){
    #**********************************************************************************
    # the function takes a vector
    # and it returns mean
    #**********************************************************************************
    my.inpu.vec<-myvec[9:28]
    
    
    period.mean <- mean(my.inpu.vec)
    
    return(period.mean)
  }
  
  #apply the aggregation function to the whole raster stack 
  Out.temp <- stackApply(T12, indices = rep(1, rnlayers), fun = stack.seq.aggregate, na.rm = FALSE)
 
  # ANOM.DATA output mean anomaly for plotting, stored the output in a single vector
  Out.vec[1]<-Out.temp
 
  
  return(Out.vec)
}


output1<-Get.aggregated.layer(fileIN,location.of.ncdfFIles)

## Warning in `[<-`(`*tmp*`, 1, value = Out.temp): implicit list embedding of S4
## objects is deprecated

library("ggplot2")

PARAMETER<-"rnd24"
location.of.ncdfFIles<-"E:\\CCAM-CABLE"

getRaster.to.dataframe <-function(Input.raster,location.of.ncdfFIles,PARAMETER){
  
    # Convert data for each time period into data file
    SPDATA1<- as(Input.raster, "SpatialPixelsDataFrame")
    SPDATA_DF1 <- as.data.frame(SPDATA1)
    SPDATA_DF1 <- fortify(SPDATA_DF1)
    
    write.csv(SPDATA_DF1,file.path(location.of.ncdfFIles, paste(PARAMETER,"mean","csv",sep = ".")), row.names = F)
    
    return(SPDATA_DF1)
    
}

output2<- getRaster.to.dataframe(output1[[1]],location.of.ncdfFIles,PARAMETER)