nctoclimarray function removed as mcera5 packge forked and pull reque…

…st issued to enable mcera5 package to provide data in correct format for microclimf

NAMESPACE

@@ -7,7 +7,6 @@ export(clumpestimate)
 export(leafrfromalb)
 export(modelin)
 export(mosaicblend)
-export(nctoclimarray)
 export(runbioclim)
 export(runmicro)
 export(runmicro_big)

R/dataprep.R

@@ -1024,84 +1024,6 @@ leafrfromalb<-function(pai, x, alb, ltrr = 0.5) {
   lref<-mask(lref,pai)
   return(list(leafr=lref,leaft=ltrr*lref,gref=.rast(gref,pai)))
 }
-#' Create climate arrays for inputting to microclimate model from a netCDF4 file
-#'
-#' @description The function `nctoclimarray` converts data in a netCDF4 file returned
-#' by [mcera5::request_era5()] to the correct formal required for running [modelina()] or
-#' [modelina_dy()].
-#'
-#' @param ncfile character vector containing the path and filename of the nc file
-#' @param dtm a SpatRaster object of elevations covering the extent of the study area (see details)
-#' @param dtr_cor_fac numeric value to be used in the diurnal temperature range
-#' correction of coastal grid cells. Default = 1.285, based on calibration against UK Met Office
-#' observations. If set to zero, no correction is applied.
-#' @return a list of the following:
-#' \describe{
-#'   \item{tme}{POSIXlt object of times corresponding to climate observations}
-#'   \item{climarray}{a list of arrays of hourly weather variables - same format as for [modelina()].}
-#'   \item{precarray}{an array of daily precipitation values - same format as for [modelina()].}
-#'   \item{dtmc}{a coarse resolution digital elevation dataset matching the resolution of input
-#'   climate data, but with a coordinate reference system and extent matching `dtm`}
-#' }
-#' @export
-#' @import ncdf4
-#' @details the model requires that input climate data are projected using a coordinate reference
-#' system in which x and y are in metres. Since values returned by [mcera5::request_era5()]
-#' are in lat long, the output data are reprojected using the coordinate reference system and
-#' extent of dtm (but retain the approximate original grid resolution of the input climate data).
-#' Returned climate data match the resolution, coordinate reference system and extent of `dtmc`.
-nctoclimarray <- function(ncfile, dtm, dtr_cor_fac = 1.285)  {
-  t2m<-rast(ncfile,subds = "t2m") # Air temperature (K)
-  d2m<-rast(ncfile,subds = "d2m") # Dewpoint temperature (K)
-  sp<-rast(ncfile,subds = "sp") # Surface pressure (Pa)
-  u10<-rast(ncfile,subds = "u10") # U-wind at 10m (m/s)
-  v10<-rast(ncfile,subds = "v10") # V-wind at 10m (m/s)
-  tp<-rast(ncfile,subds = "tp") # Total precipitation (m)
-  msnlwrf<-rast(ncfile,subds = "msnlwrf")   # Mean surface net long-wave radiation flux (W/m^2)
-  msdwlwrf<-rast(ncfile,subds = "msdwlwrf") # Mean surface downward long-wave radiation flux (W/m^2)
-  fdir<-rast(ncfile,subds = "fdir") #  Total sky direct solar radiation at surface (W/m^2)
-  ssrd<-rast(ncfile,subds = "ssrd") # Surface short-wave (solar) radiation downwards (W/m^2)
-  lsm<-rast(ncfile,subds = "lsm") # Land sea mask
-  # Create coarse-resolution dtm to use as template for resampling
-  te<-terra::project(t2m[[1]],crs(dtm))
-  agf<-res(te)[1]/res(dtm)[1]
-  dtmc<-aggregate(dtm,fact=agf,fun=mean,na.rm=T)
-  # Apply coastal correction to temperature data
-  tmn<-.ehr(.hourtoday(as.array(t2m)-273.15,min))
-  mu<-(1-as.array(lsm))*dtr_cor_fac+1
-  tc<-.rast(((as.array(t2m)-273.15)-tmn)*mu+tmn,t2m)
-  # Calculate vapour pressure
-  ea<-.rast(.satvap(as.array(d2m)-273.15),t2m)
-  # Resample all variables to match dtmc
-  tc<-terra::project(tc,dtmc)
-  ea<-terra::project(ea,dtmc)
-  sp<-terra::project(sp,dtmc)
-  u10<-terra::project(u10,dtmc)
-  v10<-terra::project(v10,dtmc)
-  tp<-terra::project(tp,dtmc)
-  msnlwrf<-terra::project(msnlwrf,dtmc)
-  msdwlwrf<-terra::project(msdwlwrf,dtmc)
-  fdir<-terra::project(fdir,dtmc)
-  ssrd<-terra::project(ssrd,dtmc)
-  # Derive varies
-  temp<-as.array(tc) # Temperature (deg c)
-  relhum<-(as.array(ea)/.satvap(temp))*100 # Relative humidity (%)
-  pres<-as.array(sp)/1000  # Surface pressure (kPa)
-  swrad<-as.array(ssrd)/3600 # Downward shortwave radiation (W/m^2)
-  difrad<-swrad-as.array(fdir)/3600 # Downward diffuse radiation (W/m^2)
-  skyem<-as.array(msdwlwrf)/as.array(msdwlwrf-msnlwrf) # sky emissivity (0-1)
-  windspeed<-sqrt(as.array(u10)^2+as.array(v10)^2)*log(67.8*2-5.42)/log(67.8*10-5.42) # Wind speed (m/s)
-  winddir<-as.array((terra::atan2(u10,v10)*180/pi+180)%%360) # Wind direction (deg from N - from)
-  precarray<-.hourtoday(as.array(tp)*1000,sum)
-  # Save lists
-  climarray<-list(temp=temp,relhum=relhum,pres=pres,swrad=swrad,difrad=difrad,
-                  skyem=skyem,windspeed=windspeed,winddir=winddir)
-  # Generate POSIXlt object of times
-  tme<-as.POSIXlt(time(t2m),tz="UTC")
-  # Output for returning
-  out<-list(tme=tme,climarray=climarray,precarray=precarray,dtmc=dtmc)
-  return(out)
-}
 #' Writes model output as ncdf4 file
 #'
 #' @description The function `writetonc` writes hourly model outputs as an ncdf4 file to a specified file