modelin: Create object of class microin

In ilyamaclean/microclimf: Fast above, below or within canopy gridded microclimate modelling with R

Create object of class microin

Description

The function 'modelin' creates an object of class microin which unpacks various component inputs and reformats as required for running the R version of the model.

Usage

modelin(
  micropoint,
  vegp,
  soilc,
  dtm,
  dtmc = NA,
  altcorrect = 0,
  runchecks = TRUE
)

Arguments

micropoint	either an object of class 'micropoint' as returned by [runpointmodel()] or [subsetpointmodel()] or a list of micropoint objects as returned by [runpointmodela()] or [subsetpointmodela()], which assumes input climate data are spatially variable.
vegp	an object of class vegparams as returned by [vegpfromhab()] (see details)
soilc	an object of class soilcharac as returned by [soilcfromtype()]
dtm	a SpatRaster object of elevations in metres (see details)
dtmc	a SpatRaster object giving the resolution, spatial extent, and projection of the weather data used in 'micropoint'. Ignored if climate data provided to 'micropoint' as a data.frame. Must give elevations in metres if climate data were arrays and 'altcorrect' > 0 or if setting runchecks to TRUE.
altcorrect	a single numeric value indicating whether to apply an elevational lapse rate correction to temperatures (0 = no correction, 1 = fixed lapse rate correction, 2 = humidity-dependent variable lapse rate correction, see details)
runchecks	optional logical indicating whether to call [checkinputs()] to run

Details

The array of Plant Area index values in 'vegp' must of the same x and y dims as 'dtm' but can contain any number of repeated measures up to the number of entries in 'weather'. Data are interpolated to the time increment of 'weather'. Other vegetation paramaters, including vegetation height are assumed time-invarient. If these are time-varient, use the c++ version of the model. The SpatRaster datasets in 'soilc' must have the same x and y dims as 'dtm'. The x,y and z units of 'dtm' must be all be in metres and the coordinate reference system must be defined. If not NA, the units of dtmc must match dtm and must be elevation data if an altitude correction is applied. If 'altcorrect'>0, the elevation difference between each pixel of dtm and dtmc is calculated and an elevation lapse rate correction is applied to the temperature and pressure data to account for these elevation differences. If 'altcorrect'= 1, a fixed lapse rate of 5 degrees per 100m is applied to the temperature data. If 'altcorrect'= 2, humidity-dependent lapse rates are calculated and applied. See also details for modelin.

Examples

# ================================================================= #
# Preparing model inputs using climate data provided as a data.frame
# ================================================================= #
# run and subset point model
micropoint<-runpointmodel(climdata, reqhgt = 0.05, dtmcaerth, vegp, soilc)
micropoint <- subsetpointmodel(micropoint)
micro <- modelin(micropoint, vegp, soilc, dtmcaerth)
# ================================================================= #
# Preparing model inputs using climate data provided as arrays
# ================================================================= #
# Create dummy array data
.ta<-function(x,dtm,xdim=5,ydim=5) {
  a<-array(rep(x,each=ydim*xdim),dim=c(ydim,xdim,length(x)))
  .rast(a,dtm)
}
dtm <- rast(dtmcaerth)
climarrayr<-list(temp = .ta(climdata$temp, dtm),
  relhum = .ta(climdata$relhum, dtm),
  pres = .ta(climdata$pres, dtm),
  swdown = .ta(climdata$swdown, dtm),
  difrad = .ta(climdata$difrad, dtm),
  lwdown = .ta(climdata$lwdown, dtm),
  windspeed = .ta(climdata$windspeed, dtm),
  winddir = .ta(climdata$winddir, dtm),
  precip = .ta(climdata$precip, dtm))
tme <- as.POSIXlt(climdata$obs_time, tz="UTC")
# Run and subset point model array
micropointa <- runpointmodela(climarrayr, tme, reqhgt = 0.05, dtmcaerth, vegp, soilc)
micropointa <- subsetpointmodela(micropointa)
# Prepare grid model input
dtmc <- resample(dtm, climarrayr$temp[[1]])
micro <- modelin(micropointa, vegp, soilc, dtm, dtmc)

ilyamaclean/microclimf documentation built on Sept. 28, 2024, 4:55 p.m.