runmicro_big: runmicro on big areas

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

runmicro on big areas

Description

The function 'runmicro' runs the grid version of the microclimate model

Usage

runmicro_big(
  micropoint,
  reqhgt,
  pathout = getwd(),
  vegp,
  soilc,
  dtm,
  dtmc = NA,
  altcorrect = 0,
  tilesize = NA,
  toverlap = 0,
  writeasnc = FALSE,
  runchecks = TRUE,
  pai_a = NA,
  tfact = 1.5,
  out = rep(TRUE, 10)
)

Arguments

micropoint	an object of class micropoint or a list of objects of class micropoint as returned by [runpointmodel()], [runpointmodela()], [subsetpointmodel()] or [subsetpointmodela()]
reqhgt	height above (postive) or below (negative) ground for which microclimate variables are required (m)
pathout	a file directory to which to save data. Data saved to a subdirectory called 'microut' in this directory. Default is working directory.
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 climate data used when running [micropointa()]. Ignored if climate data used for running the point model are provided as a data.frame. Must give elevations in metres if '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)
tilesize	optional integer of the number of pixels in x and y of each tile (returned tiles are square). Calculated automatically based on data size of not provided.
toverlap	optional integer specifying the number of pixels of overlap between adjacent tiles. Default 0, Set to > 0 and use [mosaicblend()] if output appears to have tiling effects.
writeasnc	optional logical indicating whether to write output data as netCDF4 files (default TRUE). Can only be used if all entries of 'out' are true. Alternatively data are saved as RDS files.
runchecks	optional logical indicating whether to call [checkinputs()] to run
pai_a	an array of plant area index values above 'reqhgt'. Determined from total 'pai' if not supplied.
tfact	coefficient determining sensitivity of soil moisture to variation in topographic wetness (see [soilmdistribute()])
out	optional vector of logicals indicating which variables to return ordered as for the listed outputs when ‘reqhgt > 0’' (e.g. 'out[1] = TRUE' indicates that 'Tz' is returned, 'out[2]' that 'tleaf' is returned etc). By default all variables are returned.
silent	optional logical indicating whether to report on progress (default FALSE - progress reported).

Details

The function 'runmicro_big' tiles larger studies and saves outputs for each tile

if 'writeasnc = TRUE' and all entries in 'out' are 'TRUE', a ncdf4 files for each tile are written out, unless the corresponding tile comprises all NAs. To save memory, data are written out as integers: temperatures and wind speeds are multiplied by 100 prior to doing so. If 'writeasnc = FALSE' or not all variables are required, then an RDS file is written out. a dtm (as a rwapped SpatRaster) of the corresponding tile is attached to the model outputs prior to doing so to aid with georeferencing. see [runmicro()]

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