microclimaforNMR: Extract NCEP data and run microclima for use with NicheMapR

In ilyamaclean/microclima: microclimate modelling with R

Extract NCEP data and run microclima for use with NicheMapR

Description

Extract NCEP data and run microclima for use with NicheMapR

Usage

microclimaforNMR(
  lat,
  long,
  dstart,
  dfinish,
  l,
  x,
  coastal = TRUE,
  hourlydata = NA,
  dailyprecip = NA,
  dem = NA,
  demmeso = dem,
  albr = 0.15,
  resolution = 100,
  zmin = 0,
  slope = NA,
  aspect = NA,
  horizon = NA,
  svf = NA,
  difani = TRUE,
  windthresh = 4.5,
  emthresh = 0.78,
  reanalysis2 = FALSE,
  steps = 8,
  use.raster = TRUE,
  plot.progress = TRUE,
  tidyr = FALSE,
  weather.elev = "ncep",
  cad.effects = TRUE
)

Arguments

lat	the latitude (in decimal degrees) of the location for point data are required.
long	the longitude (in decimal degrees) of the location for point data are required.
dstart	start date as character of time period required in format DD/MM/YYYY (UTC timezones assumed)
dfinish	end date as character of time period required in format DD/MM/YYYY (UTC timezones assumed)
l	a single numeric value of the leaf area index for location (see details).
x	a single numeric value representing the ratio of vertical to horizontal projections of leaf foliage for the location (see details).
coastal	an optional logical value indicating whether to calculate coastal effects using coastalNCEP().
hourlydata	an optional data frame of ourly weather and radiation data as returned by function hourlyNCEP(). Function called if data not provided.
dailyprecip	an optional data frame of ourly weather and radiation data as returned by function dailyprecipNCEP(). Function called if data not provided.
dem	an ptional raster object of elevations covering the location for which point data are required. If not provided, one is downloaded from the registry of Open Data on AWS. Used to calculate coastal, wind and radiation effects
demmeso	an optional raster object of elevations covering the location for which point data are required. Used to calculate elevation and cold air drainage effects.
albr	albedo of ground surface from which radiation is reflected (see details)
resolution	the resolution (in metres) of the dem used for downscaling (see details).
zmin	assumed sea-level height. Values below this are set to zmin (see details).
slope	an optional slope value for the location in decimal degrees. If not specified, then the slope is calculated from the retrieved dem.
aspect	an optional aspect value for the location in decimal degrees. If not specified, then the slope is calculated from the retrieved dem.
windthresh	an optional threshold wind value (m /s) above which cold air drainage is assumed not to occur
emthresh	an optional threshold emissivity value above which cold air drainage is assumed not to occur
reanalysis2	Logical. Should data be obtained from the Reanalysis II dataset (default) or from Reanalysis I (data prior to 1979).
steps	an optional integer. Coastal effects are calculated in specified directions upwind. Steps defines the total number of directions used. If the default 8 is specified, coastal effects are calculated at 45º intervals.
use.raster	an optional logical value indicating whether to mask the output values by landsea.
plot.progress	logical value indicating whether to produce plots to track progress.
tidyr	logical value indicating whether to download 30m resolution digital elevation data.
weather.elev	optional value indicating the elevation of values in hourlydata. Either a numeric value, corresponding to the elevation in (m) of the location from which hourlydata were obtained, or one of ncep (default, data derive from NOAA-NCEP reanalysis) project or era5 (derived from Copernicus ERA5 climate reanalysis).
cad.effects	optional logical indicating whether to calaculate cold air drainage effects (TRUE = Yes, slower. FALSE = No, quicker)

Details

The package NicheMapR (Kearney & Porter 2016), includes a suite of programs for mechanistic modelling of heat and mass exchange and provides a time-series of hourly estimates of above- and below‐ground conditions. It has the significant advantage over microclima in that it works entirely from first principles does not require measurements of temperature for calibration, but does not explicitly model elevation and cold-air drainage effects. The slope, aspect and canopy effects must be specified by the user, and their effect on radiation are more simplistically modelled than by microclima.

Value

a list with the following objects:

(1) hourlydata: a data frame of hourly climate data from NCEP, as returned by hourlyNCEP().

(2) hourlyradwind: A data frame with seven columns: (i) swrad: total downward shortwave radiation as a funcion of slope, aspect and canopy shading (MJ m^-2 hr^-1) as returned by shortwaveveg().(ii) skyviewfact: a topographic sky view correction factor as returned by skyviewveg(). (iii) canopyfact a canopy shading factor weighted by the ratio of direct to diffuse radiation. (iv) whselt: a ground level wind shelter coefficient as returned by windcoef(). (v) windspeed: wind speed (m /s) at 2 m, corrected for topographic sheltering. (vi) slope: the slope (decimal degrees) of the location specified by lat and long. Either the same as that input, or determined from dem. (vii) aspect: the aspect (decimal degrees) of the location specified by lat and long. Either the same as that input, or determined from dem.

(3) tref: a dataframe with five columns (i) tref the reference temperature, derived from NCEP data. (ii) elev the elevation of the location. (iii) elevncep: the mean elevation of the 2.5º grid cell corresponding to that from which NCEP data were derived. (iv) telev the expected difference in temperature due to elevation, calculated by applying lapserate(). (v) tcad the expected difference in temperature due to cold air drainage effects, determined using pcad() and cadconditions().

(4) dailyprecip a vector of daily rainfalls derived from NCEP.

(5) acoast an array of temperatures that account for coastal effects for each pixel of dem and each hour of hourlydata.

(6) basins a raster object of basins used for calculating cold air drainage.

(7) flowacc a raster object of accumulated flow.

References

Kearney MR, Porter WP (2016) NicheMapR – an R package for biophysical modelling: the microclimate model. Ecography 40: 664-674.

See Also

Function get_dem() for retrieving digital elevation data and hourlyNCEP() for retrieving and processing hourly data from NCEP and coastalNCEP() for retrieving and processing coastal effects.

Examples

mnr <- microclimaforNMR(50, -5.2, '15/01/2015', '15/02/2015', 1, 1, coastal = FALSE)
head(mnr$hourlydata)
head(mnr$hourlyradwind)
head(mnr$tref)
head(mnr$dailyprecip)

ilyamaclean/microclima documentation built on Oct. 31, 2023, 11:41 p.m.