biophys.prep: Preparation function to compile biophysical model constants...
In wpeterman/biophys: Spatially-explicit biophysical models

Description Usage Arguments Details Value Author(s) Examples

Preparation function to compile biophysical model constants and input.

op.body.temp(Tmax,
Tmin,
elev,
month = NULL,
Julian,
hours,
days = NULL,
max.active_temp,
min.active_temp,
NoData.value = -9999,
an.height = 0.005,
wind.height = 10,
u = 1.0,
pCp = 1200,
RH = 0.95,
length.m = 0.055,
phi = 0.623,
SM = 1.5708,
sigma = 5.67e-8,
e = 0.93,
es = 0.96,
cp = 29.3,
alphaS = 0.93,
alphaL = 0.96,
Fp = 0,
Fd.c = 0.8,
Fa.c = 0.5,
Fr.c = 0.5,
Fg.c = 0.5,
repro = 4.86)

`Tmax`	Maximum temperature raster object. Alternatively, a list of full paths to rasters can be supplied (see Details). The order of list elements must be them same for Tmin, month, and Julian.
`Tmin`	Minimum temperature raster object. Alternatively, a list of full paths to rasters can be supplied (see Details). The order of list elements must be them same for Tmax, month, and Julian.
`elev`	Elevation raster object
`month`	A vector of names to assign to the specified raster layer(s). If multiple months are supplied, the order must be them same as Tmax, Tmin, and Julian.
`Julian`	Julian day (1 - 365). If multiple months are supplied, the order of Julian must be them same as Tmax, Tmin, and month.
`hours`	A vector of values. Specify hours to calculate operative body temperature over.
`days`	A vector containing the number of days in each month. Order must correspond with order of months. If unspecified, each month/period will consist of 30 days.
`max.active_temp`	Maximum temprature that animals will be active (Default = 20)
`min.active_temp`	Minimum temperature that animals will be active (Default = 3)
`NoData.value`	Specify NoData value in raster layers (Default = -9999)
`an.height`	Height of animal off the ground (Default = 0.005)
`wind.height`	Height at which wind speed is measured (Default = 10)
`u`	Measured wind speed at wind meter (Default = 1.0)
`pCp`	Specific heat of air at constant pressure (Default = 1200)
`RH`	Relative humidity (Default = 0.95)
`length.m`	Length of animal in meters (Default = 0.055)
`phi`	Latitude in radians (Default = 0.623)
`SM`	Standard meridian (Default = 1.5708)
`sigma`	Stefan-Boltzmann constant (Default = 5.67e-8)
`e`	Gray body emissivity (Default = 0.93)
`es`	Gray body emissivity (Default = 0.96)
`cp`	Specific heat of air (Default = 29.3)
`alphaS`	Absorptivity in solar waveband (Default = 0.93)
`alphaL`	Absorptivity in thermal waveband (Default = 0.96)
`Fp`	ctor: ratio of projected area perpendicular to solar beam. (Default = 0)
`Fd.c`	Fd constant (Default = 0.8)
`Fa.c`	Fa constant (Default = 0.5)
`Fr.c`	Fr constant (Default = 0.5)
`Fg.c`	Fg constant (Default = 0.5)
`repro`	Energy (kJ) in 14 egg clutch (eggs 3.5 mm diameter). (Default = 4.86)

Full paths to raster files can be obtain using list.files.

For example: Tmax.files <- list.files(path = "C:/RasterFiles/", pattern = "*max", full.names = TRUE)

Assuming raster files are stored in a folder called 'RasterFiles', this create the full path to files that include 'max' in the filename. It is advised keep all raster files in a folder separate from other files, and to have a common naming scheme for both minimum and maximum surfaces.

This function returns a list object with the necessary inputs for all other biophys functions.

Bill Peterman <Bill.Peterman@gmail.com>

# Create example data
r.max <- raster(ncol=10, nrow=10)

# assign values to cells
r.max[] <- runif(ncell(r.max),10,20)
r.min <- r.max - 5
r.elev <- r.max * 10

# Make vector of hours
night.hours <- c(19:24,1:7)

biophys.input <- biophys.prep(r.max, r.min, r.elev, hour = night.hours, month = c("April"), Julian = c(106))