get_input {TTR.PGM}R Documentation

Create an input data object for make_data()

Description

This function takes the input forcing data and formats it for use by the make_data() function. The input forcing data are expected to have the units specified below. All of the forcing data should be in dataframe or matrix form. The following constant dimension sizes are expected:

nspecies : The number of species

nsites : The number of sites

nsteps : The number of timesteps

Currently only one species is supported. Depending on the model configuration different parameters need to be specified. tcur, tnur, tgrowth and tloss always need to be supplied. For the std variant of the process model, rsds has to be specified as well. For other variants photosynthesis rates can be supplied or calculated from tcur, catm and rsds. Soil water content needs to be supplied or it will be calculated from wp, fc, prec and pet. nsoil is optional. fire is currently not supported.

Usage

get_input(
  observations,
  tcur,
  tnur,
  tgrowth,
  tloss,
  seconds,
  p3 = TTR.PGM::p3,
  p4 = TTR.PGM::p4,
  lon = NULL,
  lat = NULL,
  rsds = NULL,
  catm = NULL,
  photoc3 = NULL,
  photoc4 = NULL,
  swc = NULL,
  pet = NULL,
  rain = NULL,
  wp = NULL,
  fc = NULL,
  fire = NULL,
  nsoil = NULL
)

Arguments

observations

The observation data that will be used in the statistical model, there are no checks performed, so make sure to format this in the way the user defined statistical model expects

tcur

matrix with ntimesteps rows, nsites columns, containing the temperature associated with photosynthesis [°C]

tnur

matrix with ntimesteps rows, nsites columns, containing the temperature associated with nitrogen uptake [°C]

tgrowth

matrix with ntimesteps rows, nsites columns, containing the temperature associated with growth [°C]

tloss

matrix with ntimesteps rows, nsites columns, containing the temperature associated with biomass loss [°C]

seconds

The number of seconds in a time step

p3

The parameters to be used to calculate C3 photosynthesis rates (see p3)

p4

The parameters to be used to calculate C4 photosynthesis rates (see p4)

lon

vector of length nsite containing the Longitudes of the sites

lat

vector of length nsite containing the Latitudes of the sites

rsds

matrix with ntimesteps rows, nsites columns, containing short wave downward solar radiation at the surface [W*m^(-2)]

catm

matrix with ntimesteps rows, nsites columns, containing Partial pressure of CO2 in the atmosphere [Pa]

photoc3

matrix with ntimesteps rows, nsites columns, containing c3 photosynthesis rates [mumol*m^(-2)*s^(-1)]

photoc4

matrix with ntimesteps rows, nsites columns, containing c4 photosynthesis rates [mumol*m^(-2)*s^(-1)]

swc

matrix with ntimesteps rows, nsites columns, containing soil water content scaled so that wilting point = 0 and field capacity = 100 [%]

pet

matrix with ntimesteps rows, nsites columns, containing potential evapotranspiration [kg*m^(-2)*s^(-1)]

rain

matrix with ntimesteps rows, nsites columns, containing precipitation [kg*m^(-2)*s^(-1)]

wp

vector of length nsites containing wilting points [cm^3/cm^3]

fc

vector of length nsites containing field capacities [cm^3/cm^3]

fire

matrix with ntimesteps rows, nsites columns, containing binary information on fire occurrence [no units]; currently not supported

nsoil

vector of length nsites containing the soil nitrogen content [kg/kg]

Value

A list containing the forcing data for the process model:

timeseries

All forcing variables which change with time

timeinvariant

All forcing variables which do not change with time

observations

Observations as specified above


[Package TTR.PGM version 1.0.0 Index]