VPRM_driver_data: build a VPRM_driver_data object

In Timothy-W-Hilton/VPRMLandSfcModel: R implementation of VPRM with parameter estimation

build a VPRM_driver_data object

Description

class constructor for VPRM_driver_data. Accepts all driver data necessary to run VPRM for a single eddy covariance site, calculates "derived" fields, and interpolates phenology dynamics.

Usage

VPRM_driver_data(
  name_long = "",
  name_short = "",
  lat = NA,
  lon = NA,
  PFT = NA,
  note = "",
  Tmin = 0,
  Tmax = 40,
  Topt = 20,
  Tlow = 2,
  tower_date = NA,
  NEE_obs = NA,
  T = NA,
  PAR = NA,
  date_nir = NA,
  rho_nir = NA,
  date_swir,
  rho_swir = NA,
  date_EVI,
  EVI = NA,
  refEVI = NA,
  ISA = NA,
  LSWI = NA,
  phen = NA,
  model_form = "Mahadevan07"
)

Arguments

name_long	character string; "short name" of the site. e.g. US-PFa
name_short	character string; "long name" of the site. e.g. Park Falls
lat	numeric; latitude of the site (deg N)
lon	numeric; longitude of the site (deg E)
PFT	character string; plant functional type. Will be converted to a factor.
note	character string; optional note; could be anything the user finds useful.
Tmin	numeric; minimum temperature for photosynthesis (deg C). See Mahadevan et al (2008) eq. 6.
Tmax	numeric; maximim temperature for photosynthesis (deg C). See Mahadevan et al (2008) eq. 6.
Topt	numeric; optimum temperature for photosynthesis (deg C). See Mahadevan et al (2008) eq. 6.
Tlow	numeric; minimum temperature for respiration (deg C). See Mahadevan et al (2008) eq. 10.
tower_date	chron vector; timestamps for all tower observations (NEE_obs, T, PAR)
NEE_obs	numeric vector; eddy covariance observed net ecosystem exchange (NEE, umol m-2 s-1)
T	numeric vector; observed air temperature (deg C)
PAR	numeric vector; observed photosynthetically active radiation (umol m-2 s-1)
date_nir	chron vector; timestamps for NIR reflectance.
rho_nir	numeric vector; NIR reflectance values
date_swir	chron vector; timestamps for SWIR reflectance.
rho_swir	numeric vector; SWIR reflectance values
date_EVI	chron vector; timestamps for enhanced vegetation index (EVI).
EVI	numeric vector; EVI values.
refEVI	numeric vector; reference EVI values. Only required for urbanVPRM. See Hardiman et al SI section S2.4.
ISA	numeric vector; impervious surface area values. Only required for urbanVPRM. Must vary between 0.0 and 1.0.
LSWI	numeric vector; Land Surface Water Index. If not provided will be calculated from rho_nir and rho_swir.
phen	factor; phenology dynamics. levels are ginc (onset greenness increase), gdec (onset greenness decrease), gmin (onset greenness minimum), gmax (onset greenness maximum). If not specified, phenology dynsamics are calculated from EVI using a method similar to Zhang et al (2003).
model_form	string, optional; form of VPRM model to use. Options are "Mahadevan07" (default) to use the VPRM formulation of Mahadevan et al. (2007), or "urban" to use the urbanVPRM formulation of Hardiman et al. (2017). If set to "urban".

Details

"Derived fields" denote fields that are calculated from other observed quanitities. For example, land surface water index (LSWI) is a derived field, as it is calculated from MODIS reflectances in the short infrared and near infrared bands.

Value

an object of class VPRM_driver_data. Has fields (see above arguments for definitions): name_long, name_short, lat, lon, PFT, note, Tmin, Tmax, Topt, Tlow. The data for NEE_obs, T, PAR, rho_nir, rho_swir, EVI, and phen should be accessed using the as.data.frame method.

Author(s)

Timothy W. Hilton

References

Mahadevan, P., S. C. Wofsy, D. M. Matross, X. Xiao, A. L. Dunn, J. C. Lin, C. Gerbig, J. W. Munger, V. Y. Chow, and E. W. Gottlieb (2008), A satellite-based biosphere parameterization for net ecosystem CO2 exchange: Vegetation Photosynthesis and Respiration Model (VPRM), Global Biogeochem. Cycles, 22, GB2005, doi:10.1029/2006GB002735.

Xiaoyang Zhang, Mark A. Friedl, Crystal B. Schaaf, Alan H. Strahler, John C.F. Hodges, Feng Gao, Bradley C. Reed, Alfredo Huete, Monitoring vegetation phenology using MODIS, Remote Sensing of Environment, Volume 84, Issue 3, March 2003, Pages 471-475, ISSN 0034-4257, http://dx.doi.org/10.1016/S0034-4257(02)00135-9.

Examples

data(Park_Falls)
pfa_dd <- VPRM_driver_data(name_long="Park Falls",
                           name_short = "US-PFa",
                           lat=45.9459,
                           lon=-90.2723,
                           PFT='MF',
                           tower_date=PFa_tower_obs[['date']],
                           NEE_obs=PFa_tower_obs[['FC']],
                           T=PFa_tower_obs[['TA']],
                           PAR=PFa_tower_obs[['PAR']],
                           date_nir = PFa_refl[['date']],
                           rho_nir=PFa_refl[['nir']],
                           date_swir = PFa_refl[['date']],
                           rho_swir = PFa_refl[['swir']],
                           date_EVI = PFa_evi[['date']],
                           EVI=PFa_evi[['evi']],
                           phen=NA)
print(head(as.data.frame(pfa_dd)))

Timothy-W-Hilton/VPRMLandSfcModel documentation built on July 29, 2023, 8:43 p.m.