scores.fluxnet.site: Scores for FLUXNET reference data when model run at FLUXNET...
In amber: Automated Model Benchmarking R Package

Description Usage Arguments Value Examples

This function compares model output in CSV format against FLUXNET measurements in CSV format. Use this function when running your model at each FLUXNET site individually. The performance of a model is expressed through scores that range from zero to one, where increasing values imply better performance. These scores are computed in five steps: (i) computation of a statistical metric, (ii) nondimensionalization, (iii) conversion to unit interval, (iv) spatial integration, and (v) averaging scores computed from different statistical metrics. The latter includes the bias, root-mean-square error, phase shift, inter-annual variability, and spatial distribution. The corresponding equations are documented in amber-package.

scores.fluxnet.site(long.name, mod.csv, mod.csv.path, ref.csv, mod.id,
  ref.id, unit.conv.mod, unit.conv.ref, variable.unit, sites,
  score.weights = c(1, 2, 1, 1, 1), my.xlim = c(-180, 180),
  my.ylim = c(-60, 85), plot.width = 8, plot.height = 3.8,
  numCores = 2, outputDir = FALSE, phaseMinMax = "phaseMax",
  myCex = 0.7)

`long.name`	A string that gives the full name of the variable, e.g. 'Gross primary productivity'
`mod.csv`	A string that gives the name of the model output in csv format, e.g. 'gpp_monthly.csv'
`mod.csv.path`	A string that gives the path to the model output for site-level runs
`ref.csv`	A string that gives the path and name of the csv file that contains the reference data output, e.g. '/home/reference_gpp.csv'. The columns of this file should contain latitude, longitude, date, variable of interest, and site name.
`mod.id`	A string that identifies the source of the reference data set, e.g. 'CanESM2'
`ref.id`	A string that identifies the source of the reference data set, e.g. 'MODIS'
`unit.conv.mod`	A number that is used as a factor to convert the unit of the model data, e.g. 86400
`unit.conv.ref`	A number that is used as a factor to convert the unit of the reference data, e.g. 86400
`variable.unit`	A string that gives the final units using LaTeX notation, e.g. 'gC m$^-2$ day$^-1$'
`sites`	A vector of strings that give the fluxnet site names, e.g. c('AU-Tum','BR-Sa1','CA-Qfo')
`score.weights`	R object that gives the weights of each score (S_{bias}, S_{rmse}, S_{phase}, S_{iav}, S_{dist}) that are used for computing the overall score, e.g. c(1,2,1,1,1)
`my.xlim`	An R object that gives the longitude range that you wish to plot, e.g. c(-180, 180)
`my.ylim`	An R object that gives the longitude range that you wish to plot, e.g. c(-90, 90)
`plot.width`	Number that gives the plot width, e.g. 8
`plot.height`	Number that gives the plot height, e.g. 4
`numCores`	An integer that defines the number of cores, e.g. 2
`outputDir`	A string that gives the output directory, e.g. '/home/project/study'. The output will only be written if the user specifies an output directory.
`phaseMinMax`	A string (either 'phaseMax' or 'phaseMin') that determines whether to assess the seasonal peak as a maximum or a minimum. The latter may be appropriate for variables that tend to be negative, such as net longwave radiation or net ecosystem exchange.
`myCex`	A number that determines the size of the dots in the Figure. Default is set to 0.7.

(1) Figures in PDF format that show maps of the model data at the location of FLUXNET sites (mean, mod.mean; interannual-variability, mod.iav; month of annual cycle maximum, mod.max.month), the reference data (mean, ref.mean; interannual-variability, ref.iav; month of annual cycle maximum, ref.max.month), statistical metrics (bias, bias; centralized root mean square error, crmse; time difference of the annual cycle maximum, phase), and scores (bias score, bias.score; root mean square error score, rmse.score; inter-annual variability score iav.score; annual cycle score (phase.score).

(2) Four text files: (i) score values and (ii) score inputs for each individual site, and (iii) score values and (iv) score inputs averaged across sites. when averaging over all station.

library(amber)
library(classInt)
library(doParallel)
library(foreach)
library(Hmisc)
library(latex2exp)
library(ncdf4)
library(parallel)
library(raster)
library(rgdal)
library(rgeos)
library(scico)
library(sp)
library(stats)
library(utils)
library(viridis)
library(xtable)

long.name <- 'Gross primary productivity'
mod.csv <- 'gpp_monthly.csv'
mod.csv.path <- system.file('extdata/siteLevelRun', package = 'amber')
ref.csv <- system.file('extdata/referenceRegular', 'gpp_monthly_fluxnet.csv', package = 'amber')
mod.id <- 'CLASSIC-Sitelevel' # define a model experiment ID
ref.id <- 'FLUXNET' # give reference dataset a name
unit.conv.mod <- 86400*1000 # optional unit conversion for model data
unit.conv.ref <- 1 # optional unit conversion for reference data
variable.unit <- 'gC m$^{-2}$ day$^{-1}$' # unit after conversion (LaTeX notation)

sites <- c('AU-Tum','CA-TPD', 'US-WCr')

# Short version using default settings:
scores.fluxnet.site(long.name, mod.csv, mod.csv.path, ref.csv, mod.id, ref.id,
unit.conv.mod, unit.conv.ref, variable.unit, sites)

# Additional parameters:
score.weights <- c(1,2,1,1,1) # score weights of S_bias, S_rmse, S_phase, S_iav, S_dist
my.xlim <- c(-180, 180)
my.ylim <- c(-60, 85)
plot.width <- 8
plot.height <- 3.8
numCores <- 2

scores.fluxnet.site(long.name, mod.csv, mod.csv.path, ref.csv, mod.id, ref.id,
unit.conv.mod, unit.conv.ref, variable.unit, sites, score.weights,
my.xlim, my.ylim, plot.height, numCores)

# To zoom into a particular region:
scores.fluxnet.site(long.name, mod.csv, mod.csv.path, ref.csv, mod.id, ref.id,
unit.conv.mod, unit.conv.ref, variable.unit, sites,
my.xlim = c(-150, -60), my.ylim = c(20, 60), plot.width = 6, plot.height = 3.8)
 #donttest