Internal functions for plotting SDA outputs. Interactive, post analysis time-series and bias plots in base plotting system and ggplot

Usage

interactive.plotting.sda(
  settings,
  t,
  obs.times,
  obs.mean,
  obs.cov,
  obs,
  X,
  FORECAST,
  ANALYSIS
)

postana.timeser.plotting.sda(
  settings,
  t,
  obs.times,
  obs.mean,
  obs.cov,
  obs,
  X,
  FORECAST,
  ANALYSIS
)

postana.bias.plotting.sda(
  settings,
  t,
  obs.times,
  obs.mean,
  obs.cov,
  obs,
  X,
  FORECAST,
  ANALYSIS
)

postana.bias.plotting.sda.corr(t, obs.times, X, aqq, bqq)

post.analysis.ggplot(
  settings,
  t,
  obs.times,
  obs.mean,
  obs.cov,
  obs,
  X,
  FORECAST,
  ANALYSIS,
  plot.title = NULL
)

post.analysis.ggplot.violin(
  settings,
  t,
  obs.times,
  obs.mean,
  obs.cov,
  obs,
  X,
  FORECAST,
  ANALYSIS,
  plot.title = NULL
)

post.analysis.multisite.ggplot(
  settings,
  t,
  obs.times,
  obs.mean,
  obs.cov,
  FORECAST,
  ANALYSIS,
  plot.title = NULL,
  facetg = FALSE,
  readsFF = NULL,
  Add_Map = FALSE
)

SDA_timeseries_plot(
  ANALYSIS,
  FORECAST,
  obs.mean = NULL,
  obs.cov = NULL,
  outdir,
  pft.path = NULL,
  by = "site",
  types = c("FORECAST", "ANALYSIS", "OBS"),
  CI = c(0.025, 0.975),
  unit = list(AbvGrndWood = "Mg/ha", LAI = "m2/m2", SoilMoistFrac = "", TotSoilCarb =
    "kg/m2"),
  style = list(general_color = c(FORECAST = "blue", ANALYSIS = "red", OBS = "black"),
    fill_color = c(FORECAST = "yellow", ANALYSIS = "green", OBS = "grey"), title_color =
    "red"),
  PDF_w = 20,
  PDF_h = 16,
  t.inds = NULL
)

Arguments

settings: pecan standard settings list.
t: current time - int number giving the position of the current time in obs.time.
obs.times: vector of dates of measurements
obs.mean: obs.mean
obs.cov: obs.cov
obs: list containing the mean and cov object
X: dataframe of state variables for each ensemble
FORECAST: Forecast object from the sda.output.Rdata.
ANALYSIS: Analysis object from the sda.output.Rdata.
aqq, bqq: shape parameters estimated over time for the process covariance
plot.title: character giving the title for post visualization ggplots
facetg: logical: Create a subpanel for each variable?
readsFF: optional forward forecast
Add_Map: Bool variable decide if we want to export the GIS map of Ecoregion.
outdir: physical path where the pdf will be stored.
pft.path: Physical path of pft.csv file to allow by = pft option.
by: arrange figures by var, pft, or site.
types: data types that shown in the figure.
CI: range of confidence interval.
unit: list of unit used for y axis label.
style: color option.
PDF_w: width of exported PDF file, passed on to `base::pdf()`.
PDF_h: height of exported PDF file, passed on to `base::pdf()`.
t.inds: index of period that will be plotted.

Author

Dongchen Zhang