plotData: A function to plot data

In ProfoundData: Downloading and Exploring Data from the PROFOUND Database

Description

A function to plot data of a site from the PROFOUND database.

Usage

plotData(
  dataset,
  site,
  location = NULL,
  forcingDataset = NULL,
  forcingCondition = NULL,
  species = NULL,
  variables = NULL,
  period = NULL,
  aggregated = NULL,
  FUN = mean,
  automaticPanels = T,
  quality = NULL,
  decreasing = TRUE
)

Arguments

dataset	a character string providing the name of a dataset
site	a character string providing the name of a site.
location	deprecated argument. Please use site instead.
forcingDataset	a character string providing the name of a forcingDataset. Only relevant for ISIMIP datasets.
forcingCondition	a character string providing the name of a forcingCondition. Only relevant for ISIMIP datasets.
species	a character string providing the species name or species id.
variables	a character array holding the variables to be plotted. Default is all variables.
period	a character array with either start or start and end of the subset. It must have the format "YYYY-MM-DD", or c("YYYY-MM-DD", "YYYY-MM-DD").
aggregated	a boolean indicating whether data should be aggregated for display. Possible values are date, day, month and year.
FUN	a function to use for aggregating the data
automaticPanels	a boolean indicating whether the function automatically creates panels
quality	a number indicating the quality threshold to be used. Default is none.
decreasing	a boolean indicating whether the quality threshold should be applied up- or downwards

Details

Plotting is not supported for the following datasets: OVERVIEW, SITES, SOIL(more). The aggregation of data relies on the function aggregate for zoo objects. The FUN parameter is passed to FUN from aggregate. Please check the help files of aggregate for further information. For handling NAs we recommend to pass self-defined functions (see examples).

Value

plots for the specified dataset, site and variables

Note

To report errors in the package or the data, please use the issue tracker in the GitHub repository of ProfoundData https://github.com/COST-FP1304-PROFOUND/ProfoundData

Examples

# example requires that a sql DB is registered via setDB(dbfile)
# when run without a registered DB, you will get a file query (depending on OS)

## Not run: 
# Normal plotting
plotData(dataset = "CLIMATE_LOCAL", site = "le_bray", automaticPanels = TRUE)
plotData(dataset = "TREE", site = "solling_beech",   automaticPanels = TRUE)
plotData(dataset = "CLIMATE_LOCAL", site = "le_bray", automaticPanels = FALSE)
plotData(dataset = "TREE", site = "solling_beech",   automaticPanels = FALSE)

# Plot specific forcing datasets and conditions
plotData(dataset ="CLIMATE_ISIMIP2B", site ="soro", forcingDataset="GFDLESM2M",
         forcingCondition ="rcp2p6", automaticPanels = TRUE)

# Plot specific variables
plotData(dataset ="CLIMATE_ISIMIP2B",site ="soro", forcingDataset="GFDLESM2M",
         forcingCondition ="rcp2p6", variables = "p_mm")
plotData(dataset ="TREE",site ="solling_beech", variables = "dbh1_cm")

# Plot specific species
plotData(dataset ="TREE", site ="hyytiala", species = "Pinus sylvestris",
         automaticPanels = TRUE)

# Plot specific period
plotData(dataset = "CLIMATE_LOCAL", site =  "soro",
         period = c("2011-01-01","2012-12-31"))

# Set quality threshold
plotData(dataset = "CLIMATE_LOCAL", site = "soro",
         period = c("2011-01-01","2012-12-31"), quality = 1, decreasing = FALSE)
plotData(dataset = "FLUX", site = "soro", period = c("2011-01-01","2012-12-31"),
         quality = 0, decreasing = TRUE)

# Plot aggregated data
plotData(dataset = "CLIMATE_ISIMIP2B", site ="soro",  forcingDataset= "GFDLESM2M",
         forcingCondition="rcp2p6", variables = "tmax_degC",
         period = c("2020-01-01", "2022-01-01"),
         aggregate = "month", FUN =median)
plotData(dataset = "CLIMATE_ISIMIP2B", site ="soro",  forcingDataset= "GFDLESM2M",
         forcingCondition="rcp2p6", variables = "p_mm",
         period = c("2020-01-01", "2022-01-01"),
         aggregate = "month", FUN =sum)

# Plot aggregated data with self-defined function. In this case, compare month
# mean temperature of one year to mean of all period
data <- getData(dataset = "CLIMATE_ISIMIP2B", site ="soro",  forcingDataset= "GFDLESM2M",
                forcingCondition="rcp2p6", variables = "tmax_degC")
meanTemperature <- mean(data$tmax_degC, na.rm = TRUE)
difference <- function(x) {mean(x, na.rm = TRUE) -meanTemperature}

plotData(dataset = "CLIMATE_ISIMIP2B", site ="soro",  forcingDataset= "GFDLESM2M",
         forcingCondition="rcp2p6", variables = "tmax_degC",
         period = c("2020-01-01", "2021-01-01"),
         aggregate = "month", FUN =difference)
abline(h = 0, col = "red")

## End(Not run)

ProfoundData documentation built on March 31, 2020, 5:24 p.m.