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Extract climatology data from a NetCDF file downloaded by FjordLight.

flget_climatology.Rd

This functions will conveniently extract the climatology data stored within a NetCDF file downloaded via fl_DownloadFjord. To extract the monthly bottom PAR data instead one must use flget_PARbottomMonthlyTS. There are options for how the user would like to subset the data, which data format the data should be extracted to, and if the user would like to plot the data in the process.

Usage

flget_climatology(
  fjord,
  optics = "PARbottom",
  period = "Global",
  month = NULL,
  year = NULL,
  mode = "raster",
  PLOT = FALSE
)

Arguments

fjord

Expects the object loaded via fl_LoadFjord.

optics

The PAR variable that the user would like to load. The option are: "PARbottom" (default) to load the bottom PAR values, "PAR0m" surface PAR, or "Kpar" for the extinction coefficient.

period

Here the user determines which time period of data should be loaded. To load the total average values (default) use "Global". One may chose instead to load the "Yearly" or "Monthly" values. Note that monthly values here represent the climatological average for the month, not one month in a given year. If the user would like one specific month of data (only available for bottom PAR), they should use flget_PARbottomMonthlyTS.

month

The monthly climatology to extract. Accepts an integer value from 3 to 10. This argument is ignored if period = "Yearly".

year

The yearly average to extract. Currently accepts an integer value from 2003 to 2022. This argument is ignored if period = "Monthly".

mode

Determines the format of the data loaded into the R environment. The default "raster" will load the data as a raster format. The other option "df" will load the data as a data.frame with three columns.

PLOT

Boolean argument (default = FALSE) that tells the function if the user would like the loaded data to be plotted or not.

Value

Depending on which arguments the user chooses, this function will return the chosen, global, annual, or monthly climatology data as a RasterLayer (mode = "raster") or data.frame (mode = "df"). The data.frame will contain the following columns:

longitude

degree decimals

latitude

degree decimals

optics_month|year

The column name is determined by the arguments for optics and either month or year, depending on the users choice.

Author

Bernard Gentili

Examples

# Load data
fjord_code <- "test"
fjorddata <- fl_LoadFjord(fjord_code, dirdata = system.file("extdata", package = "FjordLight"))

# PAR0m and PARbottom for July
# \donttest{
P07 <- flget_climatology(fjorddata, "PAR0m", "Clim", month = 7, PLOT = TRUE)

Pb7 <- flget_climatology(fjorddata, "PARbottom", "Clim", month = 7, PLOT = TRUE)

# }

# PARbottom Global
# \donttest{
PbG <- flget_climatology(fjorddata, "PARbottom", "Global", PLOT = TRUE)

# }

# PAR0m and kdpar for year 2012 as 3 columns data frame
P02012 <- flget_climatology(fjorddata, "PAR0m", "Yearly", year = 2012, mode = "df")
k2012 <- flget_climatology(fjorddata, "Kpar", "Yearly", year = 2012, mode = "df")

# For more examples see: https://face-it-project.github.io/FjordLight/articles/fl_example.html