VegX: Vegetation data in Veg-X

addPlotLocations

R Documentation

Adds/replaces plot location information

Description

Adds/replaces static plot location information (spatial coordinates, elevation, place names, ...) to plot elements of a VegX object from a data table where rows are plots.

Usage

addPlotLocations(
  target,
  x,
  mapping,
  proj4string = NULL,
  reset.places = FALSE,
  toWGS84 = FALSE,
  methods = list(),
  missing.values = c(NA, ""),
  missing.coords = c(NA, 0, ""),
  missing.elevation = c(NA, 0, ""),
  verbose = TRUE
)

Arguments

`target`	The initial object of class `VegX` to be modified
`x`	A data frame where each row corresponds to one plot. Columns can be varied.
`mapping`	A named list whose elements are strings that correspond to column names in `x`. Names of the list should be: `plotName` - A string identifying the vegetation plot within the data set (required). `subPlotName` - A string identifying a subplot of the plot given by `plotName` (optional). `x`, `y` - Spatial coordinates of the plot (optional). `elevation` - Elevation of the plot (optional). `authorLocation` - A string describing the location of the plot as made by the author (optional). `locationNarrative` - (optional). `placeName`, `placeType` - A string of a place name and place type (e.g. province, county, ...) (optional). Note that `placeName` and `placeType` will add new places to the list of places.
`proj4string`	A string with projection attributes (see `proj4string` of package `sp`) to be used when 'x' and 'y' are supplied. This parameter is needed if `toWGS84 = TRUE`.
`reset.places`	Whether the 'places' vector should be reset before adding new place names.
`toWGS84`	A boolean flag to indicate that coordinates should be transformed to "+proj=longlat +datum=WGS84".
`methods`	A named list with measurement methods for plot horizontal/vertical location measurements (each being an object of class `VegXMethodDefinition`). Alternatively, methods can be specified using strings if predefined methods exist (see `predefinedMeasurementMethod`). For example, `methods = c(xy = method1, elevation = method2)`. Measurement method for coordinates is not required, but that for 'elevation' is.
`missing.values`	A character vector of values that should be considered as missing data (but see the following).
`missing.coords`	A character vector of values that should be considered as missing coordinates (introduced to allow separate treatment).
`missing.elevation`	A character vector of values that should be considered as missing elevation (introduced to allow separate treatment).
`verbose`	A boolean flag to indicate console output of the data integration process.

Details

Named elements in mapping other than those used by this function will be ignored. Missing value policy:

Missing plotName values are interpreted as if the previous non-missing value has to be used to define plot.
Missing subPlotName values are interpreted in that data refers to the parent plotName.
Missing measurements (e.g. elevation, x, y, ...) are simply not added to the Veg-X document.

Value

The modified object of class VegX.

References

Wiser SK, Spencer N, De Caceres M, Kleikamp M, Boyle B & Peet RK (2011). Veg-X - an exchange standard for plot-based vegetation data

Examples

data(mokihinui)

# Define location mapping
mapping = list(plotName = "Plot", x = "Longitude", y = "Latitude")

# Create new Veg-X document with plot locations
x = addPlotLocations(newVegX(), moki_loc, mapping,
                     proj4string = "+proj=longlat +datum=WGS84")

# Summary of the new Veg-X document
showElementTable(x, "plot")

# Add 'elevation' from another table (moki_site). This implies considering subplots.
mapping = list(plotName = "Plot", subPlotName = "Subplot", elevation = "Altitude")
x = addPlotLocations(x, moki_site, mapping, 
                     methods = list(elevation = "Elevation/m"))
                     
# Summary of the updated Veg-X document
showElementTable(x, "plot")

miquelcaceres/VegX documentation built on Sept. 18, 2022, 7:04 p.m.