addPlotGeometries.Rd
Adds/replaces static plot geometry information (plot shape, dimensions, ...) to plot elements of a VegX object from a data frame where rows are plots.
The initial object of class VegX
to be modified.
A data frame where each row corresponds to one plot. Columns can be varied.
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).
area
- Area of the plot (optional).
shape
- Shape of the plot: circle/circular, rectangle/rectangular/squared, line/linear (optional).
radius
- Radius of the plot, for circular plots (optional).
width
- Width of the plot, for rectangular plots (optional).
length
- Length of the plot, for linear and rectangular plots (optional).
bandWidth
- Sampling bandwidth, for linear plots (optional).
A list measurement methods for plot geometry measurements (each being an object of class VegXMethodDefinition
).
Alternatively, methods can be specified using strings if predefined methods exist (see predefinedMeasurementMethod
).
A character vector of values that should be considered as missing data.
A boolean flag to indicate console output of the data integration process.
The modified object of class VegX
.
Named elements in mapping
beyond those used by this function will be ignored. Missing value policy:
Missing plotName
and shape
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. area
, radius
,...) are simply not added to the Veg-X document.
Wiser SK, Spencer N, De Caceres M, Kleikamp M, Boyle B & Peet RK (2011). Veg-X - an exchange standard for plot-based vegetation data
Other add functions:
addAggregateOrganismObservations()
,
addCommunityObservations()
,
addIndividualOrganismObservations()
,
addPlotLocations()
,
addPlotObservations()
,
addSiteCharacteristics()
,
addSiteObservations()
,
addStratumObservations()
,
addSurfaceCoverObservations()
,
addTaxonBySiteData()
# Load source data
data(mokihinui)
# Define location mapping
mapping = list(plotName = "Plot", subPlotName = "Subplot",
area = "PlotArea", shape = "Shape",
width = "PlotRectangleLength01", length = "PlotRectangleLength02")
# Define methods
methods = list(area = "Plot area/m2",
width = "Plot dimension/m", length = "Plot dimension/m")
# Create new Veg-X document with plot locations
x = addPlotGeometries(newVegX(), moki_site, mapping, methods)
#> Measurement method 'Plot area/m2' added for 'area'.
#> Measurement method 'Plot dimension/m' added for 'width'.
#> Measurement method 'Plot dimension/m' for 'length' already included.
#> 25 plot(s) parsed, 25 new plot(s) added.
#> 25 record(s) parsed.
# Inspect results
showElementTable(x, "plot")
#> plotName area_method area_value shape length_method length_value
#> 1 LGM08r Plot area/m2 400 rectangle Plot dimension/m 20
#> 2 LGM08r_1Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 3 LGM08r_2Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 4 LGM08r_3Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 5 LGM08r_4Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 6 LGM16l Plot area/m2 400 rectangle Plot dimension/m 20
#> 7 LGM16l_1Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 8 LGM16l_2Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 9 LGM16l_3Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 10 LGM16l_4Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 11 LGM38h Plot area/m2 400 rectangle Plot dimension/m 20
#> 12 LGM38h_1Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 13 LGM38h_2Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 14 LGM38h_3Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 15 LGM38h_4Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 16 LGM45h Plot area/m2 400 rectangle Plot dimension/m 20
#> 17 LGM45h_2Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 18 LGM45h_3Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 19 LGM45h_4Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 20 LGM43h Plot area/m2 400 rectangle Plot dimension/m 20
#> 21 LGM43h_1Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 22 LGM43h_2Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 23 LGM43h_3Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 24 LGM43h_4Q Plot area/m2 100 rectangle Plot dimension/m 10
#> 25 LGM45h_1Q Plot area/m2 100 rectangle Plot dimension/m 10
#> width_method width_value relatedPlotName plotRelationship
#> 1 Plot dimension/m 20 <NA> <NA>
#> 2 Plot dimension/m 10 LGM08r subplot
#> 3 Plot dimension/m 10 LGM08r subplot
#> 4 Plot dimension/m 10 LGM08r subplot
#> 5 Plot dimension/m 10 LGM08r subplot
#> 6 Plot dimension/m 20 <NA> <NA>
#> 7 Plot dimension/m 10 LGM16l subplot
#> 8 Plot dimension/m 10 LGM16l subplot
#> 9 Plot dimension/m 10 LGM16l subplot
#> 10 Plot dimension/m 10 LGM16l subplot
#> 11 Plot dimension/m 20 <NA> <NA>
#> 12 Plot dimension/m 10 LGM38h subplot
#> 13 Plot dimension/m 10 LGM38h subplot
#> 14 Plot dimension/m 10 LGM38h subplot
#> 15 Plot dimension/m 10 LGM38h subplot
#> 16 Plot dimension/m 20 <NA> <NA>
#> 17 Plot dimension/m 10 LGM45h subplot
#> 18 Plot dimension/m 10 LGM45h subplot
#> 19 Plot dimension/m 10 LGM45h subplot
#> 20 Plot dimension/m 20 <NA> <NA>
#> 21 Plot dimension/m 10 LGM43h subplot
#> 22 Plot dimension/m 10 LGM43h subplot
#> 23 Plot dimension/m 10 LGM43h subplot
#> 24 Plot dimension/m 10 LGM43h subplot
#> 25 Plot dimension/m 10 LGM45h subplot