addPlotLocations.RdAdds/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.
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).
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.
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.
Whether the 'places' vector should be reset before adding new place names.
A boolean flag to indicate that coordinates should be transformed to "+proj=longlat +datum=WGS84".
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.
A character vector of values that should be considered as missing data (but see the following).
A character vector of values that should be considered as missing coordinates (introduced to allow separate treatment).
A character vector of values that should be considered as missing elevation (introduced to allow separate treatment).
A boolean flag to indicate console output of the data integration process.
The modified object of class VegX.
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.
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(),
addPlotGeometries(),
addPlotObservations(),
addSiteCharacteristics(),
addSiteObservations(),
addStratumObservations(),
addSurfaceCoverObservations(),
addTaxonBySiteData()
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")
#> 5 plot(s) parsed, 5 new plot(s) added.
#> 5 record(s) parsed.
# Summary of the new Veg-X document
showElementTable(x, "plot")
#> plotName coordX coordY spatialReference
#> 1 LGM45h 172.0326 -41.5559 +proj=longlat +datum=WGS84
#> 2 LGM08r 172.1407 -41.5417 +proj=longlat +datum=WGS84
#> 3 LGM38h 172.0562 -41.5417 +proj=longlat +datum=WGS84
#> 4 LGM43h 172.0414 -41.5490 +proj=longlat +datum=WGS84
#> 5 LGM16l 172.0729 -41.5283 +proj=longlat +datum=WGS84
# 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"))
#> Measurement method 'Elevation/m' added for 'elevation'.
#> 25 plot(s) parsed, 20 new plot(s) added.
#> 25 record(s) parsed.
#> 20 record(s) with missing value(s) not added.
# Summary of the updated Veg-X document
showElementTable(x, "plot")
#> plotName coordX coordY spatialReference elevation_method
#> 1 LGM45h 172.0326 -41.5559 +proj=longlat +datum=WGS84 Elevation/m
#> 2 LGM08r 172.1407 -41.5417 +proj=longlat +datum=WGS84 Elevation/m
#> 3 LGM38h 172.0562 -41.5417 +proj=longlat +datum=WGS84 Elevation/m
#> 4 LGM43h 172.0414 -41.5490 +proj=longlat +datum=WGS84 Elevation/m
#> 5 LGM16l 172.0729 -41.5283 +proj=longlat +datum=WGS84 Elevation/m
#> 6 LGM08r_1Q NA NA <NA> <NA>
#> 7 LGM08r_2Q NA NA <NA> <NA>
#> 8 LGM08r_3Q NA NA <NA> <NA>
#> 9 LGM08r_4Q NA NA <NA> <NA>
#> 10 LGM16l_1Q NA NA <NA> <NA>
#> 11 LGM16l_2Q NA NA <NA> <NA>
#> 12 LGM16l_3Q NA NA <NA> <NA>
#> 13 LGM16l_4Q NA NA <NA> <NA>
#> 14 LGM38h_1Q NA NA <NA> <NA>
#> 15 LGM38h_2Q NA NA <NA> <NA>
#> 16 LGM38h_3Q NA NA <NA> <NA>
#> 17 LGM38h_4Q NA NA <NA> <NA>
#> 18 LGM45h_2Q NA NA <NA> <NA>
#> 19 LGM45h_3Q NA NA <NA> <NA>
#> 20 LGM45h_4Q NA NA <NA> <NA>
#> 21 LGM43h_1Q NA NA <NA> <NA>
#> 22 LGM43h_2Q NA NA <NA> <NA>
#> 23 LGM43h_3Q NA NA <NA> <NA>
#> 24 LGM43h_4Q NA NA <NA> <NA>
#> 25 LGM45h_1Q NA NA <NA> <NA>
#> elevation_value relatedPlotName plotRelationship
#> 1 82 <NA> <NA>
#> 2 95 <NA> <NA>
#> 3 50 <NA> <NA>
#> 4 77 <NA> <NA>
#> 5 94 <NA> <NA>
#> 6 NA LGM08r subplot
#> 7 NA LGM08r subplot
#> 8 NA LGM08r subplot
#> 9 NA LGM08r subplot
#> 10 NA LGM16l subplot
#> 11 NA LGM16l subplot
#> 12 NA LGM16l subplot
#> 13 NA LGM16l subplot
#> 14 NA LGM38h subplot
#> 15 NA LGM38h subplot
#> 16 NA LGM38h subplot
#> 17 NA LGM38h subplot
#> 18 NA LGM45h subplot
#> 19 NA LGM45h subplot
#> 20 NA LGM45h subplot
#> 21 NA LGM43h subplot
#> 22 NA LGM43h subplot
#> 23 NA LGM43h subplot
#> 24 NA LGM43h subplot
#> 25 NA LGM45h subplot