mergeVegX: Merge Veg-X documents

In miquelcaceres/VegX: Vegetation data in Veg-X

Merge Veg-X documents

Description

Merges two Veg-X documents while considering that some of their entities may be shared.

Usage

mergeVegX(
  x,
  y,
  allowMergePlots = FALSE,
  allowMergeOrganismIdentities = FALSE,
  verbose = TRUE
)

Arguments

x, y	The objects of class VegX to be merged.
allowMergePlots	If TRUE plots should be merged when sharing the same plotName and, if defined, plotUniqueIdentifier. If FALSE plots are never merged (i.e. the two VegX documents are considered as coming from different vegetation data sources).
allowMergeOrganismIdentities	If TRUE, allows organism identities sharing the same organismName to be merged. If FALSE organism identities are never merged (i.e. the two VegX documents are considered as coming from different vegetation data sources).
verbose	A flag to indicate console output of the data integration process.

Details

Some entities are attempted to be merged or are kept as separate entities depeding on their definition:

• projects are merged when their element title has the same value.

• plots are merged, if allowMergePlots = TRUE, when they have the same value for element plotName and, if defined, plotUniqueIdentifier are also equal.

• plotObservations are merged when both their plotID and obsStartDate elements have the same value

• organismIdentities are merged if they share the same organismName and allowMergeOrganismIdentities = TRUE because one can have the same name used in different data sets but referring to different concepts.

• methods are merged when their element name has the same value.

• strata are merged when their element stratumName has the same value and the corresponding method has the same name.

• stratumObservations are merged when both their stratumID and plotObservationID elements have the same value.

• aggregateOrganismObservations are merged when their plotObservationID and organismIdentityID (and stratumObservationID, if defined) have the same value

• individualOrganisms are merged when both their plotID and individualOrganismLabel have the same value.

• individualOrganismObservations are merged when both their plotObservationID and individualOrganismID have the same value.

• surfaceTypes are merged when their element surfaceName has the same value and the corresponding method has the same name.

• surfaceCoverObservations are merged when both their surfaceTypeID and plotObservationID elements have the same value

• siteObservations are merged into the same element when their element plotObservationID has the same value, but particular measurements are always added as if they were distinct pieces of information.

Merging to these entities may cause interruption of the process if the two entities to be merged have different value for the same element. Other entities (e.g., attributes of a method) are always considered as distinct entities between the two data sets to be merged and hence are simply copied to the result.

Value

An object of class VegX with the pooled data

See Also

VegX

Examples

data(mokihinui)

# Create document 'x' with aggregate taxon observations
taxmapping = list(plotName = "Plot", obsStartDate = "PlotObsStartDate",
              taxonName = "NVSSpeciesName",
              stratumName = "Tier", cover = "Category")
coverscale = defineOrdinalScaleMethod(name = "Recce cover scale",
               description = "Recce recording method by Hurst/Allen",
               subject = "plant cover",
               citation = "Hurst, JM and Allen, RB. (2007) 
                   The Recce method for describing New Zealand vegetation – Field protocols. 
                   Landcare Research, Lincoln.",
               codes = c("P","1","2","3", "4", "5", "6"),
               quantifiableCodes = c("1","2","3", "4", "5", "6"),
               breaks = c(0, 1, 5, 25, 50, 75, 100),
               midPoints = c(0.05, 0.5, 15, 37.5, 62.5, 87.5),
               definitions = c("Presence", "<1%", "1-5%","6-25%", "26-50%", 
                                   "51-75%", "76-100%"))
strataDef = defineMixedStrata(name = "Recce strata",
               description = "Standard Recce stratum definition",
               citation = "Hurst, JM and Allen, RB. (2007) 
                 The Recce method for describing New Zealand vegetation – Field protocols. 
                 Landcare Research, Lincoln.",
               heightStrataBreaks = c(0, 0.3,2.0,5, 12, 25, 50),
               heightStrataNames = paste0("Tier ",1:6),
               categoryStrataNames = "Tier 7",
               categoryStrataDefinition = "Epiphytes")
x = addAggregateOrganismObservations(newVegX(), moki_tcv, taxmapping,
               methods = c(cover=coverscale),
               stratumDefinition = strataDef)

# Create document 'y' with tree observations
treemapping = list(plotName = "Plot", subPlotName = "Subplot", obsStartDate = "PlotObsStartDate",
                   taxonName = "NVSSpeciesName", diameterMeasurement = "Diameter")
diamMeth = predefinedMeasurementMethod("DBH/cm")
y = addIndividualOrganismObservations(newVegX(), moki_dia, treemapping,
                   methods = c(diameterMeasurement = diamMeth))

# Merge 'x' and 'y' while keeping plots of the same name separate and
# organism identities that have the same name separated. This default behaviour
# is set assuming that 'x' and 'y' come from different data sources.
z1 = mergeVegX(x,y)
summary(z1)

# Merge 'x' and 'y' while allowing plots of the same name to be merged
# and organism identities that have the same name to be merged. This configuration
# should be used when merging two VegX objects that come from the same data source 
# (i.e. Mokihinui data)
z2 = mergeVegX(x,y, allowMergePlots = TRUE,
               allowMergeOrganismIdentities = TRUE)
summary(z2)

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