R/mergeVegX.R
In iavs-org/VegX: Vegetation data in Veg-X
Defines functions
mergeVegX
Documented in
mergeVegX
#' Merge Veg-X documents
#'
#' Merges two Veg-X documents while considering that some of their entities may be shared.
#'
#' @param x,y The objects of class \code{\linkS4class{VegX}} to be merged.
#' @param allowMergePlots If \code{TRUE} plots should be merged when sharing the same plotName and, if defined, plotUniqueIdentifier.
#' If \code{FALSE} plots are never merged (i.e. the two VegX documents are considered as coming from different vegetation data sources).
#' @param allowMergeOrganismIdentities If \code{TRUE}, allows organism identities sharing the same organismName to be merged.
#' If \code{FALSE} organism identities are never merged (i.e. the two VegX documents are considered as coming from different vegetation data sources).
#' @param verbose A flag to indicate console output of the data integration process.
#'
#' @return An object of class \code{\linkS4class{VegX}} with the pooled data
#'
#' @details Some entities are attempted to be merged or are kept as separate entities depeding on their definition:
#' \itemize{
#' \item \code{projects} are merged when their element \code{title} has the same value.
#' \item \code{plots} are merged, if \code{allowMergePlots = TRUE}, when they have the same value for element \code{plotName} and, if defined,
#' \code{plotUniqueIdentifier} are also equal.
#' \item \code{plotObservations} are merged when both their \code{plotID} and \code{obsStartDate} elements have the same value
#' \item \code{organismIdentities} are merged if they share the same organismName and \code{allowMergeOrganismIdentities = TRUE} because
#' one can have the same name used in different data sets but referring to different concepts.
#' \item \code{methods} are merged when their element \code{name} has the same value.
#' \item \code{strata} are merged when their element \code{stratumName} has the same value and the corresponding method has the same \code{name}.
#' \item \code{stratumObservations} are merged when both their \code{stratumID} and \code{plotObservationID} elements have the same value.
#' \item \code{aggregateOrganismObservations} are merged when their \code{plotObservationID} and \code{organismIdentityID} (and \code{stratumObservationID}, if defined) have the same value
#' \item \code{individualOrganisms} are merged when both their \code{plotID} and \code{individualOrganismLabel} have the same value.
#' \item \code{individualOrganismObservations} are merged when both their \code{plotObservationID} and \code{individualOrganismID} have the same value.
#' \item \code{surfaceTypes} are merged when their element \code{surfaceName} has the same value and the corresponding method has the same \code{name}.
#' \item \code{surfaceCoverObservations} are merged when both their \code{surfaceTypeID} and \code{plotObservationID} elements have the same value
#' \item \code{siteObservations} are merged into the same element when their element \code{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., \code{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.
#'
#' @seealso \code{\linkS4class{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)
#'
mergeVegX<-function(x, y,
allowMergePlots = FALSE,
allowMergeOrganismIdentities = FALSE,
verbose = TRUE) {
# uses 'x' as the target and 'y' as the source of data
if(class(x)!="VegX") stop("Wrong class for 'x'. Should be an object of class 'VegX'")
if(class(y)!="VegX") stop("Wrong class for 'y'. Should be an object of class 'VegX'")
# parties
partyIDmap = list()
nmergedparties = 0
if(length(y@parties)>0) {
for(j in 1:length(y@parties)) {
nptid = .newPartyIDByName(x, y@parties[[j]]$name)
if(nptid$new) {
x@parties[[nptid$id]] = y@parties[[j]]
} else {
x@parties[[nptid$id]] = .mergeParties(x@parties[[nlcid$id]], y@parties[[j]])
nmergedparties = nmergedparties + 1
}
partyIDmap[names(y@parties)[j]] = nptid$id
}
}
if(verbose) {
cat(paste0(" Final number of party(ies): ", length(x@parties),". Data pooled for ", nmergedparties, " party(ies).\n"))
}
# literatureCitations
litIDmap = list()
nmergedlits = 0
if(length(y@literatureCitations)>0) {
for(j in 1:length(y@literatureCitations)) {
nlcid = .newLiteratureCitationIDByCitationString(x, y@literatureCitations[[j]]$citationString)
if(nlcid$new) {
x@literatureCitations[[nlcid$id]] = y@literatureCitations[[j]]
} else {
x@literatureCitations[[nlcid$id]] = .mergeLiteratureCitations(x@literatureCitations[[nlcid$id]], y@literatureCitations[[j]])
nmergedlits = nmergedlits + 1
}
litIDmap[names(y@literatureCitations)[j]] = nlcid$id
}
}
if(verbose) {
cat(paste0(" Final number of literature citations: ", length(x@literatureCitations),". Data pooled for ", nmergedlits, " citation(s).\n"))
}
# methods/attributes
methodIDmap = list()
attIDmap = list()
nmergedmeths = 0
if(length(y@methods)>0) {
for(j in 1:length(y@methods)) {
nmetid = .newMethodIDByName(x, y@methods[[j]]$name)
if(nmetid$new) {
x@methods[[nmetid$id]] = .applyMappingsToMethod(y@methods[[j]], litIDmap)
# add attributes
attIDs = .getAttributeIDsByMethodID(y, names(y@methods)[j]) #Get attribute IDs in 'y'
if(length(attIDs)>0) {
for(i in 1:length(attIDs)) {
newAttID = .nextAttributeID(x)
x@attributes[[newAttID]] = y@attributes[[attIDs[i]]]
x@attributes[[newAttID]]$methodID = nmetid$id
attIDmap[[attIDs[i]]] = newAttID
}
}
} else { #pool information
# add attributes
xattIDs = .getAttributeIDsByMethodID(x, names(x@methods)[j]) #Get attribute IDs in 'x'
yattIDs = .getAttributeIDsByMethodID(y, names(y@methods)[j]) #Get attribute IDs in 'y'
if(length(xattIDs)>0) {
for(i in 1:length(xattIDs)) {
attIDmap[[yattIDs[i]]] = xattIDs[i]
}
}
x@methods[[nmetid$id]] = .mergeMethods(x@methods[[nmetid$id]], y@methods[[j]], litIDmap)
#TO DO: We should check the attribute correspondence here
nmergedmeths = nmergedmeths + 1
}
methodIDmap[names(y@methods)[j]] = nmetid$id
}
}
if(verbose) {
cat(paste0(" Final number of methods: ", length(x@methods),". Data pooled for ", nmergedmeths, " method(s).\n"))
cat(paste0(" Final number of attributes: ", length(x@attributes),".\n"))
}
#strata
strIDmap = list()
nmergedstr = 0
if(length(y@strata)>0) {
for(j in 1:length(y@strata)) {
methodID = methodIDmap[[y@strata[[j]]$methodID]]
y@strata[[j]]$methodID = methodID # set method ID to translated one in order to avoid matching problems (does not change id externally)
nstrid = .newStratumIDByName(x, methodID, y@strata[[j]]$stratumName)
if(nstrid$new) {
x@strata[[nstrid$id]] = y@strata[[j]]
} else { #pool information
x@strata[[nstrid$id]] = .mergeStrata(x@strata[[nstrid$id]], y@strata[[j]])
nmergedstr = nmergedstr + 1
}
strIDmap[names(y@strata)[j]] = nstrid$id
}
}
if(verbose) {
cat(paste0(" Final number of strata: ", length(x@strata),". Data pooled for ", nmergedstr, " strata.\n"))
}
#surfaceTypes
stIDmap = list()
nmergedst = 0
if(length(y@surfaceTypes)>0) {
for(j in 1:length(y@surfaceTypes)) {
methodID = methodIDmap[[y@surfaceTypes[[j]]$methodID]]
y@surfaceTypes[[j]]$methodID = methodID # set method ID to translated one in order to avoid matching problems (does not change id externally)
nstid = .newSurfaceTypeIDByName(x, methodID, y@surfaceTypes[[j]]$surfaceName)
if(nstid$new) {
x@surfaceTypes[[nstid$id]] = y@surfaceTypes[[j]]
} else { #pool information
x@surfaceTypes[[nstid$id]] = .mergeStrata(x@surfaceTypes[[nstid$id]], y@surfaceTypes[[j]])
nmergedst = nmergedst + 1
}
stIDmap[names(y@surfaceTypes)[j]] = nstid$id
}
}
if(verbose) {
cat(paste0(" Final number of surface types: ", length(x@surfaceTypes),". Data pooled for ", nmergedst, " surface types.\n"))
}
#organismNames
onIDmap = list()
nmergedons = 0
if(length(y@organismNames)>0) {
for(j in 1:length(y@organismNames)) {
nonid = .newOrganismNameIDByName(x, y@organismNames[[j]]$name, y@organismNames[[j]]$taxon)
if(nonid$new) {
x@organismNames[[nonid$id]] = y@organismNames[[j]]
} else { #pool information
x@organismNames[[nonid$id]] = .mergeOrganismNames(x@organismNames[[nonid$id]], y@organismNames[[j]])
nmergedons = nmergedons + 1
}
onIDmap[names(y@organismNames)[j]] = nonid$id
}
}
if(verbose) {
cat(paste0(" Final number of organism names: ", length(x@organismNames),". Data pooled for ", nmergedons, " organism name(s).\n"))
}
#taxonConcepts
tcIDmap = list()
nmergedtcs = 0
if(length(y@taxonConcepts)>0) {
for(j in 1:length(y@taxonConcepts)) {
ntcid = .newTaxonConceptIDByNameCitation(x, y@organismNames[[y@taxonConcepts[[j]]$organismNameID]]$name,
y@literatureCitations[[y@taxonConcepts[[j]]$citationID]]$citationString)
if(ntcid$new) {
x@taxonConcepts[[ntcid$id]] = .applyMappingsToTaxonConcept(y@taxonConcepts[[j]], onIDmap, litIDmap)
} else { #pool information
x@taxonConcepts[[ntcid$id]] = .mergeTaxonConcepts(x@taxonConcepts[[ntcid$id]], y@taxonConcepts[[j]], onIDmap, litIDmap)
nmergedtcs = nmergedtcs + 1
}
tcIDmap[names(y@taxonConcepts)[j]] = ntcid$id
}
}
if(verbose) {
cat(paste0(" Final number of taxon concepts: ", length(x@taxonConcepts),". Data pooled for ", nmergedtcs, " organism name(s).\n"))
}
#organismIdentities
oiIDmap = list()
nmergedois = 0
if(length(y@organismIdentities)>0) {
for(j in 1:length(y@organismIdentities)) {
if(allowMergeOrganismIdentities) {
organismName = .getOrganismIdentityName(y, j)
citationString = .getOrganismIdentityCitationString(y,j)
orgId = .applyMappingsToOrganismIdentity(y@organismIdentities[[j]], onIDmap, tcIDmap)
noiid = .newOrganismIdentityIDByTaxonConcept(x, organismName, citationString)
if(noiid$new) {
x@organismIdentities[[noiid$id]] = orgId
} else { #pool information
x@organismIdentities[[noiid$id]] = .mergeOrganismIdentities(x@organismIdentities[[noiid$id]], orgId)
nmergedois = nmergedois + 1
}
oiIDmap[names(y@organismIdentities)[j]] = noiid$id
} else {
newOIID = .nextOrganismIdentityID(x)
x@organismIdentities[[newOIID]] = .applyMappingsToOrganismIdentity(y@organismIdentities[[j]], onIDmap, tcIDmap)
oiIDmap[names(y@organismIdentities)[j]] = newOIID
}
}
}
if(verbose) {
cat(paste0(" Final number of organism identities: ", length(x@organismIdentities),". Data pooled for ", nmergedois, " organism identitie(s).\n"))
}
#projects
nmergedpjs = 0
projectIDmap = list()
if(length(y@projects)>0) {
for(j in 1:length(y@projects)) {
npid = .newProjectIDByTitle(x, y@projects[[j]]$title)
if(npid$new) {
x@projects[[npid$id]] = .applyMappingsToProject(y@projects[[j]], partyIDmap, litIDmap)
} else {
x@projects[[npid$id]] = .mergeProjects(x@projects[[npid$id]], y@projects[[j]])
nmergedpjs = nmergedpjs + 1
}
projectIDmap[names(y@projects)[j]] = npid$id
}
}
if(verbose) {
cat(paste0(" Final number of projects: ", length(x@projects),". Data pooled for ", nmergedpjs, " project(s).\n"))
}
#plots
plotIDmap = list()
nmergedplots = 0
if(length(y@plots)>0) {
for(j in 1:length(y@plots)) {
if(allowMergePlots) {
if("parentPlotID" %in% names(y@plots[[j]])) y@plots[[j]]$parentPlotID = plotIDmap[[y@plots[[j]]$parentPlotID]] #set parent plot ID to translated one in order to avoid matching problems
plotUniqueIdentifier = ""
if("plotUniqueIdentifier" %in% names(y@plots[[j]])) plotUniqueIdentifier = y@plots[[j]]$plotUniqueIdentifier
npid = .newPlotIDByNameAndUniqueIdentifier(x, y@plots[[j]]$plotName, plotUniqueIdentifier)
if(npid$new) {
x@plots[[npid$id]] = .applyMappingsToPlot(y@plots[[j]], partyIDmap, attIDmap)
} else { #pool information
x@plots[[npid$id]] = .mergePlots(x@plots[[npid$id]], y@plots[[j]], partyIDmap, attIDmap)
nmergedplots = nmergedplots + 1
}
plotIDmap[names(y@plots)[j]] = npid$id
} else {
newplotID = .nextPlotID(x)
x@plots[[newplotID]] = .applyMappingsToPlot(y@plots[[j]], partyIDmap, attIDmap)
plotIDmap[names(y@plots)[j]] = newplotID
}
}
}
if(verbose) {
cat(paste0(" Final number of plots: ", length(x@plots),". Data pooled for ", nmergedplots, " plot(s).\n"))
}
# individualOrganisms
indIDmap = list()
nmergedind = 0
if(length(y@individualOrganisms)>0) {
for(j in 1:length(y@individualOrganisms)) {
indOrg = .applyMappingsToIndividualOrganism(y@individualOrganisms[[j]], plotIDmap, oiIDmap)
nindid = .newIndividualOrganismIDByIndividualOrganismLabel(x, indOrg$plotID, indOrg$individualOrganismLabel)
if(nindid$new) {
x@individualOrganisms[[nindid$id]] = indOrg
} else { #pool information
x@individualOrganisms[[nindid$id]] = .mergeIndividualOrganisms(x@individualOrganisms[[nindid$id]], indOrg)
nmergedind = nmergedind + 1
}
indIDmap[names(y@individualOrganisms)[j]] = nindid$id
}
}
if(verbose) {
cat(paste0(" Final number of individual organisms: ", length(x@individualOrganisms),". Data pooled for ", nmergedind, " individual organism(s).\n"))
}
#plotObservations
plotObsIDmap = list()
nmergedplotobs = 0
if(length(y@plotObservations)>0) {
for(j in 1:length(y@plotObservations)) {
plotObs = .applyMappingsToPlotObservation(y@plotObservations[[j]], plotIDmap, projectIDmap)
npoid = .newPlotObsIDByDate(x, plotObs$plotID, plotObs$obsStartDate)
if(npoid$new) {
x@plotObservations[[npoid$id]] = plotObs
} else { #pool information
x@plotObservations[[npoid$id]] = .mergePlotObservations(x@plotObservations[[npoid$id]], plotObs)
nmergedplotobs = nmergedplotobs + 1
}
plotObsIDmap[names(y@plotObservations)[j]] = npoid$id
}
}
if(verbose) {
cat(paste0(" Final number of plot observations: ", length(x@plotObservations),". Data pooled for ", nmergedplotobs, " plot observation(s).\n"))
}
# stratumObservations
strObsIDmap = list()
nmergedstrobs = 0
if(length(y@stratumObservations)>0) {
for(j in 1:length(y@stratumObservations)) {
strObs = .applyMappingsToStratumObservation(y@stratumObservations[[j]], strIDmap, plotObsIDmap, attIDmap)
nstrobsid = .newStratumObsIDByIDs(x, strObs$plotObservationID, strObs$stratumID)
if(nstrobsid$new) {
x@stratumObservations[[nstrobsid$id]] = strObs
} else { #pool information
x@stratumObservations[[nstrobsid$id]] = .mergeStratumObservations(x@stratumObservations[[nstrobsid$id]], strObs)
nmergedstrobs = nmergedstrobs + 1
}
strObsIDmap[names(y@stratumObservations)[j]] = nstrobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of stratum observations: ", length(x@stratumObservations),". Data pooled for ", nmergedstrobs, " stratum observation(s).\n"))
}
# individualObservations
indObsIDmap = list()
nmergedindobs = 0
if(length(y@individualObservations)>0) {
for(j in 1:length(y@individualObservations)) {
indObs = .applyMappingsToIndividualOrganismObservation(y@individualObservations[[j]], plotObsIDmap, strObsIDmap, indIDmap, attIDmap)
nindobsid = .newIndividualOrganismObservationIDByIndividualID(x, indObs$plotObservationID, indObs$individualOrganismID)
if(nindobsid$new) {
x@individualObservations[[nindobsid$id]] = indObs
} else { #pool information
x@individualObservations[[nindobsid$id]] = .mergeIndividualOrganismObservations(x@individualObservations[[nindobsid$id]], indObs)
nmergedindobs = nmergedindobs + 1
}
indObsIDmap[names(y@individualObservations)[j]] = nindobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of individual organism observations: ", length(x@individualObservations),". Data pooled for ", nmergedindobs, " individual organism observation(s).\n"))
}
# aggregateObservations
aggObsIDmap = list()
nmergedaggobs = 0
if(length(y@aggregateObservations)>0) {
for(j in 1:length(y@aggregateObservations)) {
aggObs = .applyMappingsToAggregateOrganismObservation(y@aggregateObservations[[j]], plotObsIDmap, oiIDmap, strObsIDmap, attIDmap)
naggobsid = .newAggregateOrganismObservationIDByOrganismIdentityID(x,
aggObs$plotObservationID,
aggObs$stratumObservationID,
aggObs$organismIdentityID)
if(naggobsid$new) {
x@aggregateObservations[[naggobsid$id]] = aggObs
} else { #pool information
x@aggregateObservations[[naggobsid$id]] = .mergeAggregateOrganismObservations(x@aggregateObservations[[naggobsid$id]], aggObs)
nmergedaggobs = nmergedaggobs + 1
}
aggObsIDmap[names(y@aggregateObservations)[j]] = naggobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of aggregate organism observations: ", length(x@aggregateObservations),". Data pooled for ", nmergedaggobs, " aggregate organism observation(s).\n"))
}
# siteObservations
siteObsIDmap = list()
nmergedsiteobs = 0
if(length(y@siteObservations)>0) {
for(j in 1:length(y@siteObservations)) {
siteObs = .applyMappingsToSiteObservation(y@siteObservations[[j]], plotObsIDmap, attIDmap)
nsiteobsid = .newSiteObservationIDByID(x, siteObs$plotObservationID)
if(nsiteobsid$new) {
x@siteObservations[[nsiteobsid$id]] = siteObs
} else { #pool information
x@siteObservations[[nsiteobsid$id]] = .mergeSiteObservations(x@siteObservations[[nsiteobsid$id]], siteObs)
nmergedsiteobs = nmergedsiteobs + 1
}
siteObsIDmap[names(y@siteObservations)[j]] = nsiteobsid$id
# Update link in plotObservation
x@plotObservations[[x@siteObservations[[nsiteobsid$id]]$plotObservationID]]$siteObservationID = nsiteobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of site observations: ", length(x@siteObservations),". Data pooled for ", nmergedsiteobs, " site observation(s).\n"))
}
# communityObservations
commObsIDmap = list()
nmergedcommobs = 0
if(length(y@communityObservations)>0) {
for(j in 1:length(y@communityObservations)) {
commObs = .applyMappingsToCommunityObservation(y@communityObservations[[j]], plotObsIDmap, attIDmap)
ncommobsid = .newCommunityObservationIDByID(x, commObs$plotObservationID)
if(ncommobsid$new) {
x@communityObservations[[ncommobsid$id]] = commObs
} else { #pool information
x@communityObservations[[ncommobsid$id]] = .mergeCommunityObservations(x@communityObservations[[ncommobsid$id]], commObs)
nmergedcommobs = nmergedcommobs + 1
}
commObsIDmap[names(y@communityObservations)[j]] = ncommobsid$id
# Update link in plotObservation
x@plotObservations[[x@communityObservations[[ncommobsid$id]]$plotObservationID]]$communityObservationID = ncommobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of community observations: ", length(x@communityObservations),". Data pooled for ", nmergedsiteobs, " community observation(s).\n"))
}
# surfaceCoverObservations
scObsIDmap = list()
nmergedscobs = 0
if(length(y@surfaceCoverObservations)>0) {
for(j in 1:length(y@surfaceCoverObservations)) {
scObs = .applyMappingsToSurfaceCoverObservation(y@surfaceCoverObservations[[j]], stIDmap, plotObsIDmap, attIDmap)
nscobsid = .newSurfaceCoverObsIDByIDs(x, scObs$plotObservationID, scObs$surfaceTypeID)
if(nscobsid$new) {
x@surfaceCoverObservations[[nscobsid$id]] = scObs
} else { #pool information
x@surfaceCoverObservations[[nscobsid$id]] = .mergeSurfaceCoverObservations(x@surfaceCoverObservations[[nstrobsid$id]], scObs)
nmergedscobs = nmergedscobs + 1
}
scObsIDmap[names(y@surfaceCoverObservations)[j]] = nscobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of surface cover observations: ", length(x@surfaceCoverObservations),". Data pooled for ", nmergedscobs, " surface cover observation(s).\n"))
}
return(x)
}
iavs-org/VegX documentation built on Sept. 15, 2022, 5:24 a.m.
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Defines functions mergeVegX
Documented in mergeVegX
#' Merge Veg-X documents
#'
#' Merges two Veg-X documents while considering that some of their entities may be shared.
#'
#' @param x,y The objects of class \code{\linkS4class{VegX}} to be merged.
#' @param allowMergePlots If \code{TRUE} plots should be merged when sharing the same plotName and, if defined, plotUniqueIdentifier.
#' If \code{FALSE} plots are never merged (i.e. the two VegX documents are considered as coming from different vegetation data sources).
#' @param allowMergeOrganismIdentities If \code{TRUE}, allows organism identities sharing the same organismName to be merged.
#' If \code{FALSE} organism identities are never merged (i.e. the two VegX documents are considered as coming from different vegetation data sources).
#' @param verbose A flag to indicate console output of the data integration process.
#'
#' @return An object of class \code{\linkS4class{VegX}} with the pooled data
#'
#' @details Some entities are attempted to be merged or are kept as separate entities depeding on their definition:
#' \itemize{
#' \item \code{projects} are merged when their element \code{title} has the same value.
#' \item \code{plots} are merged, if \code{allowMergePlots = TRUE}, when they have the same value for element \code{plotName} and, if defined,
#' \code{plotUniqueIdentifier} are also equal.
#' \item \code{plotObservations} are merged when both their \code{plotID} and \code{obsStartDate} elements have the same value
#' \item \code{organismIdentities} are merged if they share the same organismName and \code{allowMergeOrganismIdentities = TRUE} because
#' one can have the same name used in different data sets but referring to different concepts.
#' \item \code{methods} are merged when their element \code{name} has the same value.
#' \item \code{strata} are merged when their element \code{stratumName} has the same value and the corresponding method has the same \code{name}.
#' \item \code{stratumObservations} are merged when both their \code{stratumID} and \code{plotObservationID} elements have the same value.
#' \item \code{aggregateOrganismObservations} are merged when their \code{plotObservationID} and \code{organismIdentityID} (and \code{stratumObservationID}, if defined) have the same value
#' \item \code{individualOrganisms} are merged when both their \code{plotID} and \code{individualOrganismLabel} have the same value.
#' \item \code{individualOrganismObservations} are merged when both their \code{plotObservationID} and \code{individualOrganismID} have the same value.
#' \item \code{surfaceTypes} are merged when their element \code{surfaceName} has the same value and the corresponding method has the same \code{name}.
#' \item \code{surfaceCoverObservations} are merged when both their \code{surfaceTypeID} and \code{plotObservationID} elements have the same value
#' \item \code{siteObservations} are merged into the same element when their element \code{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., \code{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.
#'
#' @seealso \code{\linkS4class{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)
#'
mergeVegX<-function(x, y,
allowMergePlots = FALSE,
allowMergeOrganismIdentities = FALSE,
verbose = TRUE) {
# uses 'x' as the target and 'y' as the source of data
if(class(x)!="VegX") stop("Wrong class for 'x'. Should be an object of class 'VegX'")
if(class(y)!="VegX") stop("Wrong class for 'y'. Should be an object of class 'VegX'")
# parties
partyIDmap = list()
nmergedparties = 0
if(length(y@parties)>0) {
for(j in 1:length(y@parties)) {
nptid = .newPartyIDByName(x, y@parties[[j]]$name)
if(nptid$new) {
x@parties[[nptid$id]] = y@parties[[j]]
} else {
x@parties[[nptid$id]] = .mergeParties(x@parties[[nlcid$id]], y@parties[[j]])
nmergedparties = nmergedparties + 1
}
partyIDmap[names(y@parties)[j]] = nptid$id
}
}
if(verbose) {
cat(paste0(" Final number of party(ies): ", length(x@parties),". Data pooled for ", nmergedparties, " party(ies).\n"))
}
# literatureCitations
litIDmap = list()
nmergedlits = 0
if(length(y@literatureCitations)>0) {
for(j in 1:length(y@literatureCitations)) {
nlcid = .newLiteratureCitationIDByCitationString(x, y@literatureCitations[[j]]$citationString)
if(nlcid$new) {
x@literatureCitations[[nlcid$id]] = y@literatureCitations[[j]]
} else {
x@literatureCitations[[nlcid$id]] = .mergeLiteratureCitations(x@literatureCitations[[nlcid$id]], y@literatureCitations[[j]])
nmergedlits = nmergedlits + 1
}
litIDmap[names(y@literatureCitations)[j]] = nlcid$id
}
}
if(verbose) {
cat(paste0(" Final number of literature citations: ", length(x@literatureCitations),". Data pooled for ", nmergedlits, " citation(s).\n"))
}
# methods/attributes
methodIDmap = list()
attIDmap = list()
nmergedmeths = 0
if(length(y@methods)>0) {
for(j in 1:length(y@methods)) {
nmetid = .newMethodIDByName(x, y@methods[[j]]$name)
if(nmetid$new) {
x@methods[[nmetid$id]] = .applyMappingsToMethod(y@methods[[j]], litIDmap)
# add attributes
attIDs = .getAttributeIDsByMethodID(y, names(y@methods)[j]) #Get attribute IDs in 'y'
if(length(attIDs)>0) {
for(i in 1:length(attIDs)) {
newAttID = .nextAttributeID(x)
x@attributes[[newAttID]] = y@attributes[[attIDs[i]]]
x@attributes[[newAttID]]$methodID = nmetid$id
attIDmap[[attIDs[i]]] = newAttID
}
}
} else { #pool information
# add attributes
xattIDs = .getAttributeIDsByMethodID(x, names(x@methods)[j]) #Get attribute IDs in 'x'
yattIDs = .getAttributeIDsByMethodID(y, names(y@methods)[j]) #Get attribute IDs in 'y'
if(length(xattIDs)>0) {
for(i in 1:length(xattIDs)) {
attIDmap[[yattIDs[i]]] = xattIDs[i]
}
}
x@methods[[nmetid$id]] = .mergeMethods(x@methods[[nmetid$id]], y@methods[[j]], litIDmap)
#TO DO: We should check the attribute correspondence here
nmergedmeths = nmergedmeths + 1
}
methodIDmap[names(y@methods)[j]] = nmetid$id
}
}
if(verbose) {
cat(paste0(" Final number of methods: ", length(x@methods),". Data pooled for ", nmergedmeths, " method(s).\n"))
cat(paste0(" Final number of attributes: ", length(x@attributes),".\n"))
}
#strata
strIDmap = list()
nmergedstr = 0
if(length(y@strata)>0) {
for(j in 1:length(y@strata)) {
methodID = methodIDmap[[y@strata[[j]]$methodID]]
y@strata[[j]]$methodID = methodID # set method ID to translated one in order to avoid matching problems (does not change id externally)
nstrid = .newStratumIDByName(x, methodID, y@strata[[j]]$stratumName)
if(nstrid$new) {
x@strata[[nstrid$id]] = y@strata[[j]]
} else { #pool information
x@strata[[nstrid$id]] = .mergeStrata(x@strata[[nstrid$id]], y@strata[[j]])
nmergedstr = nmergedstr + 1
}
strIDmap[names(y@strata)[j]] = nstrid$id
}
}
if(verbose) {
cat(paste0(" Final number of strata: ", length(x@strata),". Data pooled for ", nmergedstr, " strata.\n"))
}
#surfaceTypes
stIDmap = list()
nmergedst = 0
if(length(y@surfaceTypes)>0) {
for(j in 1:length(y@surfaceTypes)) {
methodID = methodIDmap[[y@surfaceTypes[[j]]$methodID]]
y@surfaceTypes[[j]]$methodID = methodID # set method ID to translated one in order to avoid matching problems (does not change id externally)
nstid = .newSurfaceTypeIDByName(x, methodID, y@surfaceTypes[[j]]$surfaceName)
if(nstid$new) {
x@surfaceTypes[[nstid$id]] = y@surfaceTypes[[j]]
} else { #pool information
x@surfaceTypes[[nstid$id]] = .mergeStrata(x@surfaceTypes[[nstid$id]], y@surfaceTypes[[j]])
nmergedst = nmergedst + 1
}
stIDmap[names(y@surfaceTypes)[j]] = nstid$id
}
}
if(verbose) {
cat(paste0(" Final number of surface types: ", length(x@surfaceTypes),". Data pooled for ", nmergedst, " surface types.\n"))
}
#organismNames
onIDmap = list()
nmergedons = 0
if(length(y@organismNames)>0) {
for(j in 1:length(y@organismNames)) {
nonid = .newOrganismNameIDByName(x, y@organismNames[[j]]$name, y@organismNames[[j]]$taxon)
if(nonid$new) {
x@organismNames[[nonid$id]] = y@organismNames[[j]]
} else { #pool information
x@organismNames[[nonid$id]] = .mergeOrganismNames(x@organismNames[[nonid$id]], y@organismNames[[j]])
nmergedons = nmergedons + 1
}
onIDmap[names(y@organismNames)[j]] = nonid$id
}
}
if(verbose) {
cat(paste0(" Final number of organism names: ", length(x@organismNames),". Data pooled for ", nmergedons, " organism name(s).\n"))
}
#taxonConcepts
tcIDmap = list()
nmergedtcs = 0
if(length(y@taxonConcepts)>0) {
for(j in 1:length(y@taxonConcepts)) {
ntcid = .newTaxonConceptIDByNameCitation(x, y@organismNames[[y@taxonConcepts[[j]]$organismNameID]]$name,
y@literatureCitations[[y@taxonConcepts[[j]]$citationID]]$citationString)
if(ntcid$new) {
x@taxonConcepts[[ntcid$id]] = .applyMappingsToTaxonConcept(y@taxonConcepts[[j]], onIDmap, litIDmap)
} else { #pool information
x@taxonConcepts[[ntcid$id]] = .mergeTaxonConcepts(x@taxonConcepts[[ntcid$id]], y@taxonConcepts[[j]], onIDmap, litIDmap)
nmergedtcs = nmergedtcs + 1
}
tcIDmap[names(y@taxonConcepts)[j]] = ntcid$id
}
}
if(verbose) {
cat(paste0(" Final number of taxon concepts: ", length(x@taxonConcepts),". Data pooled for ", nmergedtcs, " organism name(s).\n"))
}
#organismIdentities
oiIDmap = list()
nmergedois = 0
if(length(y@organismIdentities)>0) {
for(j in 1:length(y@organismIdentities)) {
if(allowMergeOrganismIdentities) {
organismName = .getOrganismIdentityName(y, j)
citationString = .getOrganismIdentityCitationString(y,j)
orgId = .applyMappingsToOrganismIdentity(y@organismIdentities[[j]], onIDmap, tcIDmap)
noiid = .newOrganismIdentityIDByTaxonConcept(x, organismName, citationString)
if(noiid$new) {
x@organismIdentities[[noiid$id]] = orgId
} else { #pool information
x@organismIdentities[[noiid$id]] = .mergeOrganismIdentities(x@organismIdentities[[noiid$id]], orgId)
nmergedois = nmergedois + 1
}
oiIDmap[names(y@organismIdentities)[j]] = noiid$id
} else {
newOIID = .nextOrganismIdentityID(x)
x@organismIdentities[[newOIID]] = .applyMappingsToOrganismIdentity(y@organismIdentities[[j]], onIDmap, tcIDmap)
oiIDmap[names(y@organismIdentities)[j]] = newOIID
}
}
}
if(verbose) {
cat(paste0(" Final number of organism identities: ", length(x@organismIdentities),". Data pooled for ", nmergedois, " organism identitie(s).\n"))
}
#projects
nmergedpjs = 0
projectIDmap = list()
if(length(y@projects)>0) {
for(j in 1:length(y@projects)) {
npid = .newProjectIDByTitle(x, y@projects[[j]]$title)
if(npid$new) {
x@projects[[npid$id]] = .applyMappingsToProject(y@projects[[j]], partyIDmap, litIDmap)
} else {
x@projects[[npid$id]] = .mergeProjects(x@projects[[npid$id]], y@projects[[j]])
nmergedpjs = nmergedpjs + 1
}
projectIDmap[names(y@projects)[j]] = npid$id
}
}
if(verbose) {
cat(paste0(" Final number of projects: ", length(x@projects),". Data pooled for ", nmergedpjs, " project(s).\n"))
}
#plots
plotIDmap = list()
nmergedplots = 0
if(length(y@plots)>0) {
for(j in 1:length(y@plots)) {
if(allowMergePlots) {
if("parentPlotID" %in% names(y@plots[[j]])) y@plots[[j]]$parentPlotID = plotIDmap[[y@plots[[j]]$parentPlotID]] #set parent plot ID to translated one in order to avoid matching problems
plotUniqueIdentifier = ""
if("plotUniqueIdentifier" %in% names(y@plots[[j]])) plotUniqueIdentifier = y@plots[[j]]$plotUniqueIdentifier
npid = .newPlotIDByNameAndUniqueIdentifier(x, y@plots[[j]]$plotName, plotUniqueIdentifier)
if(npid$new) {
x@plots[[npid$id]] = .applyMappingsToPlot(y@plots[[j]], partyIDmap, attIDmap)
} else { #pool information
x@plots[[npid$id]] = .mergePlots(x@plots[[npid$id]], y@plots[[j]], partyIDmap, attIDmap)
nmergedplots = nmergedplots + 1
}
plotIDmap[names(y@plots)[j]] = npid$id
} else {
newplotID = .nextPlotID(x)
x@plots[[newplotID]] = .applyMappingsToPlot(y@plots[[j]], partyIDmap, attIDmap)
plotIDmap[names(y@plots)[j]] = newplotID
}
}
}
if(verbose) {
cat(paste0(" Final number of plots: ", length(x@plots),". Data pooled for ", nmergedplots, " plot(s).\n"))
}
# individualOrganisms
indIDmap = list()
nmergedind = 0
if(length(y@individualOrganisms)>0) {
for(j in 1:length(y@individualOrganisms)) {
indOrg = .applyMappingsToIndividualOrganism(y@individualOrganisms[[j]], plotIDmap, oiIDmap)
nindid = .newIndividualOrganismIDByIndividualOrganismLabel(x, indOrg$plotID, indOrg$individualOrganismLabel)
if(nindid$new) {
x@individualOrganisms[[nindid$id]] = indOrg
} else { #pool information
x@individualOrganisms[[nindid$id]] = .mergeIndividualOrganisms(x@individualOrganisms[[nindid$id]], indOrg)
nmergedind = nmergedind + 1
}
indIDmap[names(y@individualOrganisms)[j]] = nindid$id
}
}
if(verbose) {
cat(paste0(" Final number of individual organisms: ", length(x@individualOrganisms),". Data pooled for ", nmergedind, " individual organism(s).\n"))
}
#plotObservations
plotObsIDmap = list()
nmergedplotobs = 0
if(length(y@plotObservations)>0) {
for(j in 1:length(y@plotObservations)) {
plotObs = .applyMappingsToPlotObservation(y@plotObservations[[j]], plotIDmap, projectIDmap)
npoid = .newPlotObsIDByDate(x, plotObs$plotID, plotObs$obsStartDate)
if(npoid$new) {
x@plotObservations[[npoid$id]] = plotObs
} else { #pool information
x@plotObservations[[npoid$id]] = .mergePlotObservations(x@plotObservations[[npoid$id]], plotObs)
nmergedplotobs = nmergedplotobs + 1
}
plotObsIDmap[names(y@plotObservations)[j]] = npoid$id
}
}
if(verbose) {
cat(paste0(" Final number of plot observations: ", length(x@plotObservations),". Data pooled for ", nmergedplotobs, " plot observation(s).\n"))
}
# stratumObservations
strObsIDmap = list()
nmergedstrobs = 0
if(length(y@stratumObservations)>0) {
for(j in 1:length(y@stratumObservations)) {
strObs = .applyMappingsToStratumObservation(y@stratumObservations[[j]], strIDmap, plotObsIDmap, attIDmap)
nstrobsid = .newStratumObsIDByIDs(x, strObs$plotObservationID, strObs$stratumID)
if(nstrobsid$new) {
x@stratumObservations[[nstrobsid$id]] = strObs
} else { #pool information
x@stratumObservations[[nstrobsid$id]] = .mergeStratumObservations(x@stratumObservations[[nstrobsid$id]], strObs)
nmergedstrobs = nmergedstrobs + 1
}
strObsIDmap[names(y@stratumObservations)[j]] = nstrobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of stratum observations: ", length(x@stratumObservations),". Data pooled for ", nmergedstrobs, " stratum observation(s).\n"))
}
# individualObservations
indObsIDmap = list()
nmergedindobs = 0
if(length(y@individualObservations)>0) {
for(j in 1:length(y@individualObservations)) {
indObs = .applyMappingsToIndividualOrganismObservation(y@individualObservations[[j]], plotObsIDmap, strObsIDmap, indIDmap, attIDmap)
nindobsid = .newIndividualOrganismObservationIDByIndividualID(x, indObs$plotObservationID, indObs$individualOrganismID)
if(nindobsid$new) {
x@individualObservations[[nindobsid$id]] = indObs
} else { #pool information
x@individualObservations[[nindobsid$id]] = .mergeIndividualOrganismObservations(x@individualObservations[[nindobsid$id]], indObs)
nmergedindobs = nmergedindobs + 1
}
indObsIDmap[names(y@individualObservations)[j]] = nindobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of individual organism observations: ", length(x@individualObservations),". Data pooled for ", nmergedindobs, " individual organism observation(s).\n"))
}
# aggregateObservations
aggObsIDmap = list()
nmergedaggobs = 0
if(length(y@aggregateObservations)>0) {
for(j in 1:length(y@aggregateObservations)) {
aggObs = .applyMappingsToAggregateOrganismObservation(y@aggregateObservations[[j]], plotObsIDmap, oiIDmap, strObsIDmap, attIDmap)
naggobsid = .newAggregateOrganismObservationIDByOrganismIdentityID(x,
aggObs$plotObservationID,
aggObs$stratumObservationID,
aggObs$organismIdentityID)
if(naggobsid$new) {
x@aggregateObservations[[naggobsid$id]] = aggObs
} else { #pool information
x@aggregateObservations[[naggobsid$id]] = .mergeAggregateOrganismObservations(x@aggregateObservations[[naggobsid$id]], aggObs)
nmergedaggobs = nmergedaggobs + 1
}
aggObsIDmap[names(y@aggregateObservations)[j]] = naggobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of aggregate organism observations: ", length(x@aggregateObservations),". Data pooled for ", nmergedaggobs, " aggregate organism observation(s).\n"))
}
# siteObservations
siteObsIDmap = list()
nmergedsiteobs = 0
if(length(y@siteObservations)>0) {
for(j in 1:length(y@siteObservations)) {
siteObs = .applyMappingsToSiteObservation(y@siteObservations[[j]], plotObsIDmap, attIDmap)
nsiteobsid = .newSiteObservationIDByID(x, siteObs$plotObservationID)
if(nsiteobsid$new) {
x@siteObservations[[nsiteobsid$id]] = siteObs
} else { #pool information
x@siteObservations[[nsiteobsid$id]] = .mergeSiteObservations(x@siteObservations[[nsiteobsid$id]], siteObs)
nmergedsiteobs = nmergedsiteobs + 1
}
siteObsIDmap[names(y@siteObservations)[j]] = nsiteobsid$id
# Update link in plotObservation
x@plotObservations[[x@siteObservations[[nsiteobsid$id]]$plotObservationID]]$siteObservationID = nsiteobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of site observations: ", length(x@siteObservations),". Data pooled for ", nmergedsiteobs, " site observation(s).\n"))
}
# communityObservations
commObsIDmap = list()
nmergedcommobs = 0
if(length(y@communityObservations)>0) {
for(j in 1:length(y@communityObservations)) {
commObs = .applyMappingsToCommunityObservation(y@communityObservations[[j]], plotObsIDmap, attIDmap)
ncommobsid = .newCommunityObservationIDByID(x, commObs$plotObservationID)
if(ncommobsid$new) {
x@communityObservations[[ncommobsid$id]] = commObs
} else { #pool information
x@communityObservations[[ncommobsid$id]] = .mergeCommunityObservations(x@communityObservations[[ncommobsid$id]], commObs)
nmergedcommobs = nmergedcommobs + 1
}
commObsIDmap[names(y@communityObservations)[j]] = ncommobsid$id
# Update link in plotObservation
x@plotObservations[[x@communityObservations[[ncommobsid$id]]$plotObservationID]]$communityObservationID = ncommobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of community observations: ", length(x@communityObservations),". Data pooled for ", nmergedsiteobs, " community observation(s).\n"))
}
# surfaceCoverObservations
scObsIDmap = list()
nmergedscobs = 0
if(length(y@surfaceCoverObservations)>0) {
for(j in 1:length(y@surfaceCoverObservations)) {
scObs = .applyMappingsToSurfaceCoverObservation(y@surfaceCoverObservations[[j]], stIDmap, plotObsIDmap, attIDmap)
nscobsid = .newSurfaceCoverObsIDByIDs(x, scObs$plotObservationID, scObs$surfaceTypeID)
if(nscobsid$new) {
x@surfaceCoverObservations[[nscobsid$id]] = scObs
} else { #pool information
x@surfaceCoverObservations[[nscobsid$id]] = .mergeSurfaceCoverObservations(x@surfaceCoverObservations[[nstrobsid$id]], scObs)
nmergedscobs = nmergedscobs + 1
}
scObsIDmap[names(y@surfaceCoverObservations)[j]] = nscobsid$id
}
}
if(verbose) {
cat(paste0(" Final number of surface cover observations: ", length(x@surfaceCoverObservations),". Data pooled for ", nmergedscobs, " surface cover observation(s).\n"))
}
return(x)
}
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