#' Add stratum observation records
#'
#' Adds stratum observation records to a VegX object from a data table where rows are stratum observations.
#'
#' @param target The initial object of class \code{\linkS4class{VegX}} to be modified
#' @param x A data frame where each row corresponds to one stratum observation. Columns can be varied.
#' @param mapping A named list whose elements are strings that correspond to column names in \code{x}. Names of the list should be:
#' \itemize{
#' \item{\code{plotName} - A string identifying the vegetation plot within the data set (required).}
#' \item{\code{subPlotName} - A string identifying a subplot of the plot given by \code{plotName} (optional).}
#' \item{\code{obsStartDate} - Plot observation start date (required; see \code{date.format}).}
#' \item{\code{stratumName} - A string used to identify a stratum (see \code{stratumDefinition}; required).}
#' \item{\code{lowerLimitMeasurement}, \code{upperLimitMeasurement}- Lower and upper limits, respectively, of strata (e.g. height limits in m).}
#' \item{\code{...} - User defined names used to map stratum measurements, such as percent cover (optional).}
#' }
#' @param methods A list measurement methods for \code{lowerLimitMeasurement}, \code{upperLimitMeasurement} and other stratum measurements (each one is object of class \code{\linkS4class{VegXMethodDefinition}}).
#' Alternatively, methods can be specified using strings if predefined methods exist (see \code{\link{predefinedMeasurementMethod}}).
#' @param stratumDefinition An object of class \code{\linkS4class{VegXStrataDefinition}} indicating the definition of strata.
#' @param date.format A character string specifying the input format of dates (see \code{\link{as.Date}}).
#' @param missing.values A character vector of values that should be considered as missing observations/measurements.
#' @param verbose A boolean flag to indicate console output of the data integration process.
#'
#' @return The modified object of class \code{\linkS4class{VegX}}.
#'
#' @details Missing value policy:
#' \itemize{
#' \item{Missing \code{plotName}, \code{obsStartDate} or \code{stratumName} values are interpreted as if the previous non-missing value has to be used to define plot observation.}
#' \item{Missing \code{subPlotName} values are interpreted in that observation refers to the parent plotName.}
#' \item{Missing measurements are simply not added to the Veg-X document.}
#' }
#'
#' @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
#'
#' @family add functions
#'
#' @examples
#' # Load source data
#' data(mokihinui)
#'
#' # Define mapping
#' mapping = list(plotName = "Plot", obsStartDate = "PlotObsStartDate",
#' stratumName = "Tier",
#' lowerLimitMeasurement = "TierLower", upperLimitMeasurement = "TierUpper",
#' cover = "CoverClass")
#'
#'
#' # Define cover scale
#' 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%"))
#'
#'
#' # Define strata
#' 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")
#'
#' # Create new Veg-X document with stratum observations
#' x = addStratumObservations(newVegX(), moki_str, mapping = mapping,
#' methods = list(lowerLimitMeasurement = "Stratum height/m",
#' upperLimitMeasurement = "Stratum height/m",
#' cover=coverscale),
#' stratumDefinition = strataDef)
#'
#' # Examine results
#' head(showElementTable(x, "stratumObservation"))
#'
addStratumObservations<-function(target, x, mapping,
methods,
stratumDefinition,
date.format = "%Y-%m-%d",
missing.values = c(NA, ""),
verbose = TRUE) {
if(class(target)!="VegX") stop("Wrong class for 'target'. Should be an object of class 'VegX'")
if(is.null(stratumDefinition)) stop("Stratum definition must be supplied to map stratum observations.")
x = as.data.frame(x)
nrecords = nrow(x)
nmissing = 0
#Check columns exist
for(i in 1:length(mapping)) {
if(!(mapping[i] %in% names(x))) stop(paste0("Variable '", mapping[i],"' not found in column names. Revise mapping or data."))
}
plotNames = as.character(x[[mapping[["plotName"]]]])
obsStartDates = as.Date(as.character(x[[mapping[["obsStartDate"]]]]), format = date.format)
stratumNamesData = as.character(x[[mapping[["stratumName"]]]])
#Optional mappings
subPlotFlag = ("subPlotName" %in% names(mapping))
if(subPlotFlag) {
subPlotNames = as.character(x[[mapping[["subPlotName"]]]])
}
#Check duplicate records
stratumObservationMappingsAvailable = c("plotName", "obsStartDate", "subPlotName", "stratumName")
mapcols = as.character(mapping[stratumObservationMappingsAvailable[c(T,T,subPlotFlag,T)]])
xstrings = apply(x[, mapcols],1, paste, collapse=" ")
us = length(unique(xstrings))
if(us<nrow(x)) warning(paste0(nrow(x)-us," duplicate records found!"))
#stratummeasurement
stratumMeasurementValues = list()
lowerLimitMeasurementFlag = ("lowerLimitMeasurement" %in% names(mapping))
if(lowerLimitMeasurementFlag) {
if(!("lowerLimitMeasurement" %in% names(methods))) stop("Method definition must be provided for 'lowerLimitMeasurement'.")
stratumMeasurementValues[["lowerLimitMeasurement"]] = as.character(x[[mapping[["lowerLimitMeasurement"]]]])
}
upperLimitMeasurementFlag = ("upperLimitMeasurement" %in% names(mapping))
if(upperLimitMeasurementFlag) {
if(!("upperLimitMeasurement" %in% names(methods))) stop("Method definition must be provided for 'upperLimitMeasurement'.")
stratumMeasurementValues[["upperLimitMeasurement"]] = as.character(x[[mapping[["upperLimitMeasurement"]]]])
}
strmesmapping = mapping[!(names(mapping) %in% c(stratumObservationMappingsAvailable, "lowerLimitMeasurement", "upperLimitMeasurement"))]
if(verbose) cat(paste0(" ", length(strmesmapping)," stratum measurement variables found.\n"))
if(length(strmesmapping)>0) {
for(i in 1:length(strmesmapping)){
if(!(names(strmesmapping)[[i]] %in% names(methods))) stop("Method definition must be provided for '",names(strmesmapping)[[i]],"'.")
stratumMeasurementValues[[names(strmesmapping)[i]]] = as.character(x[[strmesmapping[[i]]]])
}
}
#add methods
methodIDs = character(0)
methodCodes = list()
methodAttIDs = list()
for(m in names(methods)) {
method = methods[[m]]
if(class(method)=="character") {
method = predefinedMeasurementMethod(method)
methods[[m]] = method
}
else if (class(method) != "VegXMethodDefinition") stop(paste("Wrong class for method: ",m ,"."))
nmtid = .newMethodIDByName(target,method@name)
methodID = nmtid$id
methodIDs[[m]] = methodID
methodCodes[[m]] = character(0)
methodAttIDs[[m]] = character(0)
if(nmtid$new) {
target@methods[[methodID]] = list(name = method@name,
description = method@description,
subject = method@subject,
attributeType = method@attributeType)
if(verbose) cat(paste0(" Measurement method '", method@name,"' added for '",m,"'.\n"))
# add literature citation if necessary
if(method@citationString!="") {
ncitid = .newLiteratureCitationIDByCitationString(target, method@citationString)
if(ncitid$new) {
target@literatureCitations[[ncitid$id]] = list(citationString =method@citationString)
if(method@DOI!="") target@literatureCitations[[ncitid$id]]$DOI = method@DOI
}
target@methods[[methodID]]$citationID = ncitid$id
}
# add attributes if necessary
methodAttIDs[[m]] = character(length(method@attributes))
methodCodes[[m]] = character(length(method@attributes))
for(i in 1:length(method@attributes)) {
attid = .nextAttributeID(target)
target@attributes[[attid]] = method@attributes[[i]]
target@attributes[[attid]]$methodID = methodID
methodAttIDs[[m]][i] = attid
if(method@attributes[[i]]$type != "quantitative") methodCodes[[m]][i] = method@attributes[[i]]$code
}
} else {
methodCodes[[m]] = .getAttributeCodesByMethodID(target,methodID)
methodAttIDs[[m]] = .getAttributeIDsByMethodID(target,methodID)
if(verbose) cat(paste0(" Measurement method '", method@name,"' for '",m,"' already included.\n"))
}
}
# stratum definition
stratumDefMethod = stratumDefinition@method
snmtid = .newMethodIDByName(target,stratumDefMethod@name)
strmethodID = snmtid$id
if(snmtid$new) {
target@methods[[strmethodID]] = list(name = stratumDefMethod@name,
description = stratumDefMethod@description,
subject = stratumDefMethod@subject,
attributeType = stratumDefMethod@attributeType)
if(verbose) cat(paste0(" Stratum definition method '", stratumDefMethod@name,"' added.\n"))
# add literature citation if necessary
if(stratumDefMethod@citationString!="") {
ncitid = .newLiteratureCitationIDByCitationString(target, stratumDefMethod@citationString)
if(ncitid$new) {
target@literatureCitations[[ncitid$id]] = list(citationString =stratumDefMethod@citationString)
if(stratumDefMethod@DOI!="") target@literatureCitations[[ncitid$id]]$DOI = stratumDefMethod@DOI
}
target@methods[[strmethodID]]$citationID = ncitid$id
}
# add attributes if necessary
if(length(stratumDefMethod@attributes)>0) {
for(i in 1:length(stratumDefMethod@attributes)) {
attid = .nextAttributeID(target)
target@attributes[[attid]] = stratumDefMethod@attributes[[i]]
target@attributes[[attid]]$methodID = strmethodID
}
}
# add strata (beware of new strata)
orinstrata = length(target@strata)
nstr = length(stratumDefinition@strata)
stratumIDs = character(0)
stratumNames = character(0)
for(i in 1:nstr) {
strid = .nextStratumID(target)
stratumIDs[i] = strid
stratumNames[i] = stratumDefinition@strata[[i]]$stratumName
target@strata[[strid]] = stratumDefinition@strata[[i]]
target@strata[[strid]]$methodID = strmethodID
}
finnstrata = length(target@strata)
if(verbose) {
cat(paste0(" ", finnstrata-orinstrata, " new stratum definitions added.\n"))
}
}
else { #Read stratum IDs and stratum names from selected method
if(verbose) cat(paste0(" Stratum definition '", stratumDefMethod@name,"' already included.\n"))
stratumIDs = .getStratumIDsByMethodID(target,strmethodID)
stratumNames = .getStratumNamesByMethodID(target,strmethodID)
}
orinplots = length(target@plots)
orinplotobs = length(target@plotObservations)
orinstrobs = length(target@stratumObservations)
parsedPlots = character(0)
parsedPlotIDs = character(0)
parsedPlotObs = character(0)
parsedPlotObsIDs = character(0)
parsedStrObs = character(0)
parsedStrObsIDs = character(0)
strObsCounter = orinstrobs+1 #counter
#Record parsing loop
for(i in 1:nrecords) {
#plot
if(!(plotNames[i] %in% missing.values)) {# If plotName is missing take the previous one
plotName = plotNames[i]
}
if(!(plotName %in% parsedPlots)) {
npid = .newPlotIDByName(target, plotNames[i]) # Get the new plot ID (internal code)
plotID = npid$id
if(npid$new) target@plots[[plotID]] = list("plotName" = plotName)
parsedPlots = c(parsedPlots, plotName)
parsedPlotIDs = c(parsedPlotIDs, plotID)
} else { #this access should be faster
plotID = parsedPlotIDs[which(parsedPlots==plotName)]
}
#subplot (if defined)
if(subPlotFlag){
if(!(subPlotNames[i] %in% missing.values)) {# If subPlotName is missing use parent plot ID
subPlotCompleteName = paste0(plotNames[i],"_", subPlotNames[i])
if(!(subPlotCompleteName %in% parsedPlots)) {
parentPlotID = plotID
npid = .newPlotIDByName(target, subPlotCompleteName) # Get the new subplot ID (internal code)
plotID = npid$id
if(npid$new) target@plots[[plotID]] = list("plotName" = subPlotCompleteName,
"parentPlotID" = parentPlotID)
parsedPlots = c(parsedPlots, subPlotCompleteName)
parsedPlotIDs = c(parsedPlotIDs, plotID)
} else { #this access should be faster
plotID = parsedPlotIDs[which(parsedPlots==subPlotCompleteName)]
}
}
}
#plot observation
if(!(obsStartDates[i] %in% missing.values)) {# If observation date is missing take the previous one
obsStartDate = obsStartDates[i]
}
pObsString = paste(plotID, obsStartDate) # plotID+Date
if(!(pObsString %in% parsedPlotObs)) {
npoid = .newPlotObsIDByDate(target, plotID, obsStartDate) # Get the new plot observation ID (internal code)
plotObsID = npoid$id
if(npoid$new) {
target@plotObservations[[plotObsID]] = list("plotID" = plotID,
"obsStartDate" = obsStartDate)
}
parsedPlotObs = c(parsedPlotObs, pObsString)
parsedPlotObsIDs = c(parsedPlotObsIDs, plotObsID)
} else {
plotObsID = parsedPlotObsIDs[which(parsedPlotObs==pObsString)]
}
# stratum observations
if(!(stratumNamesData[i] %in% missing.values)) {# If stratum name is missing take the previous one
stratumName = stratumNamesData[i]
}
if(!(stratumName %in% stratumNames)) stop(paste0(stratumName," not found within stratum names. Revise stratum definition or data."))
strID = stratumIDs[which(stratumNames==stratumName)]
strObsString = paste(plotObsID, strID) # plotObsID+stratumID
if(!(strObsString %in% parsedStrObs)) {
nstroid = .newStratumObsIDByIDs(target, plotObsID, strID) # Get the new stratum observation ID (internal code)
strObsID = nstroid$id
if(nstroid$new) target@stratumObservations[[strObsID]] = list("plotObservationID" = plotObsID,
"stratumID" = strID)
parsedStrObs = c(parsedStrObs, strObsString)
parsedStrObsIDs = c(parsedStrObsIDs, strObsID)
} else {
strObsID = parsedStrObsIDs[which(parsedStrObs==strObsString)]
}
strObs = target@stratumObservations[[strObsID]]
# height limit measurements
for(m in c("lowerLimitMeasurement","upperLimitMeasurement")) {
if(m %in% names(mapping)) {
method = methods[[m]]
attIDs = methodAttIDs[[m]]
codes = methodCodes[[m]]
value = as.character(stratumMeasurementValues[[m]][i])
if(!(value %in% missing.values)) {
if(method@attributeType== "quantitative") {
value = as.numeric(value)
if(value> method@attributes[[1]]$upperLimit) {
stop(paste0("Height '", value,"' larger than upper limit of measurement definition. Please revise scale or data."))
}
else if(value < method@attributes[[1]]$lowerLimit) {
stop(paste0("Height '", value,"' smaller than lower limit of measurement definition. Please revise scale or data."))
}
strObs[[m]] = list("attributeID" = attIDs[1], "value" = value)
} else {
ind = which(codes==value)
if(length(ind)==1) {
strObs[[m]] = list("attributeID" = attIDs[ind], "value" = value)
}
else stop(paste0("Value '", value,"' not found in height measurement definition. Please revise height classes or data."))
}
} else {
nmissing = nmissing + 1
}
}
}
# stratum measurements
for(m in names(strmesmapping)) {
method = methods[[m]]
attIDs = methodAttIDs[[m]]
codes = methodCodes[[m]]
value = as.character(stratumMeasurementValues[[m]][i])
if(!((value %in% missing.values) || (value==""))) {
if(!("stratumMeasurements" %in% names(strObs))) strObs$stratumMeasurements = list()
mesID = as.character(length(strObs$stratumMeasurements)+1)
if(method@attributeType== "quantitative") {
value = as.numeric(value)
if(value> method@attributes[[1]]$upperLimit) {
stop(paste0("Value '", value,"' larger than upper limit of measurement definition for '",m,"'. Please revise scale or data."))
}
else if(value < method@attributes[[1]]$lowerLimit) {
stop(paste0("Value '", value,"' smaller than lower limit of measurement definition for '",m,"'. Please revise scale or data."))
}
strObs$stratumMeasurements[[mesID]] = list("attributeID" = attIDs[1], "value" = value)
} else {
ind = which(codes==value)
if(length(ind)==1) {
strObs$stratumMeasurements[[mesID]] = list("attributeID" = attIDs[ind], "value" = value)
}
else stop(paste0("Value '", value,"' not found in measurement definition for '",m,"'. Please revise height classes or data."))
}
}
else {
nmissing = nmissing + 1
}
}
#Store value in target
target@stratumObservations[[strObsID]] = strObs
}
finnplots = length(target@plots)
finnplotobs = length(target@plotObservations)
finnstrobs = length(target@stratumObservations)
if(verbose) {
cat(paste0(" " , length(parsedPlots)," plot(s) parsed, ", finnplots-orinplots, " new added.\n"))
cat(paste0(" " , length(parsedPlotObs)," plot observation(s) parsed, ", finnplotobs-orinplotobs, " new added.\n"))
cat(paste0(" ", nrecords," record(s) parsed, ", finnstrobs-orinstrobs, " new stratum observation(s) added.\n"))
if(nmissing>0) cat(paste0(" ", nmissing, " measurement(s) with missing value(s) not added.\n"))
}
return(target)
}
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