R/MetadataFilter.R
In TimKroeger13/ProjectMultiLake: RTools used by the Alfred wegner institut
Defines functions
MetadataFilter
Documented in
MetadataFilter
#'MetadataFilter
#'@description
#'Filters data based on the Lakedata Table and other Metadata. To see with data fits please use the ShowMetaDataFilters function.
#'@param data List of data generates by the Multivar function.
#'@param NAignore If TRUE, value that are NA don't get filtered.
#'@param Filter1
#'\cr\cr name = name of the metadata. Get this from the function ShowMetaDataFilters.
#'\cr\cr criteria = Can be "greater","smaller","TRUE" or"FALSE".
#'\cr\cr value = The filter value when greater or smaller.
#'@param Filter2 Values for Filter 2.
#'@param Filter3 Values for Filter 3.
#'@param Filter4 Values for Filter 4.
#'@param Filter5 Values for Filter 5.
#'@export
#'@return .Returns the same List but with filtert parameters
#'@author Tim Kroeger
#'@note This function has only been developed for the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research and should therefore only be used in combination with their database.
#'\cr Comma numbers are rounded up.
MetadataFilter = function(data,
NAignore = TRUE,
Filter1=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL),
Filter2=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL),
Filter3=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL),
Filter4=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL),
Filter5=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL)){
MetadataNames = data$Description[[1]][,1]
MetaDataTable = matrix(NA,ncol = length(MetadataNames), nrow = length(ls(data$Description)))
colnames(MetaDataTable) = MetadataNames
for(i in 1:length(ls(data$Description))){
MetaDataTable[i,] = data$Description[[i]][,2]
}
row.names(MetaDataTable) = MetaDataTable[,which(colnames(MetaDataTable)=="Unique CoreID")]
MetaDataList = list()
for(i in 1:dim(MetaDataTable)[2]){
if(sum(!check.numeric(na.omit(MetaDataTable[,i])))==0){
SingleMetavalue = as.numeric(MetaDataTable[,i])
names(SingleMetavalue) = MetaDataTable[,which(colnames(MetaDataTable)=="Unique CoreID")]
MetaDataList[[MetadataNames[i]]] = SingleMetavalue
}else if(sum(is.na(as.logical(na.omit(MetaDataTable[,i]))))==0){
SingleMetavalue = as.logical(MetaDataTable[,i])
names(SingleMetavalue) = MetaDataTable[,which(colnames(MetaDataTable)=="Unique CoreID")]
MetaDataList[[MetadataNames[i]]] = SingleMetavalue
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter1
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter1
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter2
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter2
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter3
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter3
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter4
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter4
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter5
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter5
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
#Filter Code name and exact name
##############################################################################
DataWasFilterd = FALSE
#Create filterDiscriptionDocument
filterDiscriptionDocument = matrix(NA, nrow = 1, ncol = 3);
filterDiscriptionDocument[,1:3] = c("name","criteria","value")
if(!Filter1["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter1)==2){Filter1 = c(Filter1,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter1)
}
if(!Filter2["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter2)==2){Filter2 = c(Filter2,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter2)
}
if(!Filter3["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter3)==2){Filter3 = c(Filter3,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter3)
}
if(!Filter4["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter4)==2){Filter4 = c(Filter4,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter4)
}
if(!Filter5["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter5)==2){Filter5 = c(Filter5,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter5)
}
if(DataWasFilterd){
#GetFilterKey
FilterKey = ""
for (i in 2:dim(filterDiscriptionDocument)[1]){
for (k in 1:dim(filterDiscriptionDocument)[2]){
FilterKey = c(FilterKey,substr(filterDiscriptionDocument[i,k], 0, 2))
}
}
#Delete the first underscor
FilterKey = FilterKey[-1]
FilterKey = paste(FilterKey, collapse = "_")
data[["Filter"]] = FilterKey
data[["FilterList"]] = filterDiscriptionDocument
}
return(data)
}
TimKroeger13/ProjectMultiLake documentation built on March 18, 2022, 2:22 p.m.
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Defines functions MetadataFilter
Documented in MetadataFilter
#'MetadataFilter
#'@description
#'Filters data based on the Lakedata Table and other Metadata. To see with data fits please use the ShowMetaDataFilters function.
#'@param data List of data generates by the Multivar function.
#'@param NAignore If TRUE, value that are NA don't get filtered.
#'@param Filter1
#'\cr\cr name = name of the metadata. Get this from the function ShowMetaDataFilters.
#'\cr\cr criteria = Can be "greater","smaller","TRUE" or"FALSE".
#'\cr\cr value = The filter value when greater or smaller.
#'@param Filter2 Values for Filter 2.
#'@param Filter3 Values for Filter 3.
#'@param Filter4 Values for Filter 4.
#'@param Filter5 Values for Filter 5.
#'@export
#'@return .Returns the same List but with filtert parameters
#'@author Tim Kroeger
#'@note This function has only been developed for the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research and should therefore only be used in combination with their database.
#'\cr Comma numbers are rounded up.
MetadataFilter = function(data,
NAignore = TRUE,
Filter1=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL),
Filter2=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL),
Filter3=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL),
Filter4=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL),
Filter5=c(name = "metdataName", criteria = c("greater","smaller","TRUE","FALSE"), value = NULL)){
MetadataNames = data$Description[[1]][,1]
MetaDataTable = matrix(NA,ncol = length(MetadataNames), nrow = length(ls(data$Description)))
colnames(MetaDataTable) = MetadataNames
for(i in 1:length(ls(data$Description))){
MetaDataTable[i,] = data$Description[[i]][,2]
}
row.names(MetaDataTable) = MetaDataTable[,which(colnames(MetaDataTable)=="Unique CoreID")]
MetaDataList = list()
for(i in 1:dim(MetaDataTable)[2]){
if(sum(!check.numeric(na.omit(MetaDataTable[,i])))==0){
SingleMetavalue = as.numeric(MetaDataTable[,i])
names(SingleMetavalue) = MetaDataTable[,which(colnames(MetaDataTable)=="Unique CoreID")]
MetaDataList[[MetadataNames[i]]] = SingleMetavalue
}else if(sum(is.na(as.logical(na.omit(MetaDataTable[,i]))))==0){
SingleMetavalue = as.logical(MetaDataTable[,i])
names(SingleMetavalue) = MetaDataTable[,which(colnames(MetaDataTable)=="Unique CoreID")]
MetaDataList[[MetadataNames[i]]] = SingleMetavalue
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter1
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter1
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter2
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter2
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter3
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter3
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter4
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter4
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
##############################################################################
##############################################################################
#Filter5
##############################################################################
##############################################################################
##############################################################################
TempFilter = Filter5
if(!TempFilter["name"]=="metdataName"){
if(!is.na(TempFilter["criteria"])){
if(TempFilter["criteria"]=="greater" || TempFilter["criteria"]=="smaller" || TempFilter["criteria"]=="TRUE" || TempFilter["criteria"]=="FALSE"){
if(sum(ls(MetaDataList)==TempFilter["name"])>0){
#Diatom
TempdataDiatom=data[["Diatom"]]
AllDiatomsNames = ls(TempdataDiatom)
counter=0
for (d in 1:length(TempdataDiatom)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataDiatom = TempdataDiatom[-counter]
counter = counter-1
}
}
}
}
data[["Diatom"]] = TempdataDiatom
#Carbon
TempdataCarbon=data[["Carbon"]]
AllDiatomsNames = ls(TempdataCarbon)
counter=0
for (d in 1:length(TempdataCarbon)){
counter=counter+1
DiatomsNames = AllDiatomsNames[d]
KeyValue = MetaDataList[[TempFilter[["name"]]]][which(names(MetaDataList[[TempFilter[["name"]]]]) == DiatomsNames)]
if(is.na(KeyValue)){
if(NAignore==TRUE){
}else{
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}else{
if(TempFilter["criteria"]=="greater"){
if(KeyValue<=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="smaller"){
if(KeyValue>=as.numeric(TempFilter["value"])){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="TRUE"){
if(KeyValue==FALSE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
if(TempFilter["criteria"]=="FALSE"){
if(KeyValue==TRUE){
TempdataCarbon = TempdataCarbon[-counter]
counter = counter-1
}
}
}
}
data[["Carbon"]] = TempdataCarbon
}else{
stop(paste("No value with the name '",TempFilter["name"],"' found",sep = ""))
}
}else{
stop(paste("No criteria with the name 'greater' or 'smaller' found",sep = ""))
}
}else{
stop(paste("Please enter a criteria",sep = ""))
}
}
##############################################################################
#Filter Code name and exact name
##############################################################################
DataWasFilterd = FALSE
#Create filterDiscriptionDocument
filterDiscriptionDocument = matrix(NA, nrow = 1, ncol = 3);
filterDiscriptionDocument[,1:3] = c("name","criteria","value")
if(!Filter1["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter1)==2){Filter1 = c(Filter1,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter1)
}
if(!Filter2["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter2)==2){Filter2 = c(Filter2,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter2)
}
if(!Filter3["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter3)==2){Filter3 = c(Filter3,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter3)
}
if(!Filter4["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter4)==2){Filter4 = c(Filter4,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter4)
}
if(!Filter5["name"]=="metdataName"){
DataWasFilterd = TRUE
if(length(Filter5)==2){Filter5 = c(Filter5,"NA")}
filterDiscriptionDocument = rbind(filterDiscriptionDocument,Filter5)
}
if(DataWasFilterd){
#GetFilterKey
FilterKey = ""
for (i in 2:dim(filterDiscriptionDocument)[1]){
for (k in 1:dim(filterDiscriptionDocument)[2]){
FilterKey = c(FilterKey,substr(filterDiscriptionDocument[i,k], 0, 2))
}
}
#Delete the first underscor
FilterKey = FilterKey[-1]
FilterKey = paste(FilterKey, collapse = "_")
data[["Filter"]] = FilterKey
data[["FilterList"]] = filterDiscriptionDocument
}
return(data)
}
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