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R/check_raising_OLD.r
In RoME: Multiple Checks on MEDITS Trawl Survey Data
# ############################################################################################################################
# # RoME: R code to perform multiple checks on MEDITS Survey data (TA, TB, TC and TE files) #
# # Authors: I. Bitetto, W. Zupa, M.T. Spedicato #
# # Coispa Tecnologia & Ricerca - Stazione sperimentale per lo Studio delle Risorse del Mare #
# # If you have any comments or suggestions please contact the following e-mail address: bitetto@coispa.it, zupa@coispa.it #
# # January 2022 #
# ############################################################################################################################
# # Check if, in case of sub-sampling in TC, the number per sex in TB is raised correctly
# if (FALSE){
# ResultDataTB = tb # RoME::TB
# ResultDataTC = tc # RoME::TC
# year=2015
# wd <- "D:\\Documents and Settings\\Utente\\Documenti\\GitHub\\RoME_appoggio\\temp" # tempdir()
# suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
# check_raising(ResultDataTB,ResultDataTC,year,wd,suffix)
# }
#
#
# check_raising_OLD<-function(ResultDataTB,ResultDataTC,year,wd,suffix){
# Format="from_2012"
#
# if (!file.exists(file.path(wd, "Logfiles"))){
# dir.create(file.path(wd, "Logfiles"), recursive = TRUE, showWarnings = FALSE)
# }
# if (!file.exists(file.path(wd,"Graphs"))){
# dir.create(file.path(wd, "Graphs"), showWarnings = FALSE)
# }
# if (!exists("suffix")){
# suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
# }
# numberError = 0
# Errors <- file.path(wd,"Logfiles",paste("Logfile_",suffix,".dat",sep=""))
# if (!file.exists(Errors)){
# file.create(Errors)
# }
#
# ### FILTERING DATA FOR THE SELECTED YEAR
# arg <- "year"
# if (!exists(arg)) {
# stop(paste0("'", arg, "' argument should be provided"))
# } else if (length(year) != 1) {
# stop(paste0("only one value should be provided for '", arg, "' argument"))
# } else if (is.na(year)) {
# stop(paste0(arg, " argument should be a numeric value"))
# }
# ResultDataTB <- ResultDataTB[ResultDataTB$YEAR == year, ]
# ResultDataTC <- ResultDataTC[ResultDataTC$YEAR == year, ]
# ########################################
#
# ResultTC = ResultDataTC
# write(paste("\n----------- check correctness of the number per sex in TB in case of sub-sampling in TC - ",ResultTC$YEAR[1]), file = Errors, append = TRUE)
#
# ResultTB = ResultDataTB
#
# ResultTB= ResultTB[,which(names(ResultTB)=="YEAR" | names(ResultTB)=="COUNTRY" | names(ResultTB)=="HAUL_NUMBER" | names(ResultTB)=="GENUS" | names(ResultTB)=="SPECIES" | names(ResultTB)=="TOTAL_WEIGHT_IN_THE_HAUL" | names(ResultTB)=="TOTAL_NUMBER_IN_THE_HAUL" | names(ResultTB)=="NB_OF_FEMALES" | names(ResultTB)=="NB_OF_MALES" | names(ResultTB)=="NB_OF_UNDETERMINED")]
#
# class(ResultTC$WEIGHT_OF_THE_FRACTION)="numeric"
#
# class(ResultTC$WEIGHT_OF_THE_SAMPLE_MEASURED)="numeric"
#
# ResultTCpivot=aggregate(ResultTC$NUMBER_OF_INDIVIDUALS_IN_THE_LENGTH_CLASS_AND_MATURITY_STAGE, by=list(ResultTC$COUNTRY, ResultTC$YEAR,ResultTC$HAUL_NUMBER,ResultTC$GENUS,ResultTC$SPECIES,as.numeric(as.character(ResultTC$WEIGHT_OF_THE_FRACTION)), as.numeric(as.character(ResultTC$WEIGHT_OF_THE_SAMPLE_MEASURED))),FUN="sum")
# colnames(ResultTCpivot)=c("COUNTRY","YEAR", "HAUL_NUMBER", "GENUS", "SPECIES","WEIGHT_OF_THE_FRACTION", "WEIGHT_OF_THE_SAMPLE_MEASURED","Sum")
#
# # check consistency between WEIGHT_OF_THE_FRACTION in TC and TOTAL_WEIGHT_IN_HAUL in TB
#
# if ( (nrow(ResultTB)!=0)){
# k=1
# for (k in 1:nrow(ResultTB)){
# foundSpec = ResultTCpivot[as.character(ResultTCpivot$COUNTRY)==as.character(ResultTB$COUNTRY[k])
# & as.character(ResultTCpivot$GENUS)==as.character(ResultTB$GENUS[k])
# & as.character(ResultTCpivot$SPECIES)==as.character(ResultTB$SPECIES[k])
# & as.numeric(ResultTCpivot$HAUL_NUMBER)==as.numeric(ResultTB$HAUL_NUMBER[k]),]
# if (nrow(foundSpec) > 1) {
# if (ResultTB[k,"TOTAL_WEIGHT_IN_THE_HAUL"]!= sum(foundSpec$WEIGHT_OF_THE_FRACTION) ){
# write(paste("Haul",ResultTB$HAUL_NUMBER[k],ResultTB$GENUS[k], ResultTB$SPECIES[k], "WEIGHT_OF_THE_FRACTION in TC is not consistent with TOTAL_WEIGHT_IN_HAUL in TB."), file = Errors, append = TRUE)
# numberError = numberError+1
# } }
# }
# }
#
#
#
#
# # check sum per sex
#
# #queryTCpivotSex = paste("SELECT YEAR, HAUL_NUMBER, GENUS, SPECIES, SEX, SUM(NUMBER_OF_INDIVIDUALS_IN_THE_LENGTH_CLASS_AND_MATURITY_STAGE) AS SumSex, WEIGHT_OF_THE_FRACTION, WEIGHT_OF_THE_SAMPLE_MEASURED from ResultTC where HAUL_NUMBER is not NULL group by YEAR, HAUL_NUMBER, GENUS, SPECIES, SEX, WEIGHT_OF_THE_FRACTION, WEIGHT_OF_THE_SAMPLE_MEASURED", sep="" )
# ResultTCpivotSex=aggregate(ResultTC$NUMBER_OF_INDIVIDUALS_IN_THE_LENGTH_CLASS_AND_MATURITY_STAGE, by=list(ResultTC$COUNTRY, ResultTC$YEAR,ResultTC$HAUL_NUMBER,ResultTC$GENUS,ResultTC$SPECIES,ResultTC$SEX,as.numeric(as.character(ResultTC$WEIGHT_OF_THE_FRACTION)), as.numeric(as.character(ResultTC$WEIGHT_OF_THE_SAMPLE_MEASURED))),FUN="sum")
# colnames(ResultTCpivotSex)=c("COUNTRY","YEAR", "HAUL_NUMBER", "GENUS", "SPECIES","SEX","WEIGHT_OF_THE_FRACTION", "WEIGHT_OF_THE_SAMPLE_MEASURED","SumSex")
#
# #ResultTCpivotSex=sqldf(queryTCpivotSex)
# #odbcClose(channelTC)
#
# ResultTCpivotSex$codedsex = ifelse(((as.character(ResultTCpivotSex$SEX)=="I") | (as.character(ResultTCpivotSex$SEX)=="N")), "I", as.character(ResultTCpivotSex$SEX))
#
#
# #write.table(ResultTCpivotSex,file="ResultTCpivotSex.csv",col.names=TRUE)
# #ResultTCpivotSexFile=read.csv("ResultTCpivotSex.csv", header=TRUE)
#
#
# #queryTCpivotSex = paste("SELECT YEAR, HAUL_NUMBER, GENUS, SPECIES, codedsex, SUM(SumSex) AS SumSexTotal, WEIGHT_OF_THE_FRACTION, WEIGHT_OF_THE_SAMPLE_MEASURED from ResultTCpivotSex where HAUL_NUMBER is not NULL ", "group by YEAR, HAUL_NUMBER, GENUS, SPECIES, codedsex, WEIGHT_OF_THE_FRACTION, WEIGHT_OF_THE_SAMPLE_MEASURED", sep="" )
#
# #ResultTCpivotSex=sqldf(queryTCpivotSex)
#
# ResultTCpivotSex=aggregate(ResultTCpivotSex$SumSex, by=list(ResultTCpivotSex$COUNTRY,ResultTCpivotSex$YEAR,ResultTCpivotSex$HAUL_NUMBER,ResultTCpivotSex$GENUS,ResultTCpivotSex$SPECIES,ResultTCpivotSex$codedsex,as.numeric(as.character(ResultTCpivotSex$WEIGHT_OF_THE_FRACTION)), as.numeric(as.character(ResultTCpivotSex$WEIGHT_OF_THE_SAMPLE_MEASURED))),FUN="sum")
# colnames(ResultTCpivotSex)=c("COUNTRY","YEAR", "HAUL_NUMBER", "GENUS", "SPECIES","SEX","WEIGHT_OF_THE_FRACTION", "WEIGHT_OF_THE_SAMPLE_MEASURED","SumSexTotal")
#
#
# #odbcClose(channel)
# #unlink(ResultTCpivotSexFile)
#
# ResultTCpivotSex[ResultTCpivotSex$WEIGHT_OF_THE_SAMPLE_MEASURED==0,"WEIGHT_OF_THE_SAMPLE_MEASURED"] <- 0.0000000000000001
# molt= as.numeric(as.character(ResultTCpivotSex$WEIGHT_OF_THE_FRACTION))/ as.numeric(as.character(ResultTCpivotSex$WEIGHT_OF_THE_SAMPLE_MEASURED))
#
# ResultTCpivotSex$raising=ResultTCpivotSex$SumSexTotal * molt
#
# #write.xlsx(ResultTCpivotSex,file="ResultTCpivotSex.xls",colNames=TRUE)
# # write.csv(ResultTCpivotSex,file="ResultTCpivotSex.csv",col.names=TRUE)
# # write.table(ResultTCpivotSex,file="ResultTCpivotSex.csv",col.names=TRUE)
# #ResultTCpivotSexFile="ResultTCpivotSex.csv"
# #channel <- odbcConnectExcel(ResultTCpivotSexFile)
# #queryTCpivotSex = paste("SELECT YEAR, HAUL_NUMBER, GENUS, SPECIES, codedsex, SUM(raising) AS Sum from ResultTCpivotSex where HAUL_NUMBER is not NULL ", "group by YEAR, HAUL_NUMBER, GENUS, SPECIES, codedsex", sep="" )
# #ResultTCpivotSex=sqldf(queryTCpivotSex)
#
# ResultTCpivotSex=aggregate(ResultTCpivotSex$raising, by=list(ResultTCpivotSex$COUNTRY,ResultTCpivotSex$YEAR,ResultTCpivotSex$HAUL_NUMBER,ResultTCpivotSex$GENUS,ResultTCpivotSex$SPECIES,ResultTCpivotSex$SEX),FUN="sum")
# colnames(ResultTCpivotSex)=c("COUNTRY","YEAR", "HAUL_NUMBER", "GENUS", "SPECIES","SEX","Sum")
#
#
# #odbcClose(channel)
# #unlink(ResultTCpivotSexFile)
#
# if ( (nrow(ResultTCpivotSex)!=0) & (numberError== 0)){
# j=17
# for (j in 1:nrow(ResultTCpivotSex)){
#
# oneRowTB = ResultTB[as.character(ResultTB$COUNTRY)==as.character(ResultTCpivotSex$COUNTRY[j])
# & as.character(ResultTB$GENUS)==as.character(ResultTCpivotSex$GENUS[j])
# & as.character(ResultTB$SPECIES)==as.character(ResultTCpivotSex$SPECIES[j])
# & as.numeric(ResultTB$HAUL_NUMBER)==as.numeric(ResultTCpivotSex$HAUL_NUMBER[j]),]
#
# TotalNumberTBSex=NA
#
# if (nrow(oneRowTB)!=0) {
# if (as.character(ResultTCpivotSex$SEX[j])=="F") {
# TotalNumberTBSex = ifelse(Format=="before_2012",oneRowTB$NUMBER_OF_FEMALES[1],oneRowTB$NB_OF_FEMALES[1])
# } else if (as.character(ResultTCpivotSex$SEX[j])=="M") {
# TotalNumberTBSex = ifelse(Format=="before_2012",oneRowTB$NUMBER_OF_MALES[1],oneRowTB$NB_OF_MALES[1])
# } else {
# TotalNumberTBSex = ifelse(Format=="before_2012",oneRowTB$NUMBER_OF_UNDETERMINED[1],oneRowTB$NB_OF_UNDETERMINED[1])
# }
#
#
# if ((round(ResultTCpivotSex$Sum[j],0))!= round(TotalNumberTBSex,0)) {
# numberError = numberError+1
#
# if (as.character(ResultTCpivotSex$SEX[j])=="F") {
# labelsex= "FEMALES"
# } else if (as.character(ResultTCpivotSex$SEX[j])=="M") {
# labelsex = "MALES"
# } else {
# labelsex = "UNDETERMINED"
# }
# write(paste("Haul ",ResultTCpivotSex$HAUL_NUMBER[j], " ",ResultTCpivotSex$COUNTRY[j], " ", ResultTCpivotSex$GENUS[j], " ", ResultTCpivotSex$SPECIES[j], " NUMBER_OF_", labelsex, " in TB (", round(TotalNumberTBSex,0),") not consistent with the sum of individuals raised per sex (",round(ResultTCpivotSex$Sum[j],0) ,") in TC", sep=""), file = Errors, append = TRUE)
# }
#
# } else {
# write(paste("Haul ",ResultTCpivotSex$HAUL_NUMBER[j], " ",ResultTCpivotSex$COUNTRY[j], " ", ResultTCpivotSex$GENUS[j], " ", ResultTCpivotSex$SPECIES[j], ": number of individuals in TB (", round(TotalNumberTBSex,0),") not consistent with the sum of individuals raised per sex (",round(ResultTCpivotSex$Sum[j],0) ,") in TC", sep=""), file = Errors, append = TRUE)
# numberError = numberError+1
# }
#
# }
# } else {
# write(paste("Found errors in TC! Check raising not executed"), file = Errors, append = TRUE)
# }
#
# if (numberError ==0) {
# write(paste("No error occurred"), file = Errors, append = TRUE)
# }
#
# # if (file.exists(file.path(tempdir(), "Logfiles"))){
# # unlink(file.path(tempdir(),"Logfiles"),recursive=T)
# # }
# # if (file.exists(file.path(tempdir(), "Graphs"))){
# # unlink(file.path(tempdir(),"Graphs"),recursive=T)
# # }
# # if (file.exists(file.path(tempdir(), "files R-Sufi"))){
# # unlink(file.path(tempdir(),"files R-Sufi"),recursive=T)
# # }
#
# if (numberError ==0) {
# return(TRUE)
# } else { return(FALSE) }
#
# }
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# ############################################################################################################################
# # RoME: R code to perform multiple checks on MEDITS Survey data (TA, TB, TC and TE files) #
# # Authors: I. Bitetto, W. Zupa, M.T. Spedicato #
# # Coispa Tecnologia & Ricerca - Stazione sperimentale per lo Studio delle Risorse del Mare #
# # If you have any comments or suggestions please contact the following e-mail address: bitetto@coispa.it, zupa@coispa.it #
# # January 2022 #
# ############################################################################################################################
# # Check if, in case of sub-sampling in TC, the number per sex in TB is raised correctly
# if (FALSE){
# ResultDataTB = tb # RoME::TB
# ResultDataTC = tc # RoME::TC
# year=2015
# wd <- "D:\\Documents and Settings\\Utente\\Documenti\\GitHub\\RoME_appoggio\\temp" # tempdir()
# suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
# check_raising(ResultDataTB,ResultDataTC,year,wd,suffix)
# }
#
#
# check_raising_OLD<-function(ResultDataTB,ResultDataTC,year,wd,suffix){
# Format="from_2012"
#
# if (!file.exists(file.path(wd, "Logfiles"))){
# dir.create(file.path(wd, "Logfiles"), recursive = TRUE, showWarnings = FALSE)
# }
# if (!file.exists(file.path(wd,"Graphs"))){
# dir.create(file.path(wd, "Graphs"), showWarnings = FALSE)
# }
# if (!exists("suffix")){
# suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
# }
# numberError = 0
# Errors <- file.path(wd,"Logfiles",paste("Logfile_",suffix,".dat",sep=""))
# if (!file.exists(Errors)){
# file.create(Errors)
# }
#
# ### FILTERING DATA FOR THE SELECTED YEAR
# arg <- "year"
# if (!exists(arg)) {
# stop(paste0("'", arg, "' argument should be provided"))
# } else if (length(year) != 1) {
# stop(paste0("only one value should be provided for '", arg, "' argument"))
# } else if (is.na(year)) {
# stop(paste0(arg, " argument should be a numeric value"))
# }
# ResultDataTB <- ResultDataTB[ResultDataTB$YEAR == year, ]
# ResultDataTC <- ResultDataTC[ResultDataTC$YEAR == year, ]
# ########################################
#
# ResultTC = ResultDataTC
# write(paste("\n----------- check correctness of the number per sex in TB in case of sub-sampling in TC - ",ResultTC$YEAR[1]), file = Errors, append = TRUE)
#
# ResultTB = ResultDataTB
#
# ResultTB= ResultTB[,which(names(ResultTB)=="YEAR" | names(ResultTB)=="COUNTRY" | names(ResultTB)=="HAUL_NUMBER" | names(ResultTB)=="GENUS" | names(ResultTB)=="SPECIES" | names(ResultTB)=="TOTAL_WEIGHT_IN_THE_HAUL" | names(ResultTB)=="TOTAL_NUMBER_IN_THE_HAUL" | names(ResultTB)=="NB_OF_FEMALES" | names(ResultTB)=="NB_OF_MALES" | names(ResultTB)=="NB_OF_UNDETERMINED")]
#
# class(ResultTC$WEIGHT_OF_THE_FRACTION)="numeric"
#
# class(ResultTC$WEIGHT_OF_THE_SAMPLE_MEASURED)="numeric"
#
# ResultTCpivot=aggregate(ResultTC$NUMBER_OF_INDIVIDUALS_IN_THE_LENGTH_CLASS_AND_MATURITY_STAGE, by=list(ResultTC$COUNTRY, ResultTC$YEAR,ResultTC$HAUL_NUMBER,ResultTC$GENUS,ResultTC$SPECIES,as.numeric(as.character(ResultTC$WEIGHT_OF_THE_FRACTION)), as.numeric(as.character(ResultTC$WEIGHT_OF_THE_SAMPLE_MEASURED))),FUN="sum")
# colnames(ResultTCpivot)=c("COUNTRY","YEAR", "HAUL_NUMBER", "GENUS", "SPECIES","WEIGHT_OF_THE_FRACTION", "WEIGHT_OF_THE_SAMPLE_MEASURED","Sum")
#
# # check consistency between WEIGHT_OF_THE_FRACTION in TC and TOTAL_WEIGHT_IN_HAUL in TB
#
# if ( (nrow(ResultTB)!=0)){
# k=1
# for (k in 1:nrow(ResultTB)){
# foundSpec = ResultTCpivot[as.character(ResultTCpivot$COUNTRY)==as.character(ResultTB$COUNTRY[k])
# & as.character(ResultTCpivot$GENUS)==as.character(ResultTB$GENUS[k])
# & as.character(ResultTCpivot$SPECIES)==as.character(ResultTB$SPECIES[k])
# & as.numeric(ResultTCpivot$HAUL_NUMBER)==as.numeric(ResultTB$HAUL_NUMBER[k]),]
# if (nrow(foundSpec) > 1) {
# if (ResultTB[k,"TOTAL_WEIGHT_IN_THE_HAUL"]!= sum(foundSpec$WEIGHT_OF_THE_FRACTION) ){
# write(paste("Haul",ResultTB$HAUL_NUMBER[k],ResultTB$GENUS[k], ResultTB$SPECIES[k], "WEIGHT_OF_THE_FRACTION in TC is not consistent with TOTAL_WEIGHT_IN_HAUL in TB."), file = Errors, append = TRUE)
# numberError = numberError+1
# } }
# }
# }
#
#
#
#
# # check sum per sex
#
# #queryTCpivotSex = paste("SELECT YEAR, HAUL_NUMBER, GENUS, SPECIES, SEX, SUM(NUMBER_OF_INDIVIDUALS_IN_THE_LENGTH_CLASS_AND_MATURITY_STAGE) AS SumSex, WEIGHT_OF_THE_FRACTION, WEIGHT_OF_THE_SAMPLE_MEASURED from ResultTC where HAUL_NUMBER is not NULL group by YEAR, HAUL_NUMBER, GENUS, SPECIES, SEX, WEIGHT_OF_THE_FRACTION, WEIGHT_OF_THE_SAMPLE_MEASURED", sep="" )
# ResultTCpivotSex=aggregate(ResultTC$NUMBER_OF_INDIVIDUALS_IN_THE_LENGTH_CLASS_AND_MATURITY_STAGE, by=list(ResultTC$COUNTRY, ResultTC$YEAR,ResultTC$HAUL_NUMBER,ResultTC$GENUS,ResultTC$SPECIES,ResultTC$SEX,as.numeric(as.character(ResultTC$WEIGHT_OF_THE_FRACTION)), as.numeric(as.character(ResultTC$WEIGHT_OF_THE_SAMPLE_MEASURED))),FUN="sum")
# colnames(ResultTCpivotSex)=c("COUNTRY","YEAR", "HAUL_NUMBER", "GENUS", "SPECIES","SEX","WEIGHT_OF_THE_FRACTION", "WEIGHT_OF_THE_SAMPLE_MEASURED","SumSex")
#
# #ResultTCpivotSex=sqldf(queryTCpivotSex)
# #odbcClose(channelTC)
#
# ResultTCpivotSex$codedsex = ifelse(((as.character(ResultTCpivotSex$SEX)=="I") | (as.character(ResultTCpivotSex$SEX)=="N")), "I", as.character(ResultTCpivotSex$SEX))
#
#
# #write.table(ResultTCpivotSex,file="ResultTCpivotSex.csv",col.names=TRUE)
# #ResultTCpivotSexFile=read.csv("ResultTCpivotSex.csv", header=TRUE)
#
#
# #queryTCpivotSex = paste("SELECT YEAR, HAUL_NUMBER, GENUS, SPECIES, codedsex, SUM(SumSex) AS SumSexTotal, WEIGHT_OF_THE_FRACTION, WEIGHT_OF_THE_SAMPLE_MEASURED from ResultTCpivotSex where HAUL_NUMBER is not NULL ", "group by YEAR, HAUL_NUMBER, GENUS, SPECIES, codedsex, WEIGHT_OF_THE_FRACTION, WEIGHT_OF_THE_SAMPLE_MEASURED", sep="" )
#
# #ResultTCpivotSex=sqldf(queryTCpivotSex)
#
# ResultTCpivotSex=aggregate(ResultTCpivotSex$SumSex, by=list(ResultTCpivotSex$COUNTRY,ResultTCpivotSex$YEAR,ResultTCpivotSex$HAUL_NUMBER,ResultTCpivotSex$GENUS,ResultTCpivotSex$SPECIES,ResultTCpivotSex$codedsex,as.numeric(as.character(ResultTCpivotSex$WEIGHT_OF_THE_FRACTION)), as.numeric(as.character(ResultTCpivotSex$WEIGHT_OF_THE_SAMPLE_MEASURED))),FUN="sum")
# colnames(ResultTCpivotSex)=c("COUNTRY","YEAR", "HAUL_NUMBER", "GENUS", "SPECIES","SEX","WEIGHT_OF_THE_FRACTION", "WEIGHT_OF_THE_SAMPLE_MEASURED","SumSexTotal")
#
#
# #odbcClose(channel)
# #unlink(ResultTCpivotSexFile)
#
# ResultTCpivotSex[ResultTCpivotSex$WEIGHT_OF_THE_SAMPLE_MEASURED==0,"WEIGHT_OF_THE_SAMPLE_MEASURED"] <- 0.0000000000000001
# molt= as.numeric(as.character(ResultTCpivotSex$WEIGHT_OF_THE_FRACTION))/ as.numeric(as.character(ResultTCpivotSex$WEIGHT_OF_THE_SAMPLE_MEASURED))
#
# ResultTCpivotSex$raising=ResultTCpivotSex$SumSexTotal * molt
#
# #write.xlsx(ResultTCpivotSex,file="ResultTCpivotSex.xls",colNames=TRUE)
# # write.csv(ResultTCpivotSex,file="ResultTCpivotSex.csv",col.names=TRUE)
# # write.table(ResultTCpivotSex,file="ResultTCpivotSex.csv",col.names=TRUE)
# #ResultTCpivotSexFile="ResultTCpivotSex.csv"
# #channel <- odbcConnectExcel(ResultTCpivotSexFile)
# #queryTCpivotSex = paste("SELECT YEAR, HAUL_NUMBER, GENUS, SPECIES, codedsex, SUM(raising) AS Sum from ResultTCpivotSex where HAUL_NUMBER is not NULL ", "group by YEAR, HAUL_NUMBER, GENUS, SPECIES, codedsex", sep="" )
# #ResultTCpivotSex=sqldf(queryTCpivotSex)
#
# ResultTCpivotSex=aggregate(ResultTCpivotSex$raising, by=list(ResultTCpivotSex$COUNTRY,ResultTCpivotSex$YEAR,ResultTCpivotSex$HAUL_NUMBER,ResultTCpivotSex$GENUS,ResultTCpivotSex$SPECIES,ResultTCpivotSex$SEX),FUN="sum")
# colnames(ResultTCpivotSex)=c("COUNTRY","YEAR", "HAUL_NUMBER", "GENUS", "SPECIES","SEX","Sum")
#
#
# #odbcClose(channel)
# #unlink(ResultTCpivotSexFile)
#
# if ( (nrow(ResultTCpivotSex)!=0) & (numberError== 0)){
# j=17
# for (j in 1:nrow(ResultTCpivotSex)){
#
# oneRowTB = ResultTB[as.character(ResultTB$COUNTRY)==as.character(ResultTCpivotSex$COUNTRY[j])
# & as.character(ResultTB$GENUS)==as.character(ResultTCpivotSex$GENUS[j])
# & as.character(ResultTB$SPECIES)==as.character(ResultTCpivotSex$SPECIES[j])
# & as.numeric(ResultTB$HAUL_NUMBER)==as.numeric(ResultTCpivotSex$HAUL_NUMBER[j]),]
#
# TotalNumberTBSex=NA
#
# if (nrow(oneRowTB)!=0) {
# if (as.character(ResultTCpivotSex$SEX[j])=="F") {
# TotalNumberTBSex = ifelse(Format=="before_2012",oneRowTB$NUMBER_OF_FEMALES[1],oneRowTB$NB_OF_FEMALES[1])
# } else if (as.character(ResultTCpivotSex$SEX[j])=="M") {
# TotalNumberTBSex = ifelse(Format=="before_2012",oneRowTB$NUMBER_OF_MALES[1],oneRowTB$NB_OF_MALES[1])
# } else {
# TotalNumberTBSex = ifelse(Format=="before_2012",oneRowTB$NUMBER_OF_UNDETERMINED[1],oneRowTB$NB_OF_UNDETERMINED[1])
# }
#
#
# if ((round(ResultTCpivotSex$Sum[j],0))!= round(TotalNumberTBSex,0)) {
# numberError = numberError+1
#
# if (as.character(ResultTCpivotSex$SEX[j])=="F") {
# labelsex= "FEMALES"
# } else if (as.character(ResultTCpivotSex$SEX[j])=="M") {
# labelsex = "MALES"
# } else {
# labelsex = "UNDETERMINED"
# }
# write(paste("Haul ",ResultTCpivotSex$HAUL_NUMBER[j], " ",ResultTCpivotSex$COUNTRY[j], " ", ResultTCpivotSex$GENUS[j], " ", ResultTCpivotSex$SPECIES[j], " NUMBER_OF_", labelsex, " in TB (", round(TotalNumberTBSex,0),") not consistent with the sum of individuals raised per sex (",round(ResultTCpivotSex$Sum[j],0) ,") in TC", sep=""), file = Errors, append = TRUE)
# }
#
# } else {
# write(paste("Haul ",ResultTCpivotSex$HAUL_NUMBER[j], " ",ResultTCpivotSex$COUNTRY[j], " ", ResultTCpivotSex$GENUS[j], " ", ResultTCpivotSex$SPECIES[j], ": number of individuals in TB (", round(TotalNumberTBSex,0),") not consistent with the sum of individuals raised per sex (",round(ResultTCpivotSex$Sum[j],0) ,") in TC", sep=""), file = Errors, append = TRUE)
# numberError = numberError+1
# }
#
# }
# } else {
# write(paste("Found errors in TC! Check raising not executed"), file = Errors, append = TRUE)
# }
#
# if (numberError ==0) {
# write(paste("No error occurred"), file = Errors, append = TRUE)
# }
#
# # if (file.exists(file.path(tempdir(), "Logfiles"))){
# # unlink(file.path(tempdir(),"Logfiles"),recursive=T)
# # }
# # if (file.exists(file.path(tempdir(), "Graphs"))){
# # unlink(file.path(tempdir(),"Graphs"),recursive=T)
# # }
# # if (file.exists(file.path(tempdir(), "files R-Sufi"))){
# # unlink(file.path(tempdir(),"files R-Sufi"),recursive=T)
# # }
#
# if (numberError ==0) {
# return(TRUE)
# } else { return(FALSE) }
#
# }
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