Nothing
R/check_distance_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 consistency of the hauls coordinates with the distance
#
# if (FALSE){
# #library(MEDITS)
# wd <- tempdir() # "D:\\Documents and Settings\\Utente\\Documenti\\GitHub\\RoME\\temp"
# suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
# DataTA = ta # RoME::TA #read.csv("~/GitHub/RoME/data/TA_GSA18_1994-2018.csv", sep=";")
# year=2015
# #DataTA[1, "SHOOTING_LATITUDE" ] <- 435.11
# check_distance(DataTA,year,wd,suffix)
# }
#
# check_distance<-function(DataTA,year, wd, suffix){
# # oldpar <- par(no.readonly = TRUE)
#
#
# lon <- lat <- NULL
#
# 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)
# }
#
# numberError = 0
# if (!exists("suffix")){
# suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
# }
#
# 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"))
# }
# DataTA <- DataTA[DataTA$YEAR == year, ]
# ########################################
#
# ResultData = DataTA[!is.na(DataTA$DISTANCE),]
# write(paste("\n----------- check consistency of the hauls coordinates with the distance - ", ResultData$YEAR[1]), file = Errors, append = TRUE)
#
#
# ResultData=ResultData[ResultData$VALIDITY=="V",]
# ResultData=MEDITS.to.dd(ResultData)
#
# i=1
# for (i in 1:nrow(ResultData)){
# ResultData$computed_distance[i]= dd.distance(ResultData[i,], unit = "m", verbose=FALSE)
# if (is.nan(ResultData$computed_distance[i])) {
# ResultData$computed_distance[i] = 0
# }
#
# if (ResultData$computed_distance[i]==0 & ResultData$SHOOTING_LATITUDE[i] == ResultData$HAULING_LATITUDE[i]) {
# write(paste("Warning: Haul",ResultData$HAUL_NUMBER[i],": the values of the SHOOTING and HAULING LATITUDE are the same. Please, check the consistency of the latitude values."), file = Errors, append = TRUE)
# }
#
# }
#
# lx = (max(ResultData$SHOOTING_LONGITUDE)+0.1) - (min(ResultData$SHOOTING_LONGITUDE)-0.1)
# ly = (max(ResultData$SHOOTING_LATITUDE)+0.1) - (min(ResultData$SHOOTING_LATITUDE)-0.1)
# ratio <- ly/lx*1.1
#
# img_width <- 12
# img_height <- img_width * ratio
# oldoptions <- options()$warn
# old_par <- list(deleteFile=TRUE)
# old_par <- par()
#
#
#
# if (nrow(ResultData)!=0){
# j=1
# for (j in 1:nrow(ResultData)){
# if ( (ResultData$DISTANCE[j]<=ResultData$computed_distance[j]-0.3*ResultData$computed_distance[j]) | (ResultData$DISTANCE[j]>=ResultData$computed_distance[j]+0.3*ResultData$computed_distance[j])){
# write(paste("Warning: Haul",ResultData$HAUL_NUMBER[j],": the distance in TA ",ResultData$DISTANCE[j],"is quite different from the computed distance",round(ResultData$computed_distance[j],4),"(haul duration:",ResultData$HAUL_DURATION[j],"min)"), file = Errors, append = TRUE)
#
#
# points_start <- data.frame(lon=ResultData[j,"SHOOTING_LONGITUDE"],lat=ResultData[j,"SHOOTING_LATITUDE"], Position ="start")
# points_end <- data.frame(lon=ResultData[j,"HAULING_LONGITUDE"],lat=ResultData[j,"HAULING_LATITUDE"], Position ="end")
# points <- rbind(points_start,points_end)
# world <- ne_countries(scale = "medium", returnclass = "sf")
# class(world)
#
# if (ratio <= 0.5) {
# text_size <- 12
# point_size <- 2
# legend_title_size <- 12
# legend_text_size <- 11
# title_text_size <- 16
# } else if (ratio >= 0.5 & ratio < 2 ) {
# text_size <- 20
# point_size <- 3.5
# legend_title_size <- 18
# legend_text_size <- 18
# title_text_size <- 22
# } else if (ratio >= 2 ) {
# text_size <- 40
# point_size <- 6
# legend_title_size <- 30
# legend_text_size <- 30
# title_text_size <- 40
# }
#
# theme_opts<-list(theme(text = element_text(size=text_size),
# plot.title = element_text(size=title_text_size),
# legend.title = element_text(size = legend_title_size),
# legend.text = element_text(size = legend_text_size),
# panel.background = element_rect(fill = 'light blue',linetype="solid",color="black"),
# panel.grid.major = element_blank(), panel.grid.minor = element_blank()))
#
# suppressMessages (
# ggplot(data=world) +
# geom_sf()+
# coord_sf(crs ="+proj=longlat +ellps=WGS84") +
# geom_point(data=points, aes(lon, lat, fill=Position),shape=21,color="black",size=point_size) +
# coord_sf(xlim = c(min(ResultData$SHOOTING_LONGITUDE)-0.1, max(ResultData$SHOOTING_LONGITUDE)+0.1),
# ylim = c(min(ResultData$SHOOTING_LATITUDE)-0.1, max(ResultData$SHOOTING_LATITUDE)+0.1),crs="+proj=longlat +ellps=WGS84")+
# ggtitle(paste("Haul",ResultData[j,"HAUL_NUMBER"],"-",ResultData[j,"YEAR"])) +
# theme_opts +
# scale_fill_manual(values=c("green", "blue"))
# )
#
#
# # tiff(file.path(wd,"Graphs",paste("haul ", ResultData[j,"HAUL_NUMBER"], " AREA ",ResultData[1,"AREA"],"_",ResultData[1,"YEAR"],".tiff",sep="")),
# # width=img_width, height=img_height,
# # bg="white", units="in", res=300,pointsize = 1/300, compression = "lzw")
# # print(p)
# ggsave(file.path(wd,"Graphs",paste("haul ", ResultData[j,"HAUL_NUMBER"], " AREA ",ResultData[1,"AREA"],"_",ResultData[1,"YEAR"],".jpeg",sep="")),width=img_width, height=img_height,dpi = 300, units="in")
# # dev.off()
#
# }
# }
# }
#
# write("Some of the hauls coordinates may be inconsistent with the computed distance. For a visual check, look at the jpeg files in Graphs directory",file = Errors, append = TRUE)
# write(paste("No error occurred"), file = Errors, append = TRUE)
#
# # on.exit(suppressWarnings(par(oldpar)))
# on.exit(c(par(mfrow=old_par$mfrow,mar=old_par$mar,fin=old_par$fin,mai=old_par$mai,omi=old_par$omi),options(warn=oldoptions))) # , unlink(paste0(normalizePath(tempdir()), "/", dir(tempdir())), recursive = TRUE)
# options(warn=-1)
#
# # 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)
# # }
#
# dev.off()
# #unlink(old_par)
# # unlink(file.path(tempdir(),list.files(file.path(tempdir()))),recursive=T)
#
# # if (file.exists(file.path(tempdir()))){
# # wd <- getwd()
# # dirl <- list.dirs(path = tempdir(), full.names = TRUE, recursive = TRUE)
# # i=1
# # for (i in 1:length(dirl)){
# # setwd(dirl[i])
# #
# # unlink(paste0(normalizePath(tempdir()), "/", dir(tempdir())), recursive = TRUE)
# # }
# # if (file.exists(file.path(tempdir()))){
# # dirl <- list.dirs(path = tempdir(), full.names = TRUE, recursive = TRUE)
# # i=1
# # for (i in 1:length(dirl)){
# # setwd(dirl[i])
# # unlink(paste0(normalizePath(tempdir()), "/", dir(tempdir())), recursive = TRUE)
# # }
# #
# # setwd (wd)
# # }
# # }
#
# return(TRUE)
#
# }
# ################################################################################
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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 consistency of the hauls coordinates with the distance
#
# if (FALSE){
# #library(MEDITS)
# wd <- tempdir() # "D:\\Documents and Settings\\Utente\\Documenti\\GitHub\\RoME\\temp"
# suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
# DataTA = ta # RoME::TA #read.csv("~/GitHub/RoME/data/TA_GSA18_1994-2018.csv", sep=";")
# year=2015
# #DataTA[1, "SHOOTING_LATITUDE" ] <- 435.11
# check_distance(DataTA,year,wd,suffix)
# }
#
# check_distance<-function(DataTA,year, wd, suffix){
# # oldpar <- par(no.readonly = TRUE)
#
#
# lon <- lat <- NULL
#
# 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)
# }
#
# numberError = 0
# if (!exists("suffix")){
# suffix=paste(as.character(Sys.Date()),format(Sys.time(), "_time_h%Hm%Ms%OS0"),sep="")
# }
#
# 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"))
# }
# DataTA <- DataTA[DataTA$YEAR == year, ]
# ########################################
#
# ResultData = DataTA[!is.na(DataTA$DISTANCE),]
# write(paste("\n----------- check consistency of the hauls coordinates with the distance - ", ResultData$YEAR[1]), file = Errors, append = TRUE)
#
#
# ResultData=ResultData[ResultData$VALIDITY=="V",]
# ResultData=MEDITS.to.dd(ResultData)
#
# i=1
# for (i in 1:nrow(ResultData)){
# ResultData$computed_distance[i]= dd.distance(ResultData[i,], unit = "m", verbose=FALSE)
# if (is.nan(ResultData$computed_distance[i])) {
# ResultData$computed_distance[i] = 0
# }
#
# if (ResultData$computed_distance[i]==0 & ResultData$SHOOTING_LATITUDE[i] == ResultData$HAULING_LATITUDE[i]) {
# write(paste("Warning: Haul",ResultData$HAUL_NUMBER[i],": the values of the SHOOTING and HAULING LATITUDE are the same. Please, check the consistency of the latitude values."), file = Errors, append = TRUE)
# }
#
# }
#
# lx = (max(ResultData$SHOOTING_LONGITUDE)+0.1) - (min(ResultData$SHOOTING_LONGITUDE)-0.1)
# ly = (max(ResultData$SHOOTING_LATITUDE)+0.1) - (min(ResultData$SHOOTING_LATITUDE)-0.1)
# ratio <- ly/lx*1.1
#
# img_width <- 12
# img_height <- img_width * ratio
# oldoptions <- options()$warn
# old_par <- list(deleteFile=TRUE)
# old_par <- par()
#
#
#
# if (nrow(ResultData)!=0){
# j=1
# for (j in 1:nrow(ResultData)){
# if ( (ResultData$DISTANCE[j]<=ResultData$computed_distance[j]-0.3*ResultData$computed_distance[j]) | (ResultData$DISTANCE[j]>=ResultData$computed_distance[j]+0.3*ResultData$computed_distance[j])){
# write(paste("Warning: Haul",ResultData$HAUL_NUMBER[j],": the distance in TA ",ResultData$DISTANCE[j],"is quite different from the computed distance",round(ResultData$computed_distance[j],4),"(haul duration:",ResultData$HAUL_DURATION[j],"min)"), file = Errors, append = TRUE)
#
#
# points_start <- data.frame(lon=ResultData[j,"SHOOTING_LONGITUDE"],lat=ResultData[j,"SHOOTING_LATITUDE"], Position ="start")
# points_end <- data.frame(lon=ResultData[j,"HAULING_LONGITUDE"],lat=ResultData[j,"HAULING_LATITUDE"], Position ="end")
# points <- rbind(points_start,points_end)
# world <- ne_countries(scale = "medium", returnclass = "sf")
# class(world)
#
# if (ratio <= 0.5) {
# text_size <- 12
# point_size <- 2
# legend_title_size <- 12
# legend_text_size <- 11
# title_text_size <- 16
# } else if (ratio >= 0.5 & ratio < 2 ) {
# text_size <- 20
# point_size <- 3.5
# legend_title_size <- 18
# legend_text_size <- 18
# title_text_size <- 22
# } else if (ratio >= 2 ) {
# text_size <- 40
# point_size <- 6
# legend_title_size <- 30
# legend_text_size <- 30
# title_text_size <- 40
# }
#
# theme_opts<-list(theme(text = element_text(size=text_size),
# plot.title = element_text(size=title_text_size),
# legend.title = element_text(size = legend_title_size),
# legend.text = element_text(size = legend_text_size),
# panel.background = element_rect(fill = 'light blue',linetype="solid",color="black"),
# panel.grid.major = element_blank(), panel.grid.minor = element_blank()))
#
# suppressMessages (
# ggplot(data=world) +
# geom_sf()+
# coord_sf(crs ="+proj=longlat +ellps=WGS84") +
# geom_point(data=points, aes(lon, lat, fill=Position),shape=21,color="black",size=point_size) +
# coord_sf(xlim = c(min(ResultData$SHOOTING_LONGITUDE)-0.1, max(ResultData$SHOOTING_LONGITUDE)+0.1),
# ylim = c(min(ResultData$SHOOTING_LATITUDE)-0.1, max(ResultData$SHOOTING_LATITUDE)+0.1),crs="+proj=longlat +ellps=WGS84")+
# ggtitle(paste("Haul",ResultData[j,"HAUL_NUMBER"],"-",ResultData[j,"YEAR"])) +
# theme_opts +
# scale_fill_manual(values=c("green", "blue"))
# )
#
#
# # tiff(file.path(wd,"Graphs",paste("haul ", ResultData[j,"HAUL_NUMBER"], " AREA ",ResultData[1,"AREA"],"_",ResultData[1,"YEAR"],".tiff",sep="")),
# # width=img_width, height=img_height,
# # bg="white", units="in", res=300,pointsize = 1/300, compression = "lzw")
# # print(p)
# ggsave(file.path(wd,"Graphs",paste("haul ", ResultData[j,"HAUL_NUMBER"], " AREA ",ResultData[1,"AREA"],"_",ResultData[1,"YEAR"],".jpeg",sep="")),width=img_width, height=img_height,dpi = 300, units="in")
# # dev.off()
#
# }
# }
# }
#
# write("Some of the hauls coordinates may be inconsistent with the computed distance. For a visual check, look at the jpeg files in Graphs directory",file = Errors, append = TRUE)
# write(paste("No error occurred"), file = Errors, append = TRUE)
#
# # on.exit(suppressWarnings(par(oldpar)))
# on.exit(c(par(mfrow=old_par$mfrow,mar=old_par$mar,fin=old_par$fin,mai=old_par$mai,omi=old_par$omi),options(warn=oldoptions))) # , unlink(paste0(normalizePath(tempdir()), "/", dir(tempdir())), recursive = TRUE)
# options(warn=-1)
#
# # 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)
# # }
#
# dev.off()
# #unlink(old_par)
# # unlink(file.path(tempdir(),list.files(file.path(tempdir()))),recursive=T)
#
# # if (file.exists(file.path(tempdir()))){
# # wd <- getwd()
# # dirl <- list.dirs(path = tempdir(), full.names = TRUE, recursive = TRUE)
# # i=1
# # for (i in 1:length(dirl)){
# # setwd(dirl[i])
# #
# # unlink(paste0(normalizePath(tempdir()), "/", dir(tempdir())), recursive = TRUE)
# # }
# # if (file.exists(file.path(tempdir()))){
# # dirl <- list.dirs(path = tempdir(), full.names = TRUE, recursive = TRUE)
# # i=1
# # for (i in 1:length(dirl)){
# # setwd(dirl[i])
# # unlink(paste0(normalizePath(tempdir()), "/", dir(tempdir())), recursive = TRUE)
# # }
# #
# # setwd (wd)
# # }
# # }
#
# return(TRUE)
#
# }
# ################################################################################
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