R/get_fleet.R
In Maritimes/Mar.bycatch: Facilitates Extraction and Linking of Commercial and Observed Fisheries Data for the Maritimes
Defines functions
get_fleet
Documented in
get_fleet
#' @title get_fleet
#' @description This function extracts all of the Vessel/Licence combinations
#' associated with a particular fleet for a particular date range.
#' @param ... other arguments passed to methods
#' @family coreFuncs
#' @return returns a data.frame with the following columns:
#' \itemize{
#' \item \code{MON_DOC_ID}
#' \item \code{GEAR_CODE }
#' \item \code{LICENCE_ID}
#' \item \code{PRO_SPC_INFO_ID}
#' \item \code{LOG_EFRT_STD_INFO_ID }
#' \item \code{T_DATE1}
#' \item \code{T_DATE2}
#' \item \code{MD_CODE}
#' \item \code{VR_NUMBER}
#' }
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
get_fleet<-function(...){
args <-list(...)
if (args$debug) t02 <-Mar.utils::where_now(returnTime = T)
MARFLEETS_LIC <- PRO_SPC_INFO <- TRIPS <- NAFO_UNIT_AREAS <- LOG_EFRT_ENTRD_DETS <- LOG_EFRT_STD_INFO <- GEARS <- NA
theseLics <- NA
for (i in 1:nrow(args$lics)){
thisL <- ifelse(is.na(args$lics$LIC_TYPE[i]),"1==1", paste0("MARFLEETS_LIC$LICENCE_TYPE_ID == ",args$lics$LIC_TYPE[i]))
thisS <- ifelse(is.na(args$lics$LIC_SUBTYPE[i]),"1==1", paste0("MARFLEETS_LIC$LICENCE_SUBTYPE_ID == ",args$lics$LIC_SUBTYPE[i]))
thisSpp <- ifelse(is.na(args$lics$LIC_SP[i]),"1==1", paste0("MARFLEETS_LIC$SPECIES_CODE == ",args$lics$LIC_SP[i]))
thisLicRow <- paste0("(",thisL, " & ",thisS," & ",thisSpp,")")
if (i==1){
theseLics <- thisLicRow
} else {
theseLics <- paste(theseLics, "|", thisLicRow)
}
}
theseLicsOra <- gsub("==", "=", gsub("\\$", "\\.", gsub("&", "AND", gsub("\\|", "OR", theseLics))))
# end -----------------------------------------------------------------------------------------------------------------------------------------------------
# sizeFilt, typeFilt and chk_Gears are used by both the Ora and loc versions of get_fleetGear ------------------------------------------------------------------------
sizeFilt <- function(df=NULL, ...){
args <- list(...)$args
if (args$debug) t03<- Mar.utils::where_now(returnTime = T)
if (!is.na(args$gearSpecs$MIN)){
#for fixed gear (CHPs), we need to keep all gillnet - don't sort as though they were hooks
#fsame for unit2 redfish
if ((args$gearSpecs$FLEET == "CHP" && grepl(pattern = "_FIXED", x = args$gearSpecs$FLEET_GEARSPECS_ID))|
(args$gearSpecs$FLEET == "REDFISH" && grepl(pattern = "UNIT2", x = args$gearSpecs$FLEET_GEARSPECS_ID))){
gn <- df[df$GEAR_CODE == 41,]
df <- df[df$GEAR_CODE != 41,]
}
theseGearSpecRelevant <- df[which(df$GR_SIZE >= args$gearSpecs$MIN &
df$GR_SIZE <= args$gearSpecs$MAX),]
if(args$keepMissingGear){
theseGearSpecUnk <- df[df$GR_SIZE == -999,]
theseGearSpecRelevant <- rbind.data.frame(theseGearSpecRelevant, theseGearSpecUnk)
}
#reattach gillnet to results
if (exists("gn")) theseGearSpecRelevant <- rbind.data.frame(theseGearSpecRelevant, gn)
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = theseGearSpecRelevant$LICENCE_ID, stepDesc = "flt_gearSize")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = theseGearSpecRelevant$VR_NUMBER, stepDesc = "flt_gearSize")
df<- theseGearSpecRelevant
}
if (args$debug) {
t03_ <- proc.time() - t03
message("\tExiting sizeFilt() (",round(t03_[1],0),"s elapsed)")
}
return(df)
}
typeFilt <- function(df=NULL, ...){
args <- list(...)$args
if (args$debug) t04<- Mar.utils::where_now(returnTime = T)
if (!is.na(args$gearSpecs$TYPE)){
#apply the requested filter
#Mesh
# "S" - SQUARE
# "D" - DIAMOND
theseGearSpecRelevant <- df[which(df$GR_TYPE %in% args$gearSpecs$TYPE),]
if(args$keepMissingGear){
theseGearSpecUnk <- df[df$GR_TYPE == "-999",]
theseGearSpecRelevant <- rbind.data.frame(theseGearSpecRelevant, theseGearSpecUnk)
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = theseGearSpecRelevant$LICENCE_ID, stepDesc = "flt_gearTypeFilt")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = theseGearSpecRelevant$VR_NUMBER, stepDesc = "flt_gearTypeFilt")
df<- theseGearSpecRelevant
}
if (args$debug) {
t04_ <- proc.time() - t04
message("\tExiting typeFilt() (",round(t04_[1],0),"s elapsed)")
}
return(df)
}
chk_Gears <- function(df=NULL, ...){
#this function figures out what categories of gears we're dealing with, and will let us determine what filters might be possible
args <- list(...)$args
if (args$debug) t05<- Mar.utils::where_now(returnTime = T)
GEARS<-unique(df$GEAR_CODE)
allGears = tolower(GEARS_MARFIS[GEARS_MARFIS$GEAR_CODE %in% GEARS,"GEAR"])
allGears = allGears[!allGears %in% c("trap net")]
matchTrap=c('trap','pot')
matchMesh=c('trawl','seine','net','midwtr', 'drag')
matchLine=c('line','jig','angli')
theseGears<-NA
if (any(grepl(pattern = paste(matchTrap, collapse = '|'), x= allGears))) theseGears <- c(theseGears,"trap")
if (any(grepl(pattern = paste(matchMesh, collapse = '|'), x= allGears))) theseGears <- c(theseGears,"mesh")
if (any(grepl(pattern = paste(matchLine, collapse = '|'), x= allGears))) theseGears <- c(theseGears,"line")
theseGears <- theseGears[!is.na(theseGears)]
if (length(theseGears)>=1){
gearType <-theseGears
}else{
gearType <- NA
}
grSpType <- NA
grSpSize <- NA
if('mesh' %in% gearType){
grSpType <- c(grSpType,31)
grSpSize <- c(grSpSize, 8,32,62,120,806)
}
if("trap" %in% gearType){
grSpType <- c(grSpType,114)
grSpSize <- c(grSpSize, 152,423,431,701)
}
if("hook" %in% gearType || "line" %in% gearType){
grSpType <- c(grSpType,5)
grSpSize <- c(grSpSize, 4,66,67)
}
if (all(is.na(gearType))) {
if (args$debug) {
t05_ <- proc.time() - t05
message("\tExiting chk_Gears() - all NA: (", round(t05_[1],0),"s elapsed)")
}
return(df)
}
#check if types exist at all for selection
grSpType <- grSpType[!is.na(grSpType)]
#check if sizes exist at all for selection
grSpSize <- grSpSize[!is.na(grSpSize)]
grSpCols <- c(grSpType, grSpSize)
sizeCols <- c(4,8,32,62,66,67,120,806,152,423,431,701)
typeCols <- c(5,31,114)
if(!args$useLocal){
RelevantQry_LE <- paste0("SELECT LOG_EFRT_STD_INFO_ID, COLUMN_DEFN_ID, DATA_VALUE from MARFISSCI.LOG_EFRT_ENTRD_DETS
WHERE
COLUMN_DEFN_ID IN (",Mar.utils::SQL_in(grSpCols,apos=F),")
AND ",Mar.utils::big_in(vec=unique(df$LOG_EFRT_STD_INFO_ID), vec.field="LOG_EFRT_STD_INFO_ID"))
LE_df <- args$cxn$thecmd(args$cxn$channel, RelevantQry_LE)
RelevantQry_MD <- paste0("SELECT MON_DOC_ID, COLUMN_DEFN_ID, DATA_VALUE from MARFISSCI.MON_DOC_ENTRD_DETS
WHERE
COLUMN_DEFN_ID IN (",Mar.utils::SQL_in(grSpCols,apos=F),")
AND ",Mar.utils::big_in(vec=unique(df$MON_DOC_ID), vec.field="MON_DOC_ID"))
MD_df <- args$cxn$thecmd(args$cxn$channel, RelevantQry_MD)
}else{
# Find all of the records that are related to the gear type (e.g. mesh/hook/trap) --------------------------------------------
Mar.utils::get_data_tables(schema = "MARFISSCI", data.dir = args$data.dir, tables = c("LOG_EFRT_ENTRD_DETS", "MON_DOC_ENTRD_DETS"),
usepkg=args$usepkg, fn.oracle.username = args$oracle.username, fn.oracle.dsn=args$oracle.dsn, fn.oracle.password = args$oracle.password,
env = environment(), quietly = TRUE, fuzzyMatch=FALSE)
LE_df <- LOG_EFRT_ENTRD_DETS[which(LOG_EFRT_ENTRD_DETS$LOG_EFRT_STD_INFO_ID %in% df$LOG_EFRT_STD_INFO_ID &
LOG_EFRT_ENTRD_DETS$COLUMN_DEFN_ID %in% grSpCols), c("LOG_EFRT_STD_INFO_ID", "COLUMN_DEFN_ID", "DATA_VALUE") ]
MD_df <- MON_DOC_ENTRD_DETS[which(MON_DOC_ENTRD_DETS$MON_DOC_ID %in% df$MON_DOC_ID &
MON_DOC_ENTRD_DETS$COLUMN_DEFN_ID %in% grSpCols), c("MON_DOC_ID","COLUMN_DEFN_ID", "DATA_VALUE"),]
}
if (nrow(LE_df)>0){
#if need convert units, do now
LE_df$COLUMN_DEFN_ID <- replace(LE_df$COLUMN_DEFN_ID, LE_df$COLUMN_DEFN_ID %in% sizeCols, "GR_SIZE")
LE_df$COLUMN_DEFN_ID <- replace(LE_df$COLUMN_DEFN_ID, LE_df$COLUMN_DEFN_ID %in% typeCols, "GR_TYPE")
LE_df <- reshape2::dcast(LE_df, LOG_EFRT_STD_INFO_ID ~ COLUMN_DEFN_ID, value.var = "DATA_VALUE")
if (!"GR_SIZE" %in% names(LE_df)) {
LE_df$GR_SIZE <- -999
}else{
LE_df$GR_SIZE <- as.numeric(LE_df$GR_SIZE)
}
if (!"GR_TYPE" %in% names(LE_df)) {
LE_df$GR_TYPE <- -999
}else{
LE_df$GR_TYPE <- toupper(LE_df$GR_TYPE)
}
colnames(LE_df)[colnames(LE_df)=="LOG_EFRT_STD_INFO_ID"] <- "ID_FLD"
LE_df$GEAR_SRC <- "LE"
}else{
LE_df <- data.frame(ID_FLD=integer(0),GR_SIZE=integer(0),GR_TYPE=character(), GEAR_SRC=character())
}
if (nrow(MD_df)>0){
#if need convert units, do now
MD_df$COLUMN_DEFN_ID <- replace(MD_df$COLUMN_DEFN_ID, MD_df$COLUMN_DEFN_ID %in% sizeCols, "GR_SIZE")
MD_df$COLUMN_DEFN_ID <- replace(MD_df$COLUMN_DEFN_ID, MD_df$COLUMN_DEFN_ID %in% typeCols, "GR_TYPE")
MD_df <- reshape2::dcast(MD_df, MON_DOC_ID ~ COLUMN_DEFN_ID, value.var = "DATA_VALUE")
if (!"GR_SIZE" %in% names(MD_df)) {
MD_df$GR_SIZE <- -999
}else{
MD_df$GR_SIZE <- as.numeric(MD_df$GR_SIZE)
}
if (!"GR_TYPE" %in% names(MD_df)) {
MD_df$GR_TYPE <- -999
}else{
MD_df$GR_TYPE <- toupper(MD_df$GR_TYPE)
}
colnames(MD_df)[colnames(MD_df)=="MON_DOC_ID"] <- "ID_FLD"
MD_df$GEAR_SRC <- "MD"
}else{
MD_df <- data.frame(ID_FLD=integer(0),GR_SIZE=integer(0),GR_TYPE=character(), GEAR_SRC=character())
}
gearSpecRelevant <- rbind.data.frame(LE_df, MD_df)
if (args$debug) {
t05_ <- proc.time() - t05
message("\tExiting chk_Gears() (",round(t05_[1],0),"s elapsed)")
}
return(gearSpecRelevant)
}
# end -----------------------------------------------------------------------------------------------------------------------------------------------------
get_fleetLicences_loc<-function(...){
args <- list(...)
if (args$debug) t06<- Mar.utils::where_now(returnTime = T)
Mar.utils::get_data_tables(schema = "MARFISSCI", data.dir = args$data.dir,
tables = c("MARFLEETS_LIC"),
usepkg=args$usepkg, fn.oracle.username = args$oracle.username, fn.oracle.dsn=args$oracle.dsn, fn.oracle.password = args$oracle.password, env = environment(), quietly = TRUE, fuzzyMatch=FALSE)
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC$LICENCE_ID, stepDesc = "flt_initial")
if (all(is.na(args$lics$LIC_TYPE))){
MARFLEETS_LIC_L <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_L <- MARFLEETS_LIC[MARFLEETS_LIC$LICENCE_TYPE_ID %in% args$lics$LIC_TYPE,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_L$LICENCE_ID, stepDesc = "flt_licType")
MARFLEETS_LIC <- MARFLEETS_LIC_L
if (all(is.na(args$lics$LIC_SUBTYPE))){
MARFLEETS_LIC_S <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_S <- MARFLEETS_LIC[MARFLEETS_LIC$LICENCE_SUBTYPE_ID %in% args$lics$LIC_SUBTYPE,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_S$LICENCE_ID, stepDesc = "flt_licSubtype")
MARFLEETS_LIC <- MARFLEETS_LIC_S
# MARFLEETS_LIC_G <- MARFLEETS_LIC[MARFLEETS_LIC$GEAR_CODE %in% unique(c(-99, args$marfGear)),]
# if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_G$LICENCE_ID, stepDesc = "flt_licGear")
# MARFLEETS_LIC <- MARFLEETS_LIC_G
if (all(is.na(args$lics$LIC_SP))){
MARFLEETS_LIC_SP <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_SP <- MARFLEETS_LIC[MARFLEETS_LIC$SPECIES_CODE %in% args$lics$LIC_SP,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_SP$LICENCE_ID, stepDesc = "flt_licSpp")
MARFLEETS_LIC <- MARFLEETS_LIC_SP
# }
MARFLEETS_LIC_new <- MARFLEETS_LIC[which(eval(parse(text=theseLics))),]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_new$LICENCE_ID, stepDesc = "flt_licTypeSubtypeSpCombo")
#if (args$debug) Mar.utils::changeDetector(pre_ = MARFLEETS_LIC, post_ = MARFLEETS_LIC_new, fields = "LICENCE_ID", flagTxt = "initial lic type/subtype/sp filter")
MARFLEETS_LIC <- MARFLEETS_LIC_new
# Filter licences by desired date range -------------------------------------------------------------------------------------------------------------------
dateFilt <- paste0("MARFLEETS_LIC$L_ORIGIN_DATE <= '", args$dateEnd, "' & MARFLEETS_LIC$L_EXPIRY_DATE >= '",args$dateStart,"'")
MARFLEETS_LIC_new <- MARFLEETS_LIC[which(eval(parse(text=dateFilt))),]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_new$LICENCE_ID, stepDesc = "flt_licDates")
#if (args$debug) Mar.utils::changeDetector(pre_ = MARFLEETS_LIC, post_ = MARFLEETS_LIC_new, fields = "LICENCE_ID", flagTxt = "lic start end dates applied")
LICDETS<- unique(MARFLEETS_LIC_new[,c("LICENCE_TYPE_ID", "LICENCE_TYPE", "LICENCE_SUBTYPE_ID", "LICENCE_SUBTYPE", "GEAR_CODE", "GEAR", "SPECIES_CODE", "SPECIES")])
licDf <- unique(MARFLEETS_LIC_new[,c("LICENCE_ID","LICENCE_TYPE_ID", "LICENCE_SUBTYPE_ID", "GEAR_CODE", "SPECIES_CODE", "L_ORIGIN_DATE", "L_EXPIRY_DATE")])
res=list()
res[["LICDETS"]]<- LICDETS
res[["licDf"]]<- licDf
if (args$debug) {
t06_ <- proc.time() - t06
message("\tExiting get_fleetLicences_loc() (",round(t06_[1],0),"s elapsed)")
}
return(res)
}
get_fleetLicences_ora<-function(...){
args <- list(...)
if (args$debug) t07<- Mar.utils::where_now(returnTime = T)
if (args$debug | !any(is.null(dbEnv$debugLics))){
# message("To handle debugging, a lot of data must first be extracted, so that each step can be checked. This step will take ~1 minute")
MARFLEETS_LIC_Qry <- paste0("SELECT *
FROM MARFISSCI.MARFLEETS_LIC WHERE ",theseLicsOra)
# AND ",Mar.utils::big_in(vec=unique(df$MON_DOC_ID), vec.field = "LOG_EFRT_STD_INFO.MON_DOC_ID"))
MARFLEETS_LIC <- args$cxn$thecmd(args$cxn$channel, MARFLEETS_LIC_Qry)
LICDETS<- unique(MARFLEETS_LIC[,c("LICENCE_TYPE_ID", "LICENCE_TYPE", "LICENCE_SUBTYPE_ID", "LICENCE_SUBTYPE", "GEAR_CODE", "GEAR", "SPECIES_CODE", "SPECIES")])
# message("Completed big extraction. To avoid this in the future, don't use debug, don't send debugLics or change to useLocal = T.")
if (all(is.na(args$lics$LIC_TYPE))){
MARFLEETS_LIC_L <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_L <- MARFLEETS_LIC[MARFLEETS_LIC$LICENCE_TYPE_ID %in% args$lics$LIC_TYPE,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_L$LICENCE_ID, stepDesc = "flt_licTypeOra")
MARFLEETS_LIC <- MARFLEETS_LIC_L
if (all(is.na(args$lics$LIC_SUBTYPE))){
MARFLEETS_LIC_S <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_S <- MARFLEETS_LIC[MARFLEETS_LIC$LICENCE_SUBTYPE_ID %in% args$lics$LIC_SUBTYPE,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_S$LICENCE_ID, stepDesc = "flt_licSubtypeOra")
MARFLEETS_LIC <- MARFLEETS_LIC_S
if (all(is.na(args$lics$LIC_SP))){
MARFLEETS_LIC_SP <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_SP <- MARFLEETS_LIC[MARFLEETS_LIC$SPECIES_CODE %in% args$lics$LIC_SP,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_SP$LICENCE_ID, stepDesc = "flt_licSppOra")
MARFLEETS_LIC <- MARFLEETS_LIC_SP
MARFLEETS_LIC_new <- MARFLEETS_LIC[which(eval(parse(text=theseLics))),]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_new$LICENCE_ID, stepDesc = "flt_licTypeSubtypeSpComboOra")
MARFLEETS_LIC <- MARFLEETS_LIC_new
dateFilt <- paste0("MARFLEETS_LIC$L_ORIGIN_DATE <= '", args$dateEnd, "' & MARFLEETS_LIC$L_EXPIRY_DATE >= '",args$dateStart,"'")
MARFLEETS_LIC_new_date <- MARFLEETS_LIC[which(eval(parse(text=dateFilt))),]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_new_date$LICENCE_ID, stepDesc = "flt_licDatesOra")
#if (args$debug) Mar.utils::changeDetector(pre_ = MARFLEETS_LIC_new, post_ = MARFLEETS_LIC_new_date, fields = "LICENCE_ID", flagTxt = "lic start end dates applied")
MARFLEETS_LIC <- MARFLEETS_LIC_new_date
# if (all(is.na(args$marfGear))){
# MARFLEETS_LIC_GR <- MARFLEETS_LIC
# } else{
# MARFLEETS_LIC_GR <- MARFLEETS_LIC[MARFLEETS_LIC$GEAR_CODE %in% unique(c(-99,args$marfGear)),]
# }
# if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_GR$LICENCE_ID, stepDesc = "flt_licGearOra")
# MARFLEETS_LIC <- MARFLEETS_LIC_GR
}else{
where_dateFilt <- paste0(" AND (MARFLEETS_LIC.L_ORIGIN_DATE <= to_date('", args$dateEnd, "','YYYY-MM-DD') AND
MARFLEETS_LIC.L_EXPIRY_DATE >= to_date('",args$dateStart,"','YYYY-MM-DD'))")
# where_gearFilt <- paste0(" AND MARFLEETS_LIC.GEAR_CODE IN (-99, ", Mar.utils::SQL_in(args$marfGear, apos = F),")")
MARFLEETS_LIC_new_Qry <- paste0("SELECT *
FROM MARFISSCI.MARFLEETS_LIC
WHERE (", theseLicsOra, ") ",where_dateFilt)
#, where_gearFilt)
MARFLEETS_LIC_new <- args$cxn$thecmd(args$cxn$channel, MARFLEETS_LIC_new_Qry)
}
LICDETS<- unique(MARFLEETS_LIC_new[,c("LICENCE_TYPE_ID", "LICENCE_TYPE", "LICENCE_SUBTYPE_ID", "LICENCE_SUBTYPE", "GEAR_CODE", "GEAR", "SPECIES_CODE", "SPECIES")])
licDf <- unique(MARFLEETS_LIC_new[,c("LICENCE_ID","LICENCE_TYPE_ID", "LICENCE_SUBTYPE_ID", "GEAR_CODE", "SPECIES_CODE", "L_ORIGIN_DATE", "L_EXPIRY_DATE")])
res=list()
res[["LICDETS"]]<- LICDETS
res[["licDf"]]<- licDf
if (args$debug) {
t07_ <- proc.time() - t07
message("\tExiting get_fleetLicences_ora() (",round(t07_[1],0),"s elapsed)")
}
return(res)
}
get_fleetActivity_loc<- function(licDf = NULL, ...){
args <- list(...)$args
if (args$debug) t08 <- Mar.utils::where_now(returnTime = T)
Mar.utils::get_data_tables(schema = "MARFISSCI", data.dir = args$data.dir,
tables = c("PRO_SPC_INFO","TRIPS","NAFO_UNIT_AREAS", "VESSELS"),
usepkg=args$usepkg, fn.oracle.username = args$oracle.username, fn.oracle.dsn=args$oracle.dsn, fn.oracle.password = args$oracle.password, env = environment(), quietly = TRUE, fuzzyMatch=FALSE)
# if ("GASP" %in% args$lics$FLEET){
# PRO_SPC_INFO= PRO_SPC_INFO[,c("LICENCE_ID","PRO_SPC_INFO_ID", "TRIP_ID", "LOG_EFRT_STD_INFO_ID","GEAR_CODE","MON_DOC_ID","NAFO_UNIT_AREA_ID", "DATE_FISHED", "LANDED_DATE")]
# TRIPS = PRO_SPC_INFO[,c("PRO_SPC_INFO_ID","DATE_FISHED", "LANDED_DATE")]
# colnames(TRIPS)[colnames(TRIPS)=="DATE_FISHED"] <- "T_DATE1"
# colnames(TRIPS)[colnames(TRIPS)=="LANDED_DATE"] <- "T_DATE2"
# }else{
PRO_SPC_INFO= PRO_SPC_INFO[,c("LICENCE_ID","PRO_SPC_INFO_ID", "TRIP_ID", "LOG_EFRT_STD_INFO_ID","GEAR_CODE","MON_DOC_ID","NAFO_UNIT_AREA_ID")]
#TRIPS
TRIPS <- TRIPS[,c("TRIP_ID","VR_NUMBER", "EARLIEST_DATE_TIME","LATEST_DATE_TIME")]
colnames(TRIPS)[colnames(TRIPS)=="EARLIEST_DATE_TIME"] <- "T_DATE1"
colnames(TRIPS)[colnames(TRIPS)=="LATEST_DATE_TIME"] <- "T_DATE2"
# }
# Handle the various data we just pulled ------------------------------------------------------------------------------------------------------------------
TRIPS$T_DATE1 <- as.Date(TRIPS$T_DATE1)
TRIPS$T_DATE2 <- as.Date(TRIPS$T_DATE2)
#NAFO
if (!"NAFO_AREA" %in% names(NAFO_UNIT_AREAS)) names(NAFO_UNIT_AREAS)[names(NAFO_UNIT_AREAS) == "AREA"] <- "NAFO_AREA"
NAFO_UNIT_AREAS <- NAFO_UNIT_AREAS[,c("AREA_ID", "NAFO_AREA")]
PRO_SPC_INFO_new <-PRO_SPC_INFO[PRO_SPC_INFO$LICENCE_ID %in% licDf$LICENCE_ID,]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = PRO_SPC_INFO_new$LICENCE_ID, stepDesc = "flt_PSLics")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = PRO_SPC_INFO_new$VR_NUMBER, stepDesc = "flt_PSLics")
if (!is.null(dbEnv$debugMARFTripIDs)) dbEnv$debugMARFTripIDs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugMARFTripIDs, expected = dbEnv$debugMARFTripIDs, expectedID = "debugMARFTripIDs", known = PRO_SPC_INFO_new$TRIP_ID, stepDesc = "flt_PSLics")
PRO_SPC_INFO <- PRO_SPC_INFO_new
# Grab fishing activity of those with valid gear code -------------------------------------------------------------------------------
PRO_SPC_INFO_new<-PRO_SPC_INFO[PRO_SPC_INFO$GEAR_CODE %in% args$marfGear,]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = PRO_SPC_INFO_new$LICENCE_ID, stepDesc = "flt_PSGrs")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = PRO_SPC_INFO_new$VR_NUMBER, stepDesc = "flt_PSGrs")
if (!is.null(dbEnv$debugMARFTripIDs)) dbEnv$debugMARFTripIDs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugMARFTripIDs, expected = dbEnv$debugMARFTripIDs, expectedID = "debugMARFTripIDs", known = PRO_SPC_INFO_new$TRIP_ID, stepDesc = "flt_PSGrs")
PRO_SPC_INFO <- PRO_SPC_INFO_new
# Limit fishing activity to desired date range ------------------------------------------------------------------------------------------------------------
TRIPS <- TRIPS[which(TRIPS$T_DATE1 <= as.Date(args$dateEnd) & TRIPS$T_DATE2 >= as.Date(args$dateStart)),]
# if ("GASP" %in% args$lics$FLEET){
# PRO_SPC_INFO_new <- PRO_SPC_INFO[PRO_SPC_INFO$PRO_SPC_INFO_ID %in% TRIPS$PRO_SPC_INFO_ID,]
# # PRO_SPC_INFO_new <- merge(PRO_SPC_INFO_new, TRIPS)
# }else{
PRO_SPC_INFO_new <- PRO_SPC_INFO[PRO_SPC_INFO$TRIP_ID %in% TRIPS$TRIP_ID,]
PRO_SPC_INFO_new <- merge(PRO_SPC_INFO_new, TRIPS)
# }
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = PRO_SPC_INFO_new$LICENCE_ID, stepDesc = "flt_PSDates")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = PRO_SPC_INFO_new$VR_NUMBER, stepDesc = "flt_PSDates")
if (!is.null(dbEnv$debugMARFTripIDs)) dbEnv$debugMARFTripIDs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugMARFTripIDs, expected = dbEnv$debugMARFTripIDs, expectedID = "debugMARFTripIDs", known = PRO_SPC_INFO_new$TRIP_ID, stepDesc = "flt_PSDates")
#if (args$debug) Mar.utils::changeDetector(pre_ = PRO_SPC_INFO, post_ = PRO_SPC_INFO_new, fields = "LICENCE_ID", flagTxt = "PS filtered by dates")
PRO_SPC_INFO <- PRO_SPC_INFO_new
# limit fishing activity to fleet-specified areas ---------------------------------------------------------------------------------------------------------
PRO_SPC_INFO = merge(PRO_SPC_INFO, NAFO_UNIT_AREAS, by.x="NAFO_UNIT_AREA_ID", by.y = "AREA_ID", all.x=T )
if (nrow(args$area)>0 & any(args$area$AREA_TYPE =="NAFO")){
nafoCode <- gsub(pattern = "%", x=args$area$AREA, replacement = "",ignore.case = T)
NAFO_UNIT_AREAS <- NAFO_UNIT_AREAS[grep(paste(nafoCode, collapse = '|'),NAFO_UNIT_AREAS$NAFO_AREA),]
PRO_SPC_INFO_new <- PRO_SPC_INFO[PRO_SPC_INFO$NAFO_UNIT_AREA_ID %in% NAFO_UNIT_AREAS$AREA_ID,]
if (!is.null(dbEnv$debugMARFTripIDs)) dbEnv$debugMARFTripIDs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugMARFTripIDs, expected = dbEnv$debugMARFTripIDs, expectedID = "debugMARFTripIDs", known = PRO_SPC_INFO_new$TRIP_ID, stepDesc = "flt_PSNAFOAreas")
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = PRO_SPC_INFO_new$LICENCE_ID, stepDesc = "flt_PSNAFOAreas")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = PRO_SPC_INFO_new$VR_NUMBER, stepDesc = "flt_PSNAFOAreas")
PRO_SPC_INFO$NAFO_AREA <- NULL
#if (args$debug) Mar.utils::changeDetector(pre_ = PRO_SPC_INFO, post_ = PRO_SPC_INFO_new, fields = "LICENCE_ID", flagTxt = "PS filtered by licenced NAFO")
PRO_SPC_INFO <- PRO_SPC_INFO_new
}
PRO_SPC_INFO <- merge(PRO_SPC_INFO, VESSELS[, c("VR_NUMBER", "LOA")], all.x = T)
# Clean results -------------------------------------------------------------------------------------------------------------------------------------------
PRO_SPC_INFO$NAFO_UNIT_AREA_ID<-PRO_SPC_INFO$TRIP_ID <- NULL
if (nrow(PRO_SPC_INFO)<1) {
stop("No fleet activity found")
}
if (args$debug) {
t08_ <- proc.time() - t08
message("\tExiting get_fleetActivity_loc() (",round(t08_[1],0),"s elapsed)")
}
return(PRO_SPC_INFO)
}
get_fleetActivity_ora<- function(licDf = NULL, ...){
args <- list(...)$args
if (args$debug) t09 <- Mar.utils::where_now(returnTime = T)
where_date <- paste0("AND (T.EARLIEST_DATE_TIME <= to_date('",args$dateEnd,"','YYYY-MM-DD') AND T.LATEST_DATE_TIME >= to_date('",args$dateStart,"','YYYY-MM-DD'))")
where_Gr <- paste0("AND PS.GEAR_CODE IN (",Mar.utils::SQL_in(args$marfGear,apos = F),")")
if (nrow(args$area)>0 & any(args$area$AREA_TYPE =="NAFO")){
where_Area <- paste0("AND (",paste0("N.AREA LIKE ('",paste0(unique(args$area$AREA),"%"),"')", collapse = " OR "),")")
}else{
where_Area = ""
}
fleetAct_qry = paste0("SELECT PS.LICENCE_ID, PS.PRO_SPC_INFO_ID, PS.LOG_EFRT_STD_INFO_ID, PS.GEAR_CODE, PS.MON_DOC_ID,
MD.VR_NUMBER, T.EARLIEST_DATE_TIME T_DATE1,T.LATEST_DATE_TIME T_DATE2,
N.AREA NAFO, V.LOA
FROM MARFISSCI.PRO_SPC_INFO PS, MARFISSCI.TRIPS T, MARFISSCI.NAFO_UNIT_AREAS N, MARFISSCI.MON_DOCS MD,
MARFISSCI.VESSELS V
WHERE
MD.MON_DOC_ID = PS.MON_DOC_ID
AND PS.TRIP_ID = T.TRIP_ID
AND MD.VR_NUMBER = V.VR_NUMBER
AND PS.NAFO_UNIT_AREA_ID = N.AREA_ID "
,where_date, " "
,where_Gr, " "
,where_Area
)
theFleet = args$cxn$thecmd(args$cxn$channel, fleetAct_qry)
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = theFleet$LICENCE_ID, stepDesc = "flt_PSDates")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = theFleet$VR_NUMBER, stepDesc = "flt_PSDates")
theFleet$NAFO <- NULL
# theFleet2 <- theFleet[paste0(theFleet$LICENCE_ID,"_", theFleet$GEAR_CODE) %in% all_LicGr,]
# if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = theFleet$LICENCE_ID, stepDesc = "flt_PSLicGears")
# if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = theFleet$VR_NUMBER, stepDesc = "flt_PSLicGears")
# if (args$debug) Mar.utils::changeDetector(pre_ = theFleet, post_ = theFleet2, fields = "LICENCE_ID", flagTxt = "PS filtered by licence/gear combo")
# theFleet <- theFleet2
if (nrow(theFleet)<1) stop("No fleet activity found")
if (args$debug) {
t09_ <- proc.time() - t09
message("\tExiting get_fleetActivity_ora() (",round(t09_[1],0),"s elapsed)")
}
return(theFleet)
}
get_fleetGear<-function(df = NULL, ...){
# this could entirely replaced by chk_Gears
args <- list(...)$args
if (args$debug) t10 <- Mar.utils::where_now(returnTime = T)
gearSpecRelevant <- do.call(chk_Gears, list(df, args=args))
if(nrow(gearSpecRelevant)<1) {
if (args$debug) {
t10_ <- proc.time() - t10
message("\tExiting get_fleetGear() - no gearSpecRelevant: (", round(t10_[1],0),"s elapsed)")
}
return(df)
}
if (nrow(args$gearSpecs)>0){
#merge the gear details from both LOG_EFRT and MON_DOC onto the df
df_merge <- unique(df[, c("PRO_SPC_INFO_ID","LOG_EFRT_STD_INFO_ID", "MON_DOC_ID")])
df_LE <- gearSpecRelevant[gearSpecRelevant$GEAR_SRC == "LE",c("ID_FLD", "GR_TYPE", "GR_SIZE")]
df_LE <- merge(df_merge, df_LE, by.x="LOG_EFRT_STD_INFO_ID", by.y = "ID_FLD")
df_MD <- gearSpecRelevant[gearSpecRelevant$GEAR_SRC == "MD",c("ID_FLD", "GR_TYPE", "GR_SIZE")]
df_MD <- merge(df_merge, df_MD, by.x="MON_DOC_ID", by.y = "ID_FLD")
allReportedGears <- rbind.data.frame(df_LE, df_MD)
df <- merge(df, allReportedGears, all.x = T)
#flag those with no gear info as -999
df[["GR_TYPE"]][is.na(df[["GR_TYPE"]])] <- -999
df[["GR_SIZE"]][is.na(df[["GR_SIZE"]])] <- -999
if (args$debug) message("n records - pre-size/type filts: ", nrow(df))
if (!is.na(args$gearSpecs$TYPE)){
df= do.call(typeFilt, list(df, args=args))
if (args$debug) message("n records - post-typeFilt: ", nrow(df))
}
if (!is.na(args$gearSpecs$MIN)){
df= do.call(sizeFilt, list(df, args=args))
if (args$debug) message("n records - post-sizeFilt: ", nrow(df))
}
}
if (nrow(df)<1){
message("\n","No fleet gear found")
}
if (args$debug) {
t10_ <- proc.time() - t10
message("\tExiting get_fleetGear() (",round(t10_[1],0),"s elapsed)")
}
return(df)
}
if (args$useLocal){
licDf_tmp <- do.call(get_fleetLicences_loc, args)
}else{
licDf_tmp <- do.call(get_fleetLicences_ora, args)
}
licDets <- licDf_tmp$LICDETS
licDf <- licDf_tmp$licDf
if (args$useLocal){
actDf <- do.call(get_fleetActivity_loc, list(licDf=licDf, args=args))
}else{
actDf <- do.call(get_fleetActivity_ora, list(licDf=licDf, args=args))
}
df <- do.call(get_fleetGear, list(df=actDf,args=args))
df$NAFO <-NULL
df <- unique(df[with(df,order(VR_NUMBER, LICENCE_ID, GEAR_CODE, LOA )),])
res <- list()
res[["LICDETS"]]<-licDets
res[["FLEET"]] <- unique(df[with(df,order(VR_NUMBER, LICENCE_ID, GEAR_CODE, LOA )),c("VR_NUMBER", "LICENCE_ID", "GEAR_CODE", "LOA")])
df$LOA <- df$NAFO_AREA <- NULL
res[["FLEET_ACTIVITY"]]<- df
if (args$debug) {
t02_ <- proc.time() - t02
message("\tExiting get_fleet() (",round(t02_[1],0),"s elapsed)")
}
return(res)
}
Maritimes/Mar.bycatch documentation built on Aug. 18, 2024, 8:43 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions get_fleet
Documented in get_fleet
#' @title get_fleet
#' @description This function extracts all of the Vessel/Licence combinations
#' associated with a particular fleet for a particular date range.
#' @param ... other arguments passed to methods
#' @family coreFuncs
#' @return returns a data.frame with the following columns:
#' \itemize{
#' \item \code{MON_DOC_ID}
#' \item \code{GEAR_CODE }
#' \item \code{LICENCE_ID}
#' \item \code{PRO_SPC_INFO_ID}
#' \item \code{LOG_EFRT_STD_INFO_ID }
#' \item \code{T_DATE1}
#' \item \code{T_DATE2}
#' \item \code{MD_CODE}
#' \item \code{VR_NUMBER}
#' }
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
get_fleet<-function(...){
args <-list(...)
if (args$debug) t02 <-Mar.utils::where_now(returnTime = T)
MARFLEETS_LIC <- PRO_SPC_INFO <- TRIPS <- NAFO_UNIT_AREAS <- LOG_EFRT_ENTRD_DETS <- LOG_EFRT_STD_INFO <- GEARS <- NA
theseLics <- NA
for (i in 1:nrow(args$lics)){
thisL <- ifelse(is.na(args$lics$LIC_TYPE[i]),"1==1", paste0("MARFLEETS_LIC$LICENCE_TYPE_ID == ",args$lics$LIC_TYPE[i]))
thisS <- ifelse(is.na(args$lics$LIC_SUBTYPE[i]),"1==1", paste0("MARFLEETS_LIC$LICENCE_SUBTYPE_ID == ",args$lics$LIC_SUBTYPE[i]))
thisSpp <- ifelse(is.na(args$lics$LIC_SP[i]),"1==1", paste0("MARFLEETS_LIC$SPECIES_CODE == ",args$lics$LIC_SP[i]))
thisLicRow <- paste0("(",thisL, " & ",thisS," & ",thisSpp,")")
if (i==1){
theseLics <- thisLicRow
} else {
theseLics <- paste(theseLics, "|", thisLicRow)
}
}
theseLicsOra <- gsub("==", "=", gsub("\\$", "\\.", gsub("&", "AND", gsub("\\|", "OR", theseLics))))
# end -----------------------------------------------------------------------------------------------------------------------------------------------------
# sizeFilt, typeFilt and chk_Gears are used by both the Ora and loc versions of get_fleetGear ------------------------------------------------------------------------
sizeFilt <- function(df=NULL, ...){
args <- list(...)$args
if (args$debug) t03<- Mar.utils::where_now(returnTime = T)
if (!is.na(args$gearSpecs$MIN)){
#for fixed gear (CHPs), we need to keep all gillnet - don't sort as though they were hooks
#fsame for unit2 redfish
if ((args$gearSpecs$FLEET == "CHP" && grepl(pattern = "_FIXED", x = args$gearSpecs$FLEET_GEARSPECS_ID))|
(args$gearSpecs$FLEET == "REDFISH" && grepl(pattern = "UNIT2", x = args$gearSpecs$FLEET_GEARSPECS_ID))){
gn <- df[df$GEAR_CODE == 41,]
df <- df[df$GEAR_CODE != 41,]
}
theseGearSpecRelevant <- df[which(df$GR_SIZE >= args$gearSpecs$MIN &
df$GR_SIZE <= args$gearSpecs$MAX),]
if(args$keepMissingGear){
theseGearSpecUnk <- df[df$GR_SIZE == -999,]
theseGearSpecRelevant <- rbind.data.frame(theseGearSpecRelevant, theseGearSpecUnk)
}
#reattach gillnet to results
if (exists("gn")) theseGearSpecRelevant <- rbind.data.frame(theseGearSpecRelevant, gn)
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = theseGearSpecRelevant$LICENCE_ID, stepDesc = "flt_gearSize")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = theseGearSpecRelevant$VR_NUMBER, stepDesc = "flt_gearSize")
df<- theseGearSpecRelevant
}
if (args$debug) {
t03_ <- proc.time() - t03
message("\tExiting sizeFilt() (",round(t03_[1],0),"s elapsed)")
}
return(df)
}
typeFilt <- function(df=NULL, ...){
args <- list(...)$args
if (args$debug) t04<- Mar.utils::where_now(returnTime = T)
if (!is.na(args$gearSpecs$TYPE)){
#apply the requested filter
#Mesh
# "S" - SQUARE
# "D" - DIAMOND
theseGearSpecRelevant <- df[which(df$GR_TYPE %in% args$gearSpecs$TYPE),]
if(args$keepMissingGear){
theseGearSpecUnk <- df[df$GR_TYPE == "-999",]
theseGearSpecRelevant <- rbind.data.frame(theseGearSpecRelevant, theseGearSpecUnk)
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = theseGearSpecRelevant$LICENCE_ID, stepDesc = "flt_gearTypeFilt")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = theseGearSpecRelevant$VR_NUMBER, stepDesc = "flt_gearTypeFilt")
df<- theseGearSpecRelevant
}
if (args$debug) {
t04_ <- proc.time() - t04
message("\tExiting typeFilt() (",round(t04_[1],0),"s elapsed)")
}
return(df)
}
chk_Gears <- function(df=NULL, ...){
#this function figures out what categories of gears we're dealing with, and will let us determine what filters might be possible
args <- list(...)$args
if (args$debug) t05<- Mar.utils::where_now(returnTime = T)
GEARS<-unique(df$GEAR_CODE)
allGears = tolower(GEARS_MARFIS[GEARS_MARFIS$GEAR_CODE %in% GEARS,"GEAR"])
allGears = allGears[!allGears %in% c("trap net")]
matchTrap=c('trap','pot')
matchMesh=c('trawl','seine','net','midwtr', 'drag')
matchLine=c('line','jig','angli')
theseGears<-NA
if (any(grepl(pattern = paste(matchTrap, collapse = '|'), x= allGears))) theseGears <- c(theseGears,"trap")
if (any(grepl(pattern = paste(matchMesh, collapse = '|'), x= allGears))) theseGears <- c(theseGears,"mesh")
if (any(grepl(pattern = paste(matchLine, collapse = '|'), x= allGears))) theseGears <- c(theseGears,"line")
theseGears <- theseGears[!is.na(theseGears)]
if (length(theseGears)>=1){
gearType <-theseGears
}else{
gearType <- NA
}
grSpType <- NA
grSpSize <- NA
if('mesh' %in% gearType){
grSpType <- c(grSpType,31)
grSpSize <- c(grSpSize, 8,32,62,120,806)
}
if("trap" %in% gearType){
grSpType <- c(grSpType,114)
grSpSize <- c(grSpSize, 152,423,431,701)
}
if("hook" %in% gearType || "line" %in% gearType){
grSpType <- c(grSpType,5)
grSpSize <- c(grSpSize, 4,66,67)
}
if (all(is.na(gearType))) {
if (args$debug) {
t05_ <- proc.time() - t05
message("\tExiting chk_Gears() - all NA: (", round(t05_[1],0),"s elapsed)")
}
return(df)
}
#check if types exist at all for selection
grSpType <- grSpType[!is.na(grSpType)]
#check if sizes exist at all for selection
grSpSize <- grSpSize[!is.na(grSpSize)]
grSpCols <- c(grSpType, grSpSize)
sizeCols <- c(4,8,32,62,66,67,120,806,152,423,431,701)
typeCols <- c(5,31,114)
if(!args$useLocal){
RelevantQry_LE <- paste0("SELECT LOG_EFRT_STD_INFO_ID, COLUMN_DEFN_ID, DATA_VALUE from MARFISSCI.LOG_EFRT_ENTRD_DETS
WHERE
COLUMN_DEFN_ID IN (",Mar.utils::SQL_in(grSpCols,apos=F),")
AND ",Mar.utils::big_in(vec=unique(df$LOG_EFRT_STD_INFO_ID), vec.field="LOG_EFRT_STD_INFO_ID"))
LE_df <- args$cxn$thecmd(args$cxn$channel, RelevantQry_LE)
RelevantQry_MD <- paste0("SELECT MON_DOC_ID, COLUMN_DEFN_ID, DATA_VALUE from MARFISSCI.MON_DOC_ENTRD_DETS
WHERE
COLUMN_DEFN_ID IN (",Mar.utils::SQL_in(grSpCols,apos=F),")
AND ",Mar.utils::big_in(vec=unique(df$MON_DOC_ID), vec.field="MON_DOC_ID"))
MD_df <- args$cxn$thecmd(args$cxn$channel, RelevantQry_MD)
}else{
# Find all of the records that are related to the gear type (e.g. mesh/hook/trap) --------------------------------------------
Mar.utils::get_data_tables(schema = "MARFISSCI", data.dir = args$data.dir, tables = c("LOG_EFRT_ENTRD_DETS", "MON_DOC_ENTRD_DETS"),
usepkg=args$usepkg, fn.oracle.username = args$oracle.username, fn.oracle.dsn=args$oracle.dsn, fn.oracle.password = args$oracle.password,
env = environment(), quietly = TRUE, fuzzyMatch=FALSE)
LE_df <- LOG_EFRT_ENTRD_DETS[which(LOG_EFRT_ENTRD_DETS$LOG_EFRT_STD_INFO_ID %in% df$LOG_EFRT_STD_INFO_ID &
LOG_EFRT_ENTRD_DETS$COLUMN_DEFN_ID %in% grSpCols), c("LOG_EFRT_STD_INFO_ID", "COLUMN_DEFN_ID", "DATA_VALUE") ]
MD_df <- MON_DOC_ENTRD_DETS[which(MON_DOC_ENTRD_DETS$MON_DOC_ID %in% df$MON_DOC_ID &
MON_DOC_ENTRD_DETS$COLUMN_DEFN_ID %in% grSpCols), c("MON_DOC_ID","COLUMN_DEFN_ID", "DATA_VALUE"),]
}
if (nrow(LE_df)>0){
#if need convert units, do now
LE_df$COLUMN_DEFN_ID <- replace(LE_df$COLUMN_DEFN_ID, LE_df$COLUMN_DEFN_ID %in% sizeCols, "GR_SIZE")
LE_df$COLUMN_DEFN_ID <- replace(LE_df$COLUMN_DEFN_ID, LE_df$COLUMN_DEFN_ID %in% typeCols, "GR_TYPE")
LE_df <- reshape2::dcast(LE_df, LOG_EFRT_STD_INFO_ID ~ COLUMN_DEFN_ID, value.var = "DATA_VALUE")
if (!"GR_SIZE" %in% names(LE_df)) {
LE_df$GR_SIZE <- -999
}else{
LE_df$GR_SIZE <- as.numeric(LE_df$GR_SIZE)
}
if (!"GR_TYPE" %in% names(LE_df)) {
LE_df$GR_TYPE <- -999
}else{
LE_df$GR_TYPE <- toupper(LE_df$GR_TYPE)
}
colnames(LE_df)[colnames(LE_df)=="LOG_EFRT_STD_INFO_ID"] <- "ID_FLD"
LE_df$GEAR_SRC <- "LE"
}else{
LE_df <- data.frame(ID_FLD=integer(0),GR_SIZE=integer(0),GR_TYPE=character(), GEAR_SRC=character())
}
if (nrow(MD_df)>0){
#if need convert units, do now
MD_df$COLUMN_DEFN_ID <- replace(MD_df$COLUMN_DEFN_ID, MD_df$COLUMN_DEFN_ID %in% sizeCols, "GR_SIZE")
MD_df$COLUMN_DEFN_ID <- replace(MD_df$COLUMN_DEFN_ID, MD_df$COLUMN_DEFN_ID %in% typeCols, "GR_TYPE")
MD_df <- reshape2::dcast(MD_df, MON_DOC_ID ~ COLUMN_DEFN_ID, value.var = "DATA_VALUE")
if (!"GR_SIZE" %in% names(MD_df)) {
MD_df$GR_SIZE <- -999
}else{
MD_df$GR_SIZE <- as.numeric(MD_df$GR_SIZE)
}
if (!"GR_TYPE" %in% names(MD_df)) {
MD_df$GR_TYPE <- -999
}else{
MD_df$GR_TYPE <- toupper(MD_df$GR_TYPE)
}
colnames(MD_df)[colnames(MD_df)=="MON_DOC_ID"] <- "ID_FLD"
MD_df$GEAR_SRC <- "MD"
}else{
MD_df <- data.frame(ID_FLD=integer(0),GR_SIZE=integer(0),GR_TYPE=character(), GEAR_SRC=character())
}
gearSpecRelevant <- rbind.data.frame(LE_df, MD_df)
if (args$debug) {
t05_ <- proc.time() - t05
message("\tExiting chk_Gears() (",round(t05_[1],0),"s elapsed)")
}
return(gearSpecRelevant)
}
# end -----------------------------------------------------------------------------------------------------------------------------------------------------
get_fleetLicences_loc<-function(...){
args <- list(...)
if (args$debug) t06<- Mar.utils::where_now(returnTime = T)
Mar.utils::get_data_tables(schema = "MARFISSCI", data.dir = args$data.dir,
tables = c("MARFLEETS_LIC"),
usepkg=args$usepkg, fn.oracle.username = args$oracle.username, fn.oracle.dsn=args$oracle.dsn, fn.oracle.password = args$oracle.password, env = environment(), quietly = TRUE, fuzzyMatch=FALSE)
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC$LICENCE_ID, stepDesc = "flt_initial")
if (all(is.na(args$lics$LIC_TYPE))){
MARFLEETS_LIC_L <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_L <- MARFLEETS_LIC[MARFLEETS_LIC$LICENCE_TYPE_ID %in% args$lics$LIC_TYPE,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_L$LICENCE_ID, stepDesc = "flt_licType")
MARFLEETS_LIC <- MARFLEETS_LIC_L
if (all(is.na(args$lics$LIC_SUBTYPE))){
MARFLEETS_LIC_S <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_S <- MARFLEETS_LIC[MARFLEETS_LIC$LICENCE_SUBTYPE_ID %in% args$lics$LIC_SUBTYPE,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_S$LICENCE_ID, stepDesc = "flt_licSubtype")
MARFLEETS_LIC <- MARFLEETS_LIC_S
# MARFLEETS_LIC_G <- MARFLEETS_LIC[MARFLEETS_LIC$GEAR_CODE %in% unique(c(-99, args$marfGear)),]
# if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_G$LICENCE_ID, stepDesc = "flt_licGear")
# MARFLEETS_LIC <- MARFLEETS_LIC_G
if (all(is.na(args$lics$LIC_SP))){
MARFLEETS_LIC_SP <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_SP <- MARFLEETS_LIC[MARFLEETS_LIC$SPECIES_CODE %in% args$lics$LIC_SP,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_SP$LICENCE_ID, stepDesc = "flt_licSpp")
MARFLEETS_LIC <- MARFLEETS_LIC_SP
# }
MARFLEETS_LIC_new <- MARFLEETS_LIC[which(eval(parse(text=theseLics))),]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_new$LICENCE_ID, stepDesc = "flt_licTypeSubtypeSpCombo")
#if (args$debug) Mar.utils::changeDetector(pre_ = MARFLEETS_LIC, post_ = MARFLEETS_LIC_new, fields = "LICENCE_ID", flagTxt = "initial lic type/subtype/sp filter")
MARFLEETS_LIC <- MARFLEETS_LIC_new
# Filter licences by desired date range -------------------------------------------------------------------------------------------------------------------
dateFilt <- paste0("MARFLEETS_LIC$L_ORIGIN_DATE <= '", args$dateEnd, "' & MARFLEETS_LIC$L_EXPIRY_DATE >= '",args$dateStart,"'")
MARFLEETS_LIC_new <- MARFLEETS_LIC[which(eval(parse(text=dateFilt))),]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_new$LICENCE_ID, stepDesc = "flt_licDates")
#if (args$debug) Mar.utils::changeDetector(pre_ = MARFLEETS_LIC, post_ = MARFLEETS_LIC_new, fields = "LICENCE_ID", flagTxt = "lic start end dates applied")
LICDETS<- unique(MARFLEETS_LIC_new[,c("LICENCE_TYPE_ID", "LICENCE_TYPE", "LICENCE_SUBTYPE_ID", "LICENCE_SUBTYPE", "GEAR_CODE", "GEAR", "SPECIES_CODE", "SPECIES")])
licDf <- unique(MARFLEETS_LIC_new[,c("LICENCE_ID","LICENCE_TYPE_ID", "LICENCE_SUBTYPE_ID", "GEAR_CODE", "SPECIES_CODE", "L_ORIGIN_DATE", "L_EXPIRY_DATE")])
res=list()
res[["LICDETS"]]<- LICDETS
res[["licDf"]]<- licDf
if (args$debug) {
t06_ <- proc.time() - t06
message("\tExiting get_fleetLicences_loc() (",round(t06_[1],0),"s elapsed)")
}
return(res)
}
get_fleetLicences_ora<-function(...){
args <- list(...)
if (args$debug) t07<- Mar.utils::where_now(returnTime = T)
if (args$debug | !any(is.null(dbEnv$debugLics))){
# message("To handle debugging, a lot of data must first be extracted, so that each step can be checked. This step will take ~1 minute")
MARFLEETS_LIC_Qry <- paste0("SELECT *
FROM MARFISSCI.MARFLEETS_LIC WHERE ",theseLicsOra)
# AND ",Mar.utils::big_in(vec=unique(df$MON_DOC_ID), vec.field = "LOG_EFRT_STD_INFO.MON_DOC_ID"))
MARFLEETS_LIC <- args$cxn$thecmd(args$cxn$channel, MARFLEETS_LIC_Qry)
LICDETS<- unique(MARFLEETS_LIC[,c("LICENCE_TYPE_ID", "LICENCE_TYPE", "LICENCE_SUBTYPE_ID", "LICENCE_SUBTYPE", "GEAR_CODE", "GEAR", "SPECIES_CODE", "SPECIES")])
# message("Completed big extraction. To avoid this in the future, don't use debug, don't send debugLics or change to useLocal = T.")
if (all(is.na(args$lics$LIC_TYPE))){
MARFLEETS_LIC_L <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_L <- MARFLEETS_LIC[MARFLEETS_LIC$LICENCE_TYPE_ID %in% args$lics$LIC_TYPE,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_L$LICENCE_ID, stepDesc = "flt_licTypeOra")
MARFLEETS_LIC <- MARFLEETS_LIC_L
if (all(is.na(args$lics$LIC_SUBTYPE))){
MARFLEETS_LIC_S <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_S <- MARFLEETS_LIC[MARFLEETS_LIC$LICENCE_SUBTYPE_ID %in% args$lics$LIC_SUBTYPE,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_S$LICENCE_ID, stepDesc = "flt_licSubtypeOra")
MARFLEETS_LIC <- MARFLEETS_LIC_S
if (all(is.na(args$lics$LIC_SP))){
MARFLEETS_LIC_SP <- MARFLEETS_LIC
} else{
MARFLEETS_LIC_SP <- MARFLEETS_LIC[MARFLEETS_LIC$SPECIES_CODE %in% args$lics$LIC_SP,]
}
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_SP$LICENCE_ID, stepDesc = "flt_licSppOra")
MARFLEETS_LIC <- MARFLEETS_LIC_SP
MARFLEETS_LIC_new <- MARFLEETS_LIC[which(eval(parse(text=theseLics))),]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_new$LICENCE_ID, stepDesc = "flt_licTypeSubtypeSpComboOra")
MARFLEETS_LIC <- MARFLEETS_LIC_new
dateFilt <- paste0("MARFLEETS_LIC$L_ORIGIN_DATE <= '", args$dateEnd, "' & MARFLEETS_LIC$L_EXPIRY_DATE >= '",args$dateStart,"'")
MARFLEETS_LIC_new_date <- MARFLEETS_LIC[which(eval(parse(text=dateFilt))),]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_new_date$LICENCE_ID, stepDesc = "flt_licDatesOra")
#if (args$debug) Mar.utils::changeDetector(pre_ = MARFLEETS_LIC_new, post_ = MARFLEETS_LIC_new_date, fields = "LICENCE_ID", flagTxt = "lic start end dates applied")
MARFLEETS_LIC <- MARFLEETS_LIC_new_date
# if (all(is.na(args$marfGear))){
# MARFLEETS_LIC_GR <- MARFLEETS_LIC
# } else{
# MARFLEETS_LIC_GR <- MARFLEETS_LIC[MARFLEETS_LIC$GEAR_CODE %in% unique(c(-99,args$marfGear)),]
# }
# if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = MARFLEETS_LIC_GR$LICENCE_ID, stepDesc = "flt_licGearOra")
# MARFLEETS_LIC <- MARFLEETS_LIC_GR
}else{
where_dateFilt <- paste0(" AND (MARFLEETS_LIC.L_ORIGIN_DATE <= to_date('", args$dateEnd, "','YYYY-MM-DD') AND
MARFLEETS_LIC.L_EXPIRY_DATE >= to_date('",args$dateStart,"','YYYY-MM-DD'))")
# where_gearFilt <- paste0(" AND MARFLEETS_LIC.GEAR_CODE IN (-99, ", Mar.utils::SQL_in(args$marfGear, apos = F),")")
MARFLEETS_LIC_new_Qry <- paste0("SELECT *
FROM MARFISSCI.MARFLEETS_LIC
WHERE (", theseLicsOra, ") ",where_dateFilt)
#, where_gearFilt)
MARFLEETS_LIC_new <- args$cxn$thecmd(args$cxn$channel, MARFLEETS_LIC_new_Qry)
}
LICDETS<- unique(MARFLEETS_LIC_new[,c("LICENCE_TYPE_ID", "LICENCE_TYPE", "LICENCE_SUBTYPE_ID", "LICENCE_SUBTYPE", "GEAR_CODE", "GEAR", "SPECIES_CODE", "SPECIES")])
licDf <- unique(MARFLEETS_LIC_new[,c("LICENCE_ID","LICENCE_TYPE_ID", "LICENCE_SUBTYPE_ID", "GEAR_CODE", "SPECIES_CODE", "L_ORIGIN_DATE", "L_EXPIRY_DATE")])
res=list()
res[["LICDETS"]]<- LICDETS
res[["licDf"]]<- licDf
if (args$debug) {
t07_ <- proc.time() - t07
message("\tExiting get_fleetLicences_ora() (",round(t07_[1],0),"s elapsed)")
}
return(res)
}
get_fleetActivity_loc<- function(licDf = NULL, ...){
args <- list(...)$args
if (args$debug) t08 <- Mar.utils::where_now(returnTime = T)
Mar.utils::get_data_tables(schema = "MARFISSCI", data.dir = args$data.dir,
tables = c("PRO_SPC_INFO","TRIPS","NAFO_UNIT_AREAS", "VESSELS"),
usepkg=args$usepkg, fn.oracle.username = args$oracle.username, fn.oracle.dsn=args$oracle.dsn, fn.oracle.password = args$oracle.password, env = environment(), quietly = TRUE, fuzzyMatch=FALSE)
# if ("GASP" %in% args$lics$FLEET){
# PRO_SPC_INFO= PRO_SPC_INFO[,c("LICENCE_ID","PRO_SPC_INFO_ID", "TRIP_ID", "LOG_EFRT_STD_INFO_ID","GEAR_CODE","MON_DOC_ID","NAFO_UNIT_AREA_ID", "DATE_FISHED", "LANDED_DATE")]
# TRIPS = PRO_SPC_INFO[,c("PRO_SPC_INFO_ID","DATE_FISHED", "LANDED_DATE")]
# colnames(TRIPS)[colnames(TRIPS)=="DATE_FISHED"] <- "T_DATE1"
# colnames(TRIPS)[colnames(TRIPS)=="LANDED_DATE"] <- "T_DATE2"
# }else{
PRO_SPC_INFO= PRO_SPC_INFO[,c("LICENCE_ID","PRO_SPC_INFO_ID", "TRIP_ID", "LOG_EFRT_STD_INFO_ID","GEAR_CODE","MON_DOC_ID","NAFO_UNIT_AREA_ID")]
#TRIPS
TRIPS <- TRIPS[,c("TRIP_ID","VR_NUMBER", "EARLIEST_DATE_TIME","LATEST_DATE_TIME")]
colnames(TRIPS)[colnames(TRIPS)=="EARLIEST_DATE_TIME"] <- "T_DATE1"
colnames(TRIPS)[colnames(TRIPS)=="LATEST_DATE_TIME"] <- "T_DATE2"
# }
# Handle the various data we just pulled ------------------------------------------------------------------------------------------------------------------
TRIPS$T_DATE1 <- as.Date(TRIPS$T_DATE1)
TRIPS$T_DATE2 <- as.Date(TRIPS$T_DATE2)
#NAFO
if (!"NAFO_AREA" %in% names(NAFO_UNIT_AREAS)) names(NAFO_UNIT_AREAS)[names(NAFO_UNIT_AREAS) == "AREA"] <- "NAFO_AREA"
NAFO_UNIT_AREAS <- NAFO_UNIT_AREAS[,c("AREA_ID", "NAFO_AREA")]
PRO_SPC_INFO_new <-PRO_SPC_INFO[PRO_SPC_INFO$LICENCE_ID %in% licDf$LICENCE_ID,]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = PRO_SPC_INFO_new$LICENCE_ID, stepDesc = "flt_PSLics")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = PRO_SPC_INFO_new$VR_NUMBER, stepDesc = "flt_PSLics")
if (!is.null(dbEnv$debugMARFTripIDs)) dbEnv$debugMARFTripIDs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugMARFTripIDs, expected = dbEnv$debugMARFTripIDs, expectedID = "debugMARFTripIDs", known = PRO_SPC_INFO_new$TRIP_ID, stepDesc = "flt_PSLics")
PRO_SPC_INFO <- PRO_SPC_INFO_new
# Grab fishing activity of those with valid gear code -------------------------------------------------------------------------------
PRO_SPC_INFO_new<-PRO_SPC_INFO[PRO_SPC_INFO$GEAR_CODE %in% args$marfGear,]
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = PRO_SPC_INFO_new$LICENCE_ID, stepDesc = "flt_PSGrs")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = PRO_SPC_INFO_new$VR_NUMBER, stepDesc = "flt_PSGrs")
if (!is.null(dbEnv$debugMARFTripIDs)) dbEnv$debugMARFTripIDs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugMARFTripIDs, expected = dbEnv$debugMARFTripIDs, expectedID = "debugMARFTripIDs", known = PRO_SPC_INFO_new$TRIP_ID, stepDesc = "flt_PSGrs")
PRO_SPC_INFO <- PRO_SPC_INFO_new
# Limit fishing activity to desired date range ------------------------------------------------------------------------------------------------------------
TRIPS <- TRIPS[which(TRIPS$T_DATE1 <= as.Date(args$dateEnd) & TRIPS$T_DATE2 >= as.Date(args$dateStart)),]
# if ("GASP" %in% args$lics$FLEET){
# PRO_SPC_INFO_new <- PRO_SPC_INFO[PRO_SPC_INFO$PRO_SPC_INFO_ID %in% TRIPS$PRO_SPC_INFO_ID,]
# # PRO_SPC_INFO_new <- merge(PRO_SPC_INFO_new, TRIPS)
# }else{
PRO_SPC_INFO_new <- PRO_SPC_INFO[PRO_SPC_INFO$TRIP_ID %in% TRIPS$TRIP_ID,]
PRO_SPC_INFO_new <- merge(PRO_SPC_INFO_new, TRIPS)
# }
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = PRO_SPC_INFO_new$LICENCE_ID, stepDesc = "flt_PSDates")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = PRO_SPC_INFO_new$VR_NUMBER, stepDesc = "flt_PSDates")
if (!is.null(dbEnv$debugMARFTripIDs)) dbEnv$debugMARFTripIDs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugMARFTripIDs, expected = dbEnv$debugMARFTripIDs, expectedID = "debugMARFTripIDs", known = PRO_SPC_INFO_new$TRIP_ID, stepDesc = "flt_PSDates")
#if (args$debug) Mar.utils::changeDetector(pre_ = PRO_SPC_INFO, post_ = PRO_SPC_INFO_new, fields = "LICENCE_ID", flagTxt = "PS filtered by dates")
PRO_SPC_INFO <- PRO_SPC_INFO_new
# limit fishing activity to fleet-specified areas ---------------------------------------------------------------------------------------------------------
PRO_SPC_INFO = merge(PRO_SPC_INFO, NAFO_UNIT_AREAS, by.x="NAFO_UNIT_AREA_ID", by.y = "AREA_ID", all.x=T )
if (nrow(args$area)>0 & any(args$area$AREA_TYPE =="NAFO")){
nafoCode <- gsub(pattern = "%", x=args$area$AREA, replacement = "",ignore.case = T)
NAFO_UNIT_AREAS <- NAFO_UNIT_AREAS[grep(paste(nafoCode, collapse = '|'),NAFO_UNIT_AREAS$NAFO_AREA),]
PRO_SPC_INFO_new <- PRO_SPC_INFO[PRO_SPC_INFO$NAFO_UNIT_AREA_ID %in% NAFO_UNIT_AREAS$AREA_ID,]
if (!is.null(dbEnv$debugMARFTripIDs)) dbEnv$debugMARFTripIDs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugMARFTripIDs, expected = dbEnv$debugMARFTripIDs, expectedID = "debugMARFTripIDs", known = PRO_SPC_INFO_new$TRIP_ID, stepDesc = "flt_PSNAFOAreas")
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = PRO_SPC_INFO_new$LICENCE_ID, stepDesc = "flt_PSNAFOAreas")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = PRO_SPC_INFO_new$VR_NUMBER, stepDesc = "flt_PSNAFOAreas")
PRO_SPC_INFO$NAFO_AREA <- NULL
#if (args$debug) Mar.utils::changeDetector(pre_ = PRO_SPC_INFO, post_ = PRO_SPC_INFO_new, fields = "LICENCE_ID", flagTxt = "PS filtered by licenced NAFO")
PRO_SPC_INFO <- PRO_SPC_INFO_new
}
PRO_SPC_INFO <- merge(PRO_SPC_INFO, VESSELS[, c("VR_NUMBER", "LOA")], all.x = T)
# Clean results -------------------------------------------------------------------------------------------------------------------------------------------
PRO_SPC_INFO$NAFO_UNIT_AREA_ID<-PRO_SPC_INFO$TRIP_ID <- NULL
if (nrow(PRO_SPC_INFO)<1) {
stop("No fleet activity found")
}
if (args$debug) {
t08_ <- proc.time() - t08
message("\tExiting get_fleetActivity_loc() (",round(t08_[1],0),"s elapsed)")
}
return(PRO_SPC_INFO)
}
get_fleetActivity_ora<- function(licDf = NULL, ...){
args <- list(...)$args
if (args$debug) t09 <- Mar.utils::where_now(returnTime = T)
where_date <- paste0("AND (T.EARLIEST_DATE_TIME <= to_date('",args$dateEnd,"','YYYY-MM-DD') AND T.LATEST_DATE_TIME >= to_date('",args$dateStart,"','YYYY-MM-DD'))")
where_Gr <- paste0("AND PS.GEAR_CODE IN (",Mar.utils::SQL_in(args$marfGear,apos = F),")")
if (nrow(args$area)>0 & any(args$area$AREA_TYPE =="NAFO")){
where_Area <- paste0("AND (",paste0("N.AREA LIKE ('",paste0(unique(args$area$AREA),"%"),"')", collapse = " OR "),")")
}else{
where_Area = ""
}
fleetAct_qry = paste0("SELECT PS.LICENCE_ID, PS.PRO_SPC_INFO_ID, PS.LOG_EFRT_STD_INFO_ID, PS.GEAR_CODE, PS.MON_DOC_ID,
MD.VR_NUMBER, T.EARLIEST_DATE_TIME T_DATE1,T.LATEST_DATE_TIME T_DATE2,
N.AREA NAFO, V.LOA
FROM MARFISSCI.PRO_SPC_INFO PS, MARFISSCI.TRIPS T, MARFISSCI.NAFO_UNIT_AREAS N, MARFISSCI.MON_DOCS MD,
MARFISSCI.VESSELS V
WHERE
MD.MON_DOC_ID = PS.MON_DOC_ID
AND PS.TRIP_ID = T.TRIP_ID
AND MD.VR_NUMBER = V.VR_NUMBER
AND PS.NAFO_UNIT_AREA_ID = N.AREA_ID "
,where_date, " "
,where_Gr, " "
,where_Area
)
theFleet = args$cxn$thecmd(args$cxn$channel, fleetAct_qry)
if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = theFleet$LICENCE_ID, stepDesc = "flt_PSDates")
if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = theFleet$VR_NUMBER, stepDesc = "flt_PSDates")
theFleet$NAFO <- NULL
# theFleet2 <- theFleet[paste0(theFleet$LICENCE_ID,"_", theFleet$GEAR_CODE) %in% all_LicGr,]
# if (!is.null(dbEnv$debugLics)) dbEnv$debugLics <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugLics, expected = dbEnv$debugLics, expectedID = "debugLics", known = theFleet$LICENCE_ID, stepDesc = "flt_PSLicGears")
# if (!is.null(dbEnv$debugVRs)) dbEnv$debugVRs <- Mar.utils::updateExpected(quietly = TRUE, df=dbEnv$debugVRs, expected = dbEnv$debugVRs, expectedID = "debugVRs", known = theFleet$VR_NUMBER, stepDesc = "flt_PSLicGears")
# if (args$debug) Mar.utils::changeDetector(pre_ = theFleet, post_ = theFleet2, fields = "LICENCE_ID", flagTxt = "PS filtered by licence/gear combo")
# theFleet <- theFleet2
if (nrow(theFleet)<1) stop("No fleet activity found")
if (args$debug) {
t09_ <- proc.time() - t09
message("\tExiting get_fleetActivity_ora() (",round(t09_[1],0),"s elapsed)")
}
return(theFleet)
}
get_fleetGear<-function(df = NULL, ...){
# this could entirely replaced by chk_Gears
args <- list(...)$args
if (args$debug) t10 <- Mar.utils::where_now(returnTime = T)
gearSpecRelevant <- do.call(chk_Gears, list(df, args=args))
if(nrow(gearSpecRelevant)<1) {
if (args$debug) {
t10_ <- proc.time() - t10
message("\tExiting get_fleetGear() - no gearSpecRelevant: (", round(t10_[1],0),"s elapsed)")
}
return(df)
}
if (nrow(args$gearSpecs)>0){
#merge the gear details from both LOG_EFRT and MON_DOC onto the df
df_merge <- unique(df[, c("PRO_SPC_INFO_ID","LOG_EFRT_STD_INFO_ID", "MON_DOC_ID")])
df_LE <- gearSpecRelevant[gearSpecRelevant$GEAR_SRC == "LE",c("ID_FLD", "GR_TYPE", "GR_SIZE")]
df_LE <- merge(df_merge, df_LE, by.x="LOG_EFRT_STD_INFO_ID", by.y = "ID_FLD")
df_MD <- gearSpecRelevant[gearSpecRelevant$GEAR_SRC == "MD",c("ID_FLD", "GR_TYPE", "GR_SIZE")]
df_MD <- merge(df_merge, df_MD, by.x="MON_DOC_ID", by.y = "ID_FLD")
allReportedGears <- rbind.data.frame(df_LE, df_MD)
df <- merge(df, allReportedGears, all.x = T)
#flag those with no gear info as -999
df[["GR_TYPE"]][is.na(df[["GR_TYPE"]])] <- -999
df[["GR_SIZE"]][is.na(df[["GR_SIZE"]])] <- -999
if (args$debug) message("n records - pre-size/type filts: ", nrow(df))
if (!is.na(args$gearSpecs$TYPE)){
df= do.call(typeFilt, list(df, args=args))
if (args$debug) message("n records - post-typeFilt: ", nrow(df))
}
if (!is.na(args$gearSpecs$MIN)){
df= do.call(sizeFilt, list(df, args=args))
if (args$debug) message("n records - post-sizeFilt: ", nrow(df))
}
}
if (nrow(df)<1){
message("\n","No fleet gear found")
}
if (args$debug) {
t10_ <- proc.time() - t10
message("\tExiting get_fleetGear() (",round(t10_[1],0),"s elapsed)")
}
return(df)
}
if (args$useLocal){
licDf_tmp <- do.call(get_fleetLicences_loc, args)
}else{
licDf_tmp <- do.call(get_fleetLicences_ora, args)
}
licDets <- licDf_tmp$LICDETS
licDf <- licDf_tmp$licDf
if (args$useLocal){
actDf <- do.call(get_fleetActivity_loc, list(licDf=licDf, args=args))
}else{
actDf <- do.call(get_fleetActivity_ora, list(licDf=licDf, args=args))
}
df <- do.call(get_fleetGear, list(df=actDf,args=args))
df$NAFO <-NULL
df <- unique(df[with(df,order(VR_NUMBER, LICENCE_ID, GEAR_CODE, LOA )),])
res <- list()
res[["LICDETS"]]<-licDets
res[["FLEET"]] <- unique(df[with(df,order(VR_NUMBER, LICENCE_ID, GEAR_CODE, LOA )),c("VR_NUMBER", "LICENCE_ID", "GEAR_CODE", "LOA")])
df$LOA <- df$NAFO_AREA <- NULL
res[["FLEET_ACTIVITY"]]<- df
if (args$debug) {
t02_ <- proc.time() - t02
message("\tExiting get_fleet() (",round(t02_[1],0),"s elapsed)")
}
return(res)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.