In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
title: "Bycatch Data Submission"
author: "Lobster Group, Science Branch "
output: tint::tintPdf
1. Data was collected
dat$Y<- convert.dd.dddd(dat$LATDDMM, format="dec.deg")
dat$X<- convert.dd.dddd(dat$LONGDDMM, format="dec.deg")*-1
dat$EID<- 1:nrow(dat)
xlim = c(min(dat$X)-0.5, max(dat$X)+0.5)
ylim = c(min(dat$Y)-0.5, max(dat$Y)+0.5)
x11(10,10)
LobsterMap(ylim=ylim ,xlim=xlim, labels = 'lfa')
attr(dat,"projection") <- "LL"
addPoints(dat, pch = 21, cex=1.5, bg='red')
ll<-unique(dat$COMAREA_ID)
lll<-ifelse(nchar(ll)==3,3,4)
ll<-substr(ll,2,lll)
title(paste0("LFA", ll))
2. What group entered the data and the name of the data file that was imported
cat(paste("<br> <ul>", unique(dat$OWNER_GROUP),unique(dat$TRIP),"</br> </ul>"))
if(!grepl(unique(dat$TRIP),nm)){
print(paste("<br><ul> \textcolor{red}{Trip File Name does not match TRIP column in Data Sheet. Check ",Fi[i],"} </br></ul>",sep=" "))
}
3. Do the coordinates match the Grids and LFA?
dat$COMAREA_ID[which(dat$COMAREA_ID =="L31A")]<-311
dat$COMAREA_ID[which(dat$COMAREA_ID =="L31B")]<-312
ll=unique(dat$COMAREA_ID)
if(!unique(dat$COMAREA_ID) %in% c(311,312)){
ll<-unique(dat$COMAREA_ID)
lll<-ifelse(nchar(ll)==3,3,4)
ll<-substr(ll,2,lll)
}
LFAs<-subset(LFAS, PID ==ll )
LFAgrid<-subset(LFAGrid, PID == ll)
#Convert to Decimal Degrees
dat$Y<-convert.dd.dddd(dat$LATDDMM, format="dec.deg")
dat$X<-(convert.dd.dddd(dat$LONGDDMM, format="dec.deg")*-1)
dat$EID = 1:nrow(dat)
#Check LFA Locations
locCheck<-findPolys(dat, LFAs)
if(is.null(locCheck)){
cat(paste0("<br> <ul> \textcolor{red}{ERROR:Wrong LFA identified} </br> </ul>"))
}else{
missingLoc<-merge(dat, locCheck, all.x = T, by = "EID")
missedLoc<-subset(missingLoc, is.na(PID))
if(nrow(missedLoc)>0){
print(paste0("<br> <ul> \textcolor{red}{ERROR:LFA locations missing or incorrect. Check line(s)",paste(as.numeric(row.names(missedLoc))+1, collapse=" , "),"}", sep=" ", "</br> </ul>"))
} else {print("<br> <ul> <center> All locations match LFA </br> </ul> </center>")
}
#Check Grid Locations
glocCheck<-findPolys(dat, LFAgrid)
#Find missing grid locations - or locations that don't pair with corresponding grids
missingGLoc<-merge(dat, glocCheck, all.x = T, by = "EID")
missedGLoc<-subset(missingGLoc, is.na(PID))
if(nrow(missedGLoc)>0){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Grid locations missing or incorrect. Check line(s) ", paste(as.numeric(row.names(missedGLoc))+1,collapse=","), "}", sep=" ", "</br> </ul>"))
} else {cat("<br> <ul> All locations match grids </br> </ul>")
}
}
4. Are males berried or notched?
dat$SEXCHECK<-NA
dat$SEXCHECK<- ifelse(dat$SPECCD_ID ==2550 & dat$SEXCD_ID == 1 & !is.na(dat$VNOTCH) , 1, dat$SEXCHECK)
notchcheck<-any(dat$SEXCHECK == 1, na.rm = T)
notchmales<-which(dat$SEXCHECK == 1)
if(notchcheck == T){
print(paste0("<br> <ul> \textcolor{red}{ERROR:Check SEX and NOTCH. Errors on line(s) ",paste(notchmales+1, collapse=" , "), "}", sep=" ", "</br> </ul>"))
}else {cat("<br> <ul> No Males are V-notched </br> </ul>")
}
dat$SEXCHECK <- NULL
5. Is the length between a reasonable size 30-250mm?
dat$CLCHECK<-NA
dat$CLCHECK<- ifelse(dat$SPECCD_ID == 2550 & (dat$FISH_LENGTH <=30 | dat$FISH_LENGTH >=250), 1, dat$CLCHECK)
sizecheck<-any(dat$CLCHECK ==1, na.rm=T)
wrongsize<-which(dat$CLCHECK==1)
if(sizecheck == T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Sizes are not reasonable. Check for errors on line(s) ", paste(wrongsize+1, collapse=" , "), "}", sep= " ", "</br> </ul>"))
}else{cat("<br> <ul> Carapace sizes reasonable </br> </ul>")}
dat$CLCHECK <- NULL
6. Is Length, Shell, Disease, Sex and Condition recorded for all Lobster?
dat$LENGTHDAT<-NA
dat$LENGTHDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$FISH_LENGTH), 1, dat$LENGTHDAT)
lengthcheck<-any(dat$LENGTHDAT == 1, na.rm=T)
nolength<-which(dat$LENGTHDAT==1)
if(lengthcheck == T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for carapace length. Check line(s) ", paste(nolength+1, collapse=" , "), "}", sep=" ", "</br> </ul>"))
}else{ cat("<br> <ul> Carapace lengths recorded </br> </ul> ")
}
dat$SHELLDAT<-NA
dat$SHELLDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$SHELL), 1, dat$SHELLDAT)
shellcheck<-any(dat$SHELLDAT == 1, na.rm=T)
noshell<-which(dat$SHELLDAT==1)
if(shellcheck == T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for shell hardness. Check line(s) ", paste(noshell+1, collapse=" , "),"}", sep = " ", "</br> </ul>"))
}else{ cat("<br> <ul> Shell hardness recorded </br> </ul>")
}
dat$SICDAT<-NA
dat$SICDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$DISEASE), 1, dat$SICDAT)
siccheck<-any(dat$SICDAT == 1, na.rm=T)
nosic<-which(dat$SICDAT==1)
if(siccheck == T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for disease. Check line(s) ", paste(nosic+1, collapse=" , "), "}", sep = " ", "</br> </ul>"))
}else{ cat("<br> <ul> Disease status recorded </br> </ul>")
}
dat$SEXDAT<-NA
dat$SEXDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$SEXCD_ID), 1, dat$SEXDAT)
sexcheck<-any(dat$SEXDAT == 1, na.rm=T)
nosex<-which(dat$SEXDAT==1)
if(sexcheck == T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for sex. Check line(s) ", paste(nosex+1, collapse=" , "), "}",sep=" ", "</br> </ul>"))
}else{ cat("<br> <ul> Sex recorded </br> </ul>")
}
dat$CONDAT<-NA
dat$CONDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$CONDITION_CD), 1, dat$CONDAT)
concheck<-any(dat$CONDAT == 1, na.rm=T)
nocon<-which(dat$CONDAT==1)
if(concheck == T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for condition. Check line(s) ", paste(nocon+1, collapse=" , "), "}", sep=" ", "</br> </ul>"))
}else{ cat("<br> <ul> Condition recorded </br> </ul>")
}
7. Is the depth less than a maximum fishing depth ?
dat$DEPTHCHECK<-NA
dat$DEPTHCHECK<-ifelse(dat$DEPTH <= 300,0,1)
deepcheck<-any(dat$DEPTHCHECK ==1,na.rm=T)
baddepth<-which(dat$DEPTHCHECK==1)
if(deepcheck==T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Depths exceed a maximum fishing depth. Check line(s) ", paste(baddepth+1, collapse=" , "), "}", sep = " ", "</br> </ul>"))
}else{cat("<br> <ul> Depths within reasonable range </br> </ul>")}
dat$DEPTHCHECK <- NULL
8. Were any lobster kept below the MLS for the given LFA?
```r
MLS=82.5
dat$smallretained <-0
if(unique(dat$COMAREA_ID) %in% c("L28","L29")){
MLS=84 }
dat$smallretained[which(dat$SPECCD_ID ==2550 & dat$FISH_LENGTH < MLS & dat$KEPT == 1)]<-1
if(any(dat$smallretained ==1) ){
ij<-which(dat$smallretained==1)
print(paste0("<br> <ul> \textcolor{red}{ERROR:Lobsters kept below MLS. Check line(s) ", paste(ij+1, collapse=" , "), "}",sep = " ", "</br> </ul>"))
}else{cat("<br> <ul> No small lobsters retained </br> </ul>")}
dat$smallretained = NULL
**9. Were female between 114-124mm kept in LFA 31a?**
```r
dat$window<- 0
dat$window<- ifelse(dat$COMAREA_ID %in% c(311) & dat$SEXCD_ID %in% c(2,3) & dat$SPECCD_ID == 2550 & dat$FISH_LENGTH %in% c(114:124) & dat$KEPT %in% c(1), 1, 0)
if(any(dat$window == 1)){
ko<-which(dat$window ==1)
print(paste0("<br> <ul> \textcolor{red}{ERROR:Lobsters kept between 114-124mm in 31a. Check line(s)", paste(ko+1, collapse=" , "), "}", sep = " ", "</br> </ul>"))
} else {
cat("<br> <ul> No window restricted lobsters were kept </br> </ul>")
}
dat$window = NULL
10. Were v-notched lobster retained in prohibited LFAs?
dat$keepnotch<-0
if(any(is.na(dat$KEPT))) dat$KEPT[which(is.na(dat$KEPT))] <- 0
dat$keepnotch<- ifelse(dat$COMAREA_ID %ni% c("L27","L31A") & !is.na(dat$VNOTCH) & dat$KEPT == 1,1,0)
if(any(dat$keepnotch ==1)){
pl<- which(dat$keepnotch==1)
print(paste0("<br> <ul> \textcolor{red}{ERROR:V-notched lobsters retained in prohibited LFA. Check line(s) ", paste(pl+1, collapse=" , "), "}", sep = " ", "</br> </ul>"))
}else{
cat("<br> <ul> No vnotched lobster retained in prohibited area </br> </ul>")
}
dat$keepnotch =NULL
11. Is abundance greater than 1 for anything other than whelks, starfish, urchins?
dat$AMOUNT<-NA
dat$AMOUNT<- ifelse((dat$SPECSCD_ID <= 1000 | dat$SPECCD_ID %in% c(2550,2513,2511,2531,2520,2526)) & (dat$ABUNDANCE > 1), 1, 0)
amountcheck<- any(dat$AMOUNT ==1, na.rm=T)
wrongamount<-which(dat$AMOUNT==1)
if(amountcheck ==T){
print(paste0("<br> <ul> \textcolor{red}{ERROR:Check Abundance. Error on line(s)", paste(wrongamount+1, collapse=" , "), "}", sep = " ", "</br> </ul>"))
} else {
cat("<br> <ul> Abundance is correct </br> </ul>")
}
dat$AMOUNT<-NULL
12. If species is not a berried lobster does it have clutch and egg categories filled out?
dat$BERRIED<-NA
dat$BERRIED<- ifelse(dat$SPECCD_ID ==2550 & dat$SEXCD_ID %in% c(1,2) & c(!is.na(dat$CLUTCH) | !is.na(dat$EGG_STAGE)),1,0)
notberried<- any(dat$BERRIED == 1, na.rm=T)
noberries<-which(dat$BERRIED==1)
if(notberried ==T){
print(paste0("<br> <ul> \textcolor{red}{ERROR:Check SEX, CLUTCH, an/or EGG STAGE. Error on line(s) ", paste(noberries+1, collapse=" , "), "}", sep = " ", "</br> </ul>"))
} else {
cat("<br> <ul> Only berried females have egg and clutch information </br> </ul>")
}
dat$BERRIED<-NULL
13. If a lobster is berried is egg stage and clutch size recorded?
dat$BERRIES<-NA
dat$BERRIES<- ifelse(dat$SPECCD_ID ==2550 & dat$SEXCD_ID== 3 & c(is.na(dat$CLUTCH) | is.na(dat$EGG_STAGE)),1,0)
berried<- any(dat$BERRIES == 1, na.rm=T)
noberried<-which(dat$BERRIES==1)
if(berried ==T){
print(paste0("<br> <ul> \textcolor{red}{ERROR:Check CLUTCH and/or EGG STAGE. Error on line(s) ", paste(noberried+1, collapse=" , "), "}", sep= " ", "</br> </ul>"))
} else {
cat("<br> <ul> Berried females have egg and clutch information </br> </ul>")
}
dat$BERRIES<-NULL
14. Do all crab species entries have length, sex and condition recorded?
dat$CRABBIE<-NA
dat$CRABBIE<- ifelse(dat$SPECCD_ID %in% c(2513,2511,2531,2520,2526) & (dat$FISH_LENGTH < 1 | is.na(dat$FISH_LENGTH)) & (!dat$SEXCD_ID %in% c(1,2,3) | is.na(dat$SEXCD_ID)), 1, 0)
crabinfo<- any(dat$CRABBIE ==1, na.rm=T)
nocrab<- which(dat$CRABBIE ==1)
if(crabinfo ==T){
print(paste0("<br> <ul> <center> \textcolor{red}{ERROR:Check SEX and/or FISH LENGTH. Error on line(s) ", paste(nocrab+1, collapse=" , "), "}", sep= " ", "</br> </ul> </center>"))
} else {
cat("<br> <ul> All crabs have length and sex recorded </br> </ul>")
}
dat$CRABBIE<- NULL
dat$CCONDAT<-NA
dat$CCONDAT<-ifelse(dat$SPECCD_ID %in% c(2513,2511,2531,2520,2526) & is.na(dat$CONDITION_CD), 1, dat$CCONDAT)
cconcheck<-any(dat$CCONDAT == 1, na.rm=T)
noccon<-which(dat$CCONDAT==1)
if(cconcheck == T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for condition. Check line(s) ", paste(nocon+1, collapse=" , "), "}", sep= " ","</br> </ul>"))
} else {
cat("<br> <ul> Condition recorded </br> </ul>")
}
dat$CCONDAT <- NULL
15. Does anything other than a lobster have the notch category filled out?
dat$NOTCHED<- NA
dat$NOTCHED<- ifelse(!dat$SPECCD_ID==2550 & !is.na(dat$VNOTCH),1,0)
nonotch<- any(dat$NOTCHED==1, na.rm=T)
notchless<- which(dat$NOTCHED ==1)
if(nonotch ==T){
print(paste0("<br> <ul> \textcolor{red}{ERROR:Check NOTCH on line(s) ", paste(notchless+1, collapse=" , "),"}", sep= " ", "</br> </ul>"))
} else {
cat("<br> <ul> Only lobster have notches </br> </ul>")
}
dat$NOTCHED<-NULL
16. Do all Fish species entries have length, condition recorded?
dat$FISHY<-NA
dat$FISHY<- ifelse(dat$SPECCD_ID <1000 & c(dat$FISH_LENGTH < 1 | is.na(dat$FISH_LENGTH)), 1, 0)
fishinfo<- any(dat$FISHY ==1, na.rm=T)
nofish<- which(dat$FISHY ==1)
if(fishinfo ==T){
print(paste0("<br> <ul> \textcolor{red}{ERROR: Check FISH LENGTH on line(s) ", paste(nofish+1, collapse=" , "),"}", "</br> </ul>",sep=" "))
} else {
cat("<br> <ul> All fish have length recorded </br> </ul>")
}
dat$FISHY<- NULL
dat$CCONDAT<-NA
dat$CCONDAT<-ifelse(dat$SPECCD_ID %in% c(1:1000,2513,2511,2531,2520,2526) & is.na(dat$CONDITION_CD), 1, dat$CCONDAT)
cconcheck<-any(dat$CCONDAT == 1, na.rm=T)
noccon<-which(dat$CCONDAT==1)
if(cconcheck == T){
cat(paste0(" \textcolor{red}{ERROR: Missing information for CONDITION. Check line(s) ", paste(noccon+1, collapse=" , "),"}", sep=" "))
} else {
cat("<br> <ul> All fish have condition recorded </br> </ul>")
}
dat$CCONDAT <- NULL
17. What is the trap sampling frequency per string?
trapnum<-as.data.frame(unique(cbind(dat$SET_NO,dat$TRAP_NO)))
trapnum<-trapnum[order(trapnum$V1,trapnum$V2),]
trapfreq<-aggregate(V2~V1, data=trapnum,FUN = function(x) mean(diff(x)))
trapfreq$test<-round(trapfreq$V2,0)
names(trapfreq)[1:2]<-c("String", "Frequency")
irrfreq<-which(trapfreq$Frequency != trapfreq$test)
trapfreq$test <-NULL
if(length(irrfreq)> 0){
print(paste0("<br> <ul> \textcolor{red}{ERROR:Irregular trap sampling frequencies in string(s) ", trapfreq[irrfreq,"String"], "}", sep=" ", "</br> </ul>" ))
}
if(length(irrfreq)<nrow(trapfreq)){
cat("<br> <ul> Trap sampling frequencies by string </br> </ul>")
if(length(irrfreq)>=0)cat(paste0("<ul> One in ", unique(trapfreq[-irrfreq,'Frequency']), " traps sampled per string </ul>"))
}
18. What is the total number of traps sampled and total traps hauled
sampled<-length(unique(paste(dat$TRAP_NO,dat$SET_NO,sep="-")))
if(length(sampled)>0){
cat(paste0("<br> <ul> Total number of traps sampled: ", sampled, "</br> </ul>"))
}
totaltrap<-as.data.frame(unique(cbind(dat$SET_NO, dat$NUM_HOOK_HAUL)))
if(sum(totaltrap$V2, na.rm = T)< sampled){
print("<br> <ul> \textcolor{red}{ERROR: Check SET NO and NUM HOOK HAUL numbers do not add up to total traps sampled.}, </br> </ul>")
} else {cat(paste0("<br> <ul> Total number of traps hauled: ", sum(totaltrap$V2),"</br> </ul>"))
}
19. What was the total number of lobsters and other species sampled?
numlob<-length(which(dat$SPECCD_ID==2550))
if(length(numlob>0)){
cat(paste0("<br> <ul> Total number of lobsters sampled: ", numlob, "</br> </ul>"))
}
numother<-length(which(dat$SPECCD_ID != 2550))
if(length(numother>0)){
cat(paste0("<br> <ul> Total number of non lobsters sampled: ", numother, "</br> </ul>"))
}
numother<-length(unique(dat$SPECCD_ID))
if(length(numother>0)){
cat(paste0("<br> <ul> Total number of species: ", numother, "</br> </ul>"))
}
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
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title: "Bycatch Data Submission" author: "Lobster Group, Science Branch " output: tint::tintPdf
1. Data was collected
dat$Y<- convert.dd.dddd(dat$LATDDMM, format="dec.deg") dat$X<- convert.dd.dddd(dat$LONGDDMM, format="dec.deg")*-1 dat$EID<- 1:nrow(dat) xlim = c(min(dat$X)-0.5, max(dat$X)+0.5) ylim = c(min(dat$Y)-0.5, max(dat$Y)+0.5) x11(10,10) LobsterMap(ylim=ylim ,xlim=xlim, labels = 'lfa') attr(dat,"projection") <- "LL" addPoints(dat, pch = 21, cex=1.5, bg='red') ll<-unique(dat$COMAREA_ID) lll<-ifelse(nchar(ll)==3,3,4) ll<-substr(ll,2,lll) title(paste0("LFA", ll))
2. What group entered the data and the name of the data file that was imported
cat(paste("<br> <ul>", unique(dat$OWNER_GROUP),unique(dat$TRIP),"</br> </ul>")) if(!grepl(unique(dat$TRIP),nm)){ print(paste("<br><ul> \textcolor{red}{Trip File Name does not match TRIP column in Data Sheet. Check ",Fi[i],"} </br></ul>",sep=" ")) }
3. Do the coordinates match the Grids and LFA?
dat$COMAREA_ID[which(dat$COMAREA_ID =="L31A")]<-311 dat$COMAREA_ID[which(dat$COMAREA_ID =="L31B")]<-312 ll=unique(dat$COMAREA_ID) if(!unique(dat$COMAREA_ID) %in% c(311,312)){ ll<-unique(dat$COMAREA_ID) lll<-ifelse(nchar(ll)==3,3,4) ll<-substr(ll,2,lll) } LFAs<-subset(LFAS, PID ==ll ) LFAgrid<-subset(LFAGrid, PID == ll) #Convert to Decimal Degrees dat$Y<-convert.dd.dddd(dat$LATDDMM, format="dec.deg") dat$X<-(convert.dd.dddd(dat$LONGDDMM, format="dec.deg")*-1) dat$EID = 1:nrow(dat) #Check LFA Locations locCheck<-findPolys(dat, LFAs) if(is.null(locCheck)){ cat(paste0("<br> <ul> \textcolor{red}{ERROR:Wrong LFA identified} </br> </ul>")) }else{ missingLoc<-merge(dat, locCheck, all.x = T, by = "EID") missedLoc<-subset(missingLoc, is.na(PID)) if(nrow(missedLoc)>0){ print(paste0("<br> <ul> \textcolor{red}{ERROR:LFA locations missing or incorrect. Check line(s)",paste(as.numeric(row.names(missedLoc))+1, collapse=" , "),"}", sep=" ", "</br> </ul>")) } else {print("<br> <ul> <center> All locations match LFA </br> </ul> </center>") } #Check Grid Locations glocCheck<-findPolys(dat, LFAgrid) #Find missing grid locations - or locations that don't pair with corresponding grids missingGLoc<-merge(dat, glocCheck, all.x = T, by = "EID") missedGLoc<-subset(missingGLoc, is.na(PID)) if(nrow(missedGLoc)>0){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Grid locations missing or incorrect. Check line(s) ", paste(as.numeric(row.names(missedGLoc))+1,collapse=","), "}", sep=" ", "</br> </ul>")) } else {cat("<br> <ul> All locations match grids </br> </ul>") } }
4. Are males berried or notched?
dat$SEXCHECK<-NA dat$SEXCHECK<- ifelse(dat$SPECCD_ID ==2550 & dat$SEXCD_ID == 1 & !is.na(dat$VNOTCH) , 1, dat$SEXCHECK) notchcheck<-any(dat$SEXCHECK == 1, na.rm = T) notchmales<-which(dat$SEXCHECK == 1) if(notchcheck == T){ print(paste0("<br> <ul> \textcolor{red}{ERROR:Check SEX and NOTCH. Errors on line(s) ",paste(notchmales+1, collapse=" , "), "}", sep=" ", "</br> </ul>")) }else {cat("<br> <ul> No Males are V-notched </br> </ul>") } dat$SEXCHECK <- NULL
5. Is the length between a reasonable size 30-250mm?
dat$CLCHECK<-NA dat$CLCHECK<- ifelse(dat$SPECCD_ID == 2550 & (dat$FISH_LENGTH <=30 | dat$FISH_LENGTH >=250), 1, dat$CLCHECK) sizecheck<-any(dat$CLCHECK ==1, na.rm=T) wrongsize<-which(dat$CLCHECK==1) if(sizecheck == T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Sizes are not reasonable. Check for errors on line(s) ", paste(wrongsize+1, collapse=" , "), "}", sep= " ", "</br> </ul>")) }else{cat("<br> <ul> Carapace sizes reasonable </br> </ul>")} dat$CLCHECK <- NULL
6. Is Length, Shell, Disease, Sex and Condition recorded for all Lobster?
dat$LENGTHDAT<-NA dat$LENGTHDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$FISH_LENGTH), 1, dat$LENGTHDAT) lengthcheck<-any(dat$LENGTHDAT == 1, na.rm=T) nolength<-which(dat$LENGTHDAT==1) if(lengthcheck == T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for carapace length. Check line(s) ", paste(nolength+1, collapse=" , "), "}", sep=" ", "</br> </ul>")) }else{ cat("<br> <ul> Carapace lengths recorded </br> </ul> ") } dat$SHELLDAT<-NA dat$SHELLDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$SHELL), 1, dat$SHELLDAT) shellcheck<-any(dat$SHELLDAT == 1, na.rm=T) noshell<-which(dat$SHELLDAT==1) if(shellcheck == T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for shell hardness. Check line(s) ", paste(noshell+1, collapse=" , "),"}", sep = " ", "</br> </ul>")) }else{ cat("<br> <ul> Shell hardness recorded </br> </ul>") } dat$SICDAT<-NA dat$SICDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$DISEASE), 1, dat$SICDAT) siccheck<-any(dat$SICDAT == 1, na.rm=T) nosic<-which(dat$SICDAT==1) if(siccheck == T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for disease. Check line(s) ", paste(nosic+1, collapse=" , "), "}", sep = " ", "</br> </ul>")) }else{ cat("<br> <ul> Disease status recorded </br> </ul>") } dat$SEXDAT<-NA dat$SEXDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$SEXCD_ID), 1, dat$SEXDAT) sexcheck<-any(dat$SEXDAT == 1, na.rm=T) nosex<-which(dat$SEXDAT==1) if(sexcheck == T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for sex. Check line(s) ", paste(nosex+1, collapse=" , "), "}",sep=" ", "</br> </ul>")) }else{ cat("<br> <ul> Sex recorded </br> </ul>") } dat$CONDAT<-NA dat$CONDAT<-ifelse(dat$SPECCD_ID == 2550 & is.na(dat$CONDITION_CD), 1, dat$CONDAT) concheck<-any(dat$CONDAT == 1, na.rm=T) nocon<-which(dat$CONDAT==1) if(concheck == T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for condition. Check line(s) ", paste(nocon+1, collapse=" , "), "}", sep=" ", "</br> </ul>")) }else{ cat("<br> <ul> Condition recorded </br> </ul>") }
7. Is the depth less than a maximum fishing depth ?
dat$DEPTHCHECK<-NA dat$DEPTHCHECK<-ifelse(dat$DEPTH <= 300,0,1) deepcheck<-any(dat$DEPTHCHECK ==1,na.rm=T) baddepth<-which(dat$DEPTHCHECK==1) if(deepcheck==T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Depths exceed a maximum fishing depth. Check line(s) ", paste(baddepth+1, collapse=" , "), "}", sep = " ", "</br> </ul>")) }else{cat("<br> <ul> Depths within reasonable range </br> </ul>")} dat$DEPTHCHECK <- NULL
8. Were any lobster kept below the MLS for the given LFA? ```r MLS=82.5 dat$smallretained <-0
if(unique(dat$COMAREA_ID) %in% c("L28","L29")){
MLS=84 }
dat$smallretained[which(dat$SPECCD_ID ==2550 & dat$FISH_LENGTH < MLS & dat$KEPT == 1)]<-1
if(any(dat$smallretained ==1) ){
ij<-which(dat$smallretained==1)
print(paste0("<br> <ul> \textcolor{red}{ERROR:Lobsters kept below MLS. Check line(s) ", paste(ij+1, collapse=" , "), "}",sep = " ", "</br> </ul>"))
}else{cat("<br> <ul> No small lobsters retained </br> </ul>")}
dat$smallretained = NULL
**9. Were female between 114-124mm kept in LFA 31a?**
```r
dat$window<- 0
dat$window<- ifelse(dat$COMAREA_ID %in% c(311) & dat$SEXCD_ID %in% c(2,3) & dat$SPECCD_ID == 2550 & dat$FISH_LENGTH %in% c(114:124) & dat$KEPT %in% c(1), 1, 0)
if(any(dat$window == 1)){
ko<-which(dat$window ==1)
print(paste0("<br> <ul> \textcolor{red}{ERROR:Lobsters kept between 114-124mm in 31a. Check line(s)", paste(ko+1, collapse=" , "), "}", sep = " ", "</br> </ul>"))
} else {
cat("<br> <ul> No window restricted lobsters were kept </br> </ul>")
}
dat$window = NULL
10. Were v-notched lobster retained in prohibited LFAs?
dat$keepnotch<-0 if(any(is.na(dat$KEPT))) dat$KEPT[which(is.na(dat$KEPT))] <- 0 dat$keepnotch<- ifelse(dat$COMAREA_ID %ni% c("L27","L31A") & !is.na(dat$VNOTCH) & dat$KEPT == 1,1,0) if(any(dat$keepnotch ==1)){ pl<- which(dat$keepnotch==1) print(paste0("<br> <ul> \textcolor{red}{ERROR:V-notched lobsters retained in prohibited LFA. Check line(s) ", paste(pl+1, collapse=" , "), "}", sep = " ", "</br> </ul>")) }else{ cat("<br> <ul> No vnotched lobster retained in prohibited area </br> </ul>") } dat$keepnotch =NULL
11. Is abundance greater than 1 for anything other than whelks, starfish, urchins?
dat$AMOUNT<-NA dat$AMOUNT<- ifelse((dat$SPECSCD_ID <= 1000 | dat$SPECCD_ID %in% c(2550,2513,2511,2531,2520,2526)) & (dat$ABUNDANCE > 1), 1, 0) amountcheck<- any(dat$AMOUNT ==1, na.rm=T) wrongamount<-which(dat$AMOUNT==1) if(amountcheck ==T){ print(paste0("<br> <ul> \textcolor{red}{ERROR:Check Abundance. Error on line(s)", paste(wrongamount+1, collapse=" , "), "}", sep = " ", "</br> </ul>")) } else { cat("<br> <ul> Abundance is correct </br> </ul>") } dat$AMOUNT<-NULL
12. If species is not a berried lobster does it have clutch and egg categories filled out?
dat$BERRIED<-NA dat$BERRIED<- ifelse(dat$SPECCD_ID ==2550 & dat$SEXCD_ID %in% c(1,2) & c(!is.na(dat$CLUTCH) | !is.na(dat$EGG_STAGE)),1,0) notberried<- any(dat$BERRIED == 1, na.rm=T) noberries<-which(dat$BERRIED==1) if(notberried ==T){ print(paste0("<br> <ul> \textcolor{red}{ERROR:Check SEX, CLUTCH, an/or EGG STAGE. Error on line(s) ", paste(noberries+1, collapse=" , "), "}", sep = " ", "</br> </ul>")) } else { cat("<br> <ul> Only berried females have egg and clutch information </br> </ul>") } dat$BERRIED<-NULL
13. If a lobster is berried is egg stage and clutch size recorded?
dat$BERRIES<-NA dat$BERRIES<- ifelse(dat$SPECCD_ID ==2550 & dat$SEXCD_ID== 3 & c(is.na(dat$CLUTCH) | is.na(dat$EGG_STAGE)),1,0) berried<- any(dat$BERRIES == 1, na.rm=T) noberried<-which(dat$BERRIES==1) if(berried ==T){ print(paste0("<br> <ul> \textcolor{red}{ERROR:Check CLUTCH and/or EGG STAGE. Error on line(s) ", paste(noberried+1, collapse=" , "), "}", sep= " ", "</br> </ul>")) } else { cat("<br> <ul> Berried females have egg and clutch information </br> </ul>") } dat$BERRIES<-NULL
14. Do all crab species entries have length, sex and condition recorded?
dat$CRABBIE<-NA dat$CRABBIE<- ifelse(dat$SPECCD_ID %in% c(2513,2511,2531,2520,2526) & (dat$FISH_LENGTH < 1 | is.na(dat$FISH_LENGTH)) & (!dat$SEXCD_ID %in% c(1,2,3) | is.na(dat$SEXCD_ID)), 1, 0) crabinfo<- any(dat$CRABBIE ==1, na.rm=T) nocrab<- which(dat$CRABBIE ==1) if(crabinfo ==T){ print(paste0("<br> <ul> <center> \textcolor{red}{ERROR:Check SEX and/or FISH LENGTH. Error on line(s) ", paste(nocrab+1, collapse=" , "), "}", sep= " ", "</br> </ul> </center>")) } else { cat("<br> <ul> All crabs have length and sex recorded </br> </ul>") } dat$CRABBIE<- NULL dat$CCONDAT<-NA dat$CCONDAT<-ifelse(dat$SPECCD_ID %in% c(2513,2511,2531,2520,2526) & is.na(dat$CONDITION_CD), 1, dat$CCONDAT) cconcheck<-any(dat$CCONDAT == 1, na.rm=T) noccon<-which(dat$CCONDAT==1) if(cconcheck == T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Missing information for condition. Check line(s) ", paste(nocon+1, collapse=" , "), "}", sep= " ","</br> </ul>")) } else { cat("<br> <ul> Condition recorded </br> </ul>") } dat$CCONDAT <- NULL
15. Does anything other than a lobster have the notch category filled out?
dat$NOTCHED<- NA dat$NOTCHED<- ifelse(!dat$SPECCD_ID==2550 & !is.na(dat$VNOTCH),1,0) nonotch<- any(dat$NOTCHED==1, na.rm=T) notchless<- which(dat$NOTCHED ==1) if(nonotch ==T){ print(paste0("<br> <ul> \textcolor{red}{ERROR:Check NOTCH on line(s) ", paste(notchless+1, collapse=" , "),"}", sep= " ", "</br> </ul>")) } else { cat("<br> <ul> Only lobster have notches </br> </ul>") } dat$NOTCHED<-NULL
16. Do all Fish species entries have length, condition recorded?
dat$FISHY<-NA dat$FISHY<- ifelse(dat$SPECCD_ID <1000 & c(dat$FISH_LENGTH < 1 | is.na(dat$FISH_LENGTH)), 1, 0) fishinfo<- any(dat$FISHY ==1, na.rm=T) nofish<- which(dat$FISHY ==1) if(fishinfo ==T){ print(paste0("<br> <ul> \textcolor{red}{ERROR: Check FISH LENGTH on line(s) ", paste(nofish+1, collapse=" , "),"}", "</br> </ul>",sep=" ")) } else { cat("<br> <ul> All fish have length recorded </br> </ul>") } dat$FISHY<- NULL dat$CCONDAT<-NA dat$CCONDAT<-ifelse(dat$SPECCD_ID %in% c(1:1000,2513,2511,2531,2520,2526) & is.na(dat$CONDITION_CD), 1, dat$CCONDAT) cconcheck<-any(dat$CCONDAT == 1, na.rm=T) noccon<-which(dat$CCONDAT==1) if(cconcheck == T){ cat(paste0(" \textcolor{red}{ERROR: Missing information for CONDITION. Check line(s) ", paste(noccon+1, collapse=" , "),"}", sep=" ")) } else { cat("<br> <ul> All fish have condition recorded </br> </ul>") } dat$CCONDAT <- NULL
17. What is the trap sampling frequency per string?
trapnum<-as.data.frame(unique(cbind(dat$SET_NO,dat$TRAP_NO))) trapnum<-trapnum[order(trapnum$V1,trapnum$V2),] trapfreq<-aggregate(V2~V1, data=trapnum,FUN = function(x) mean(diff(x))) trapfreq$test<-round(trapfreq$V2,0) names(trapfreq)[1:2]<-c("String", "Frequency") irrfreq<-which(trapfreq$Frequency != trapfreq$test) trapfreq$test <-NULL if(length(irrfreq)> 0){ print(paste0("<br> <ul> \textcolor{red}{ERROR:Irregular trap sampling frequencies in string(s) ", trapfreq[irrfreq,"String"], "}", sep=" ", "</br> </ul>" )) } if(length(irrfreq)<nrow(trapfreq)){ cat("<br> <ul> Trap sampling frequencies by string </br> </ul>") if(length(irrfreq)>=0)cat(paste0("<ul> One in ", unique(trapfreq[-irrfreq,'Frequency']), " traps sampled per string </ul>")) }
18. What is the total number of traps sampled and total traps hauled
sampled<-length(unique(paste(dat$TRAP_NO,dat$SET_NO,sep="-"))) if(length(sampled)>0){ cat(paste0("<br> <ul> Total number of traps sampled: ", sampled, "</br> </ul>")) } totaltrap<-as.data.frame(unique(cbind(dat$SET_NO, dat$NUM_HOOK_HAUL))) if(sum(totaltrap$V2, na.rm = T)< sampled){ print("<br> <ul> \textcolor{red}{ERROR: Check SET NO and NUM HOOK HAUL numbers do not add up to total traps sampled.}, </br> </ul>") } else {cat(paste0("<br> <ul> Total number of traps hauled: ", sum(totaltrap$V2),"</br> </ul>")) }
19. What was the total number of lobsters and other species sampled?
numlob<-length(which(dat$SPECCD_ID==2550)) if(length(numlob>0)){ cat(paste0("<br> <ul> Total number of lobsters sampled: ", numlob, "</br> </ul>")) } numother<-length(which(dat$SPECCD_ID != 2550)) if(length(numother>0)){ cat(paste0("<br> <ul> Total number of non lobsters sampled: ", numother, "</br> </ul>")) } numother<-length(unique(dat$SPECCD_ID)) if(length(numother>0)){ cat(paste0("<br> <ul> Total number of species: ", numother, "</br> </ul>")) }
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