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readICES works with CA=NULL #21

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48 changes: 28 additions & 20 deletions DATRAS/R/read_datras.R
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Original file line number Diff line number Diff line change
Expand Up @@ -116,14 +116,19 @@ readICES <- function(file="IBTS.csv",na.strings=c("-9","-9.0","-9.00","-9.0000")
})

## Data components must come in specific order
d <- d[c("CA", "HH", "HL")]
dout <- vector("list", 3)
if (!is.null(d$CA)) dout[[1]] <- d$CA
if (!is.null(d$HH)) dout[[2]] <- d$HH
if (!is.null(d$HL)) dout[[3]] <- d$HL
names(dout) <- c("CA","HH","HL")
d <- dout
cat("Classes of the variables\n")
print(lapply(d,function(x)sapply(x,class)))
if(sum(sapply(d,nrow)) + length(i) != length(lines))stop("csv file appears to be corrupt.")
if(sum(sapply(d[!sapply(d, is.null)],nrow)) + length(i) != length(lines))stop("csv file appears to be corrupt.")
## Inconsistencies with variable names are resolved here
## =====================================================
## Ices-square variable should have the same name ("StatRec") in age and hydro data.
if(is.null(d[[1]]$StatRec))d[[1]]$StatRec <- d[[1]]$AreaCode
if(!is.null(d$CA) && is.null(d[[1]]$StatRec))d[[1]]$StatRec <- d[[1]]$AreaCode
d <- addExtraVariables(d)
d <- fixMissingHaulIds(d,strict=strict)
class(d) <- "DATRASraw"
Expand Down Expand Up @@ -392,19 +397,21 @@ c.DATRASraw <- function(...){
unionNames <- do.call("Map",c(list("union"),argnames))
addMissingVariables <- function(x){
out <- lapply(1:3,function(i){
ans <- x[[i]]
missingVariables <- setdiff( unionNames[[i]],names(ans) )
if(length(missingVariables)>0){
warning("Incomplete DATRASraw? Missing ",names(x)[i],"-record(s): ",
paste(missingVariables,collapse=", "),
". NA will be inserted.")
if(nrow(ans)>0){
ans[missingVariables] <- NA
} else {
for(ii in 1:length(missingVariables)) ans[,missingVariables[ii]] <- logical(0)
ans <- x[[i]]
if (!is.null(ans)) {
missingVariables <- setdiff( unionNames[[i]],names(ans) )
if(length(missingVariables)>0){
warning("Incomplete DATRASraw? Missing ",names(x)[i],"-record(s): ",
paste(missingVariables,collapse=", "),
". NA will be inserted.")
if(nrow(ans)>0){
ans[missingVariables] <- NA
} else {
for(ii in 1:length(missingVariables)) ans[,missingVariables[ii]] <- logical(0)
}
}
}
}
ans
ans
})
names(out) <- names(x)
out
Expand Down Expand Up @@ -484,12 +491,13 @@ addExtraVariables <- function(IBTS){
## are not different from the submissions with data type R.
## HLNoAtLngt for DataTypes R and S should be multiplied with SubFactor!
## Note, some BITS hauls (all LT and some DK) have dataType C but SubFactor>1 - two multipliers needed!
d3 <- merge(d3,d2[c("haul.id","HaulDur","DataType")],by="haul.id",all.x=TRUE,sort=FALSE)
d3 <- merge(d3[!(colnames(d3) %in% c("HaulDur","DataType"))],
d2[c("haul.id","HaulDur","DataType")],by="haul.id",all.x=TRUE,sort=FALSE)
multiplier1 <- ifelse(d3$DataType=="C",d3$HaulDur/60,1)
multiplier2 <- ifelse(!is.na(d3$SubFactor),d3$SubFactor,1)
d3$Count <- d3$HLNoAtLngt*multiplier1*multiplier2

d2$abstime <- local(Year+(Month-1)*1/12+(Day-1)/365,d2)
d2$abstime <- local(as.integer(Year)+(Month-1)*1/12+(Day-1)/365,d2)
d2$timeOfYear <- local((Month-1)*1/12+(Day-1)/365,d2)
d2$TimeShotHour=as.integer(d2$TimeShot/100) + (d2$TimeShot%%100)/60;
d2 <- transform(d2,lon=ShootLong,lat=ShootLat)
Expand All @@ -506,9 +514,9 @@ addExtraVariables <- function(IBTS){
## ---------------------------------------------------------------------------
diff <- setdiff(levels(d2$haul.id),levels(d3$haul.id)) ## Hauls for which length is missing
if(length(diff)>0){
cat("========= WARNING: ============\n")
cat("Hauls without length info will be interpreted as empty hauls:\n")
print(diff)
cat("========= WARNING: ============\n")
cat("Hauls without length info will be interpreted as empty hauls:\n")
print(diff)
}

## Identical haul levels
Expand Down