R/logbook.db.r
In jae0/bio.snowcrab: Snow crab assessment suite using aegis* and associated projects and data streams.
Defines functions
logbook.db
logbook.db = function( DS, prorate=T, p=NULL, yrs=NULL, fn_root=project.datadirectory("bio.snowcrab") ) {
if (DS %in% c("rawdata.logbook", "rawdata.logbook.redo")) {
fn.loc = file.path( fn_root, "data", "logbook", "datadump" )
dir.create( fn.loc, recursive = TRUE, showWarnings = FALSE )
if (DS=="rawdata.logbook") {
out = NULL
for ( YR in yrs ) {
fny = file.path( fn.loc, paste( YR, "rdata", sep="."))
if (file.exists(fny)) {
load (fny)
out = rbind( out, logbook )
}
}
return (out)
}
con=ROracle::dbConnect(DBI::dbDriver("Oracle"),dbname=oracle.snowcrab.server , username=oracle.snowcrab.user, password=oracle.snowcrab.password, believeNRows=F)
for ( YR in yrs ) {
fny = file.path( fn.loc, paste( YR,"rdata", sep="."))
query = paste(
"SELECT * from marfissci.marfis_crab ",
"where target_spc=705",
"AND EXTRACT(YEAR from DATE_LANDED) = ", YR )
logbook = NULL
#in following line replaced sqlQuery (Rrawdata) with dbGetQuery (ROracle)
logbook = ROracle::dbGetQuery(con, query )
save( logbook, file=fny, compress=T)
gc() # garbage collection
print(YR)
}
ROracle::dbDisconnect(con)
return (yrs)
}
# -------------------------
if (DS %in% c("rawdata.licence.redo", "rawdata.licence" ) ) {
fn.loc = file.path( fn_root, "data", "logbook" )
dir.create( fn.loc, recursive = TRUE, showWarnings = FALSE )
filename.licence = file.path( fn.loc, "lic.datadump.rdata" )
if (DS=="rawdata.licence") {
load(filename.licence)
return (lic)
}
con=ROracle::dbConnect(DBI::dbDriver("Oracle"),dbname=oracle.snowcrab.server , username=oracle.snowcrab.user, password=oracle.snowcrab.password, believeNRows=F)
lic = ROracle::dbGetQuery(con, "select * from marfissci.licence_areas")
save(lic, file=filename.licence, compress=T)
ROracle::dbDisconnect(con)
}
if (DS %in% c("rawdata.areas.redo", "rawdata.areas" ) ) {
fn.loc = file.path( fn_root, "data", "logbook" )
dir.create( fn.loc, recursive = TRUE, showWarnings = FALSE )
filename.areas = file.path( fn.loc, "areas.datadump.rdata" )
if (DS=="rawdata.areas") {
load(filename.areas)
return (areas)
}
con=ROracle::dbConnect(DBI::dbDriver("Oracle"),dbname=oracle.snowcrab.server , username=oracle.snowcrab.user, password=oracle.snowcrab.password, believeNRows=F)
areas = ROracle::dbGetQuery(con, "select * from marfissci.areas")
save(areas, file=filename.areas, compress=T)
ROracle::dbDisconnect(con)
return ("Complete")
}
# -------
if (DS %in% c("logbook.filtered.positions", "logbook.filtered.positions.redo")) {
# exclude data that have positions that are incorrect
filename = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "logbook.filtered.positions.rdata" )
if (DS=="logbook.filtered.positions") {
load( filename )
return(lgbk)
}
lgbk = logbook.db( DS="logbook" )
h = which( !is.na( lgbk$lon + lgbk$lat ) )
lgbk = lgbk[h,]
i = polygon_inside( lgbk[, c("lon", "lat")], region="cfaall")
lgbk = lgbk[i,]
j = polygon_inside( lgbk[, c("lon", "lat")], region="isobath1000m")
lgbk = lgbk[j,]
# additional constraint ..
# remove data that are strange in location .. land
crs_lonlat = st_crs( projection_proj4string("lonlat_wgs84") )
mp = st_multipoint(cbind(p$corners$lon, p$corners$lat))
bbox = st_as_sfc(st_bbox( mp) )
st_crs(bbox) = crs_lonlat
coast = st_transform( st_as_sf(coastline_db( p=p )), crs=crs_lonlat )
coast = (
st_intersection( coast, bbox )
%>% st_buffer(0.01)
%>% st_union()
%>% st_cast("POLYGON" )
%>% st_union()
%>% st_make_valid()
)
inside = st_points_in_polygons(
pts =st_as_sf( lgbk[,c("lon", "lat")], coords=c("lon","lat"), crs=crs_lonlat ),
polys = coast
)
onland = which (is.finite(inside))
if (length(onland)>0) lgbk = lgbk[-onland, ]
# filter by depth ..
# use the match/map syntax in bathymetry and filter out shallow sets .. < 10 m? TODO
# keep those in the domain and deeper than depth=10 m
pL = aegis.bathymetry::bathymetry_parameters( project_class="stmv" )
LUT= aegis_survey_lookuptable( aegis_project="bathymetry",
project_class="core", DS="aggregated_data", pL=pL )
z = aegis_lookup( pL=pL,, LOCS=lgbk[, c("lon", "lat")], LUT=LUT,
output_format="points" ,
space_resolution=p$pres*2, variable_name="z.mean" ) # core=="rawdata"
aoi = which( z > 10 ) # negative = above land
lgbk = lgbk[ aoi,]
# only accept "correctly" positioned data within each subarea ... in case miscoded data have a large effect
icfa4x = polygon_inside( lgbk[, c("lon", "lat")], "cfa4x")
icfanorth = polygon_inside( lgbk[, c("lon", "lat")], "cfanorth")
icfa23 = polygon_inside( lgbk[, c("lon", "lat")], "cfa23")
icfa24 = polygon_inside( lgbk[, c("lon", "lat")], "cfa24")
gooddata = sort( unique( c(icfa4x, icfanorth, icfa23, icfa24 ) ) )
lgbk = lgbk[gooddata, ]
save( lgbk, file=filename, compress=T )
return(filename)
}
# -------
if (DS %in% c("logbook", "logbook.redo")) {
filename = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "logbook.rdata" )
if (DS=="logbook") {
load( filename )
return(logbook)
}
# stop(" MUST ADD EXTERNAL DATA -- landings in GULF ")
# logbooks from historical data tables (1996-2003; but 2002 and 2003 seem to be partial records)
lb.historical = logbook.db( DS="fisheries.historical" )
lb.historical$cfa = NA
lb.historical$date.fished = paste( lb.historical$date.fished, "01:00:00" )
#lb.historical$date.landed = as.POSIXct( lb.historical$date.landed )
# logbooks from marfissci tables
x = logbook.db( DS="rawdata.logbook", yrs=1996:(p$year.assessment + 1) ) # add one to catch 4X effort/landings in next year
names( x ) = tolower( names( x ) )
names( x ) = rename.bio.snowcrab.variables(names( x ))
to.char = c( "cfa", "licence_id_old", "licence", "date.fished",
"captain", "vessel", "doc_id", "doc_type")
for (i in to.char) x[,i] = as.character(x[,i])
iy = which(!is.finite(x$year))
if (length(iy) > 0) {
x$year[iy] = lubridate::year(x$date.landed) [iy]
iy = which(!is.finite(x$year))
if (length(iy) > 0) x = x[ -iy, ]
}
prorate=FALSE
# if (prorate) x = logbook.prorate( x ) # assume pro-rating not required for historical data as it was maintained manually by Moncton
x$soak.time = x$soak_days * 24 # make into hours
x$trap.type = "" # dummy value until this can be added to the views .. check with Alan
x$status = "" # "" "" ""
# datelanded = matrix(unlist(strsplit(x$date.landed, " ", fixed=T)), ncol=2, byrow=T)[,1]
# x$date.landed = lubridate::ymd( datelanded, tz="America/Halifax" )
x$date.landed = with_tz( x$date.landed, "UTC" )
x$landings = x$pro_rated_slip_wt_lbs * 0.45359 # convert to kg
x$cpue = x$landings / x$effort
x$depth = x$depth_fm*1.83
x$lat = round( as.numeric(substring(x$lat, 1,2)) + as.numeric(substring(x$lat, 3,6))/6000 ,6)
x$lon = - round((as.numeric(substring(x$lon, 1,2)) + as.numeric(substring(x$lon, 3,6))/6000), 6)
to.extract = c( "year","lat","lon","depth","landings","effort","soak.time",
"cpue","trap.type","cfv","status","licence",
"date.landed", "date.fished", "cfa" )
lb.marfis = x[, to.extract ]
# lb.historical$date.landed = as.POSIXct(lb.historical$date.landed)
a = lb.historical$date.fished
b = paste(substr(a, 1, 4), "/", substr(a, 5, 6), "/", substr(a, 7, 8), sep="")
lb.historical$date.fished = as.POSIXct(b)
x = NULL
x = rbind( lb.historical, lb.marfis )
# dups = which(duplicated(x))
# toremove = sort(unique(c(iy, dups)))
# if (length(toremove) > 0) x = x[-toremove,]
# known errors: manual fixes
ix = which( round(x$lat)==46 & round(x$lon)==-5930 )
if (length(ix) > 0) x$lon[ ix ] = x$lon[ ix ] / 100
x = logbook.determine.region(x) # using licence info and geographics
i.cfa4x = which( x$cfa == "cfa4x" )
i.offset = which( lubridate::month(x$date.landed) >= 1 & lubridate::month(x$date.landed) <= 6 )
to.offset = intersect( i.cfa4x, i.offset)
x$yr = x$year
x$yr[to.offset] = x$yr[to.offset] - 1
# x$yr[i.cfa4x] = x$yr[i.cfa4x] + 1 # ie:: fishery from 1999-2000 in 4X is now coded as 2000
message( "Fishing 'yr' for CFA 4X has been set to starting year:: 2001-2002 -> 2001, etc.")
a= x[which(x$cfa0=='cfa4x'),]
head(a)
# enforce bounds in effort and cpue
oo = which( x$cpue > 650 * 0.454 ) # 600 - 650 lbs / trap is a real/reasonable upper limit
if ( length(oo) > 0 ) x$cpue[oo] = NA
pp = which ( x$effort > 240 ) # small traps were used at times with large 240 trap compliments
if ( length(pp) > 0 ) x$effort[pp] = NA
x = lonlat2planar( x, proj.type=p$aegis_proj4string_planar_km )
logbook = x
save (logbook, file=filename, compress=T ) # this is for plotting maps, etc
return( "Complete" )
}
# ---------------------
if (DS %in% c( "fishing.grounds.annual", "fishing.grounds.global", "fishing.grounds.redo")) {
fn1 = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "fishing.grounds.global.rdata")
fn2 = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "fishing.grounds.annual.rdata")
if (DS=="fishing.grounds.global") {
load( fn1 )
return (fg)
}
if (DS=="fishing.grounds.annual") {
load( fn2 )
return (fg)
}
out = NULL
fg.res = p$fisheries.grid.resolution
x = logbook.db( DS="logbook.filtered.positions" )
grid = spatial_grid(p=p, DS="planar.coords")
x$plon = grid_internal( x$plon, grid$plon )
x$plat = grid_internal( x$plat, grid$plat )
yrs = c(T,F)
message ("The following warnings are ok: JC ... just a few NA's created which will be removed..")
for ( Y in yrs ) {
if (Y) {
fn = fn2
x$gridid = paste(x$plon%/%fg.res*fg.res, x$plat%/%fg.res*fg.res, x$year, sep="." )
ncols=3
} else {
fn = fn1
x$gridid = paste(x$plon%/%fg.res*fg.res, x$plat%/%fg.res*fg.res, sep="." )
ncols=2
}
v = "visits"
x$visits=1
w = x[is.finite(x[,v]),]
tmp = as.data.frame( xtabs( as.integer(x[,v]) ~ as.factor(x[,"gridid"]), exclude="" ) )
names(tmp) = c("gridid", "total.visits")
out = tmp
v = "landings"
w = x[is.finite(x[,v]),]
tmp = as.data.frame( xtabs( as.integer(x[,v]) ~ as.factor(x[,"gridid"]), exclude="" ) )
names(tmp) = c("gridid", "total.landings")
out = merge( out, tmp, by="gridid", all=T, sort=F)
v = "effort"
w = x[is.finite(x[,v]),]
tmp = as.data.frame( xtabs( as.integer(x[,v]) ~ as.factor(x[,"gridid"]), exclude="" ) )
names(tmp) = c("gridid", "total.effort")
out = merge( out, tmp, by="gridid", all=T, sort=F)
out$total.cpue = out$total.landings / out$total.effort
tmp = matrix(unlist(strsplit(as.character(out$gridid), ".", fixed=T)), ncol=ncols, byrow=T)
out$plat = as.numeric(tmp[,2])
out$plon = as.numeric(tmp[,1])
out$gridid = as.character( out$gridid )
if (Y) out$yr = as.numeric(tmp[,3])
fg = out[ which(is.finite(out$plat+out$plon)), ]
save( fg, file=fn, compress=T )
}
return( "Complete")
}
# -----------------------------
if (DS %in% c("fisheries.historical", "fisheries.historical.redo" )) {
fn = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "logbook.historical.rdata" )
if (DS=="fisheries.historical") {
logs = NULL
if (file.exists(fn)) load( fn)
return( logs )
}
historicaldataloc = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "archive")
files = c("logbooks1996.csv", "logbooks1997.csv", "logbooks1998.csv", "logbooks1999.csv", "logbooks2000.csv", "logbooks2001.csv")
out = NULL
for (g in files) {
f = file.path(historicaldataloc, g )
a = read.table(file=f, skip=1, as.is=T, strip.white=T, sep=";")
a = a[,c(1:14)]
names(a) = c("cfv", "areas", "status", "licence", "date.landed", "date.fished", "lat", "lon",
"landings.kg", "landings.lbs", "effort", "soak.time", "cpue", "trap.type" )
a$file = f
a$yr = as.numeric(gsub("[[:alpha:]]", "", f))
out = rbind(out, a)
}
f4x = read.table(file=file.path(historicaldataloc, "logbooks4x.csv"), skip=1, as.is=T, strip.white=T, sep=";")
names(f4x) = c("cfv", "areas", "date.landed", "date.fished", "lat", "lon",
"landings.kg", "landings.lbs", "effort", "soak.time", "cpue", "trap.type" )
f4x$areas="4X"
f4x$status = NA
f4x$licence = NA
f4x$file = "logbooks4x.csv"
f4x$yr = floor(f4x$date.landed/10000)
f4x = f4x[, names(out) ]
logs = rbind (out, f4x)
logs$lon = -logs$lon
logs$depth = NA
logs$year = logs$yr
logs$landings = logs$landings.kg
logs$cpue = logs$landings / logs$effort
i = which( nchar(logs$date.landed) <10 & !is.na(logs$date.landed) )
dt = logs[i, "date.landed"]
yr = substring(dt,1,4)
mon = substring(dt,5,6)
da = substring(dt,7,8)
logs[i, "date.landed"] = paste( mon, da, yr, sep="/")
logs$date.landed = lubridate::mdy( logs$date.landed, tz="America/Halifax" )
logs$date.landed = with_tz( logs$date.landed, "UTC" )
to.extract = c( "year","lat","lon","depth","landings","effort","soak.time",
"cpue","trap.type","cfv","status","licence",
"date.landed", "date.fished")
logs = logs[, to.extract]
logs = logs[ -which( !is.finite(logs$year) ), ]
save(logs, file=fn, compress=T)
return( "completed")
} # end if historical
# -------------------------
if (DS %in% c("fisheries.complete", "fisheries.complete.redo" )) {
fn = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "logbook.complete.rdata" )
if (DS=="fisheries.complete") {
load( fn)
return( logbook )
}
logbook = logbook.db(DS="logbook.filtered.positions")
nl0 = nrow( logbook )
grid = spatial_grid(p=p, DS="planar.coords")
logbook$plon = grid_internal( logbook$plon, grid$plon )
logbook$plat = grid_internal( logbook$plat, grid$plat )
logbook$timestamp = as.POSIXct( logbook$date.landed, tz="America/Halifax", origin=lubridate::origin )
logbook$timestamp = with_tz( logbook$timestamp, "UTC")
logbook$dyear = lubridate::decimal_date( logbook$timestamp ) - lubridate::year(logbook$timestamp )
logbook = logbook[which(logbook$yr<=p$year.assessment),]
# bring in time invariant features:: depth
logbook$z = logbook$depth
logbook$depth = NULL
oo = which( logbook$z < 10 | logbook$z > 500 ) # screen out large z's
if (length(oo) > 0 ) logbook$z[ oo ] = NA
ii = which(!is.finite(logbook$z))
if (length(ii)>0) {
pL = aegis.bathymetry::bathymetry_parameters( project_class="stmv" )
LUT= aegis_survey_lookuptable( aegis_project="bathymetry",
project_class="core", DS="aggregated_data", pL=pL )
logbook$z[ii] = aegis_lookup(
pL=pL, LOCS=logbook[ ii, c("lon", "lat")], LUT=LUT,
project_class="core", output_format="points",
space_resolution=p$pres*2, variable_name="z.mean" ) # core=="rawdata"
}
logbook$z = log( logbook$z )
ii = which( ! is.finite( logbook$z) )
if (length(ii)>0) logbook = logbook[ -ii, ]
# bring in time varing features:: temperature
ii = which(!is.finite(logbook$t))
if (length(ii)>0){
pL = aegis.temperature::temperature_parameters( project_class="core", yrs=p$yrs )
LUT= aegis_survey_lookuptable( aegis_project="temperature",
project_class="core", DS="aggregated_data", pL=pL )
logbook$t[ii] = aegis_lookup( pL=pL,
LOCS=logbook[ ii, c("lon", "lat", "timestamp")], LUT=LUT,
project_class="core", output_format="points",
space_resolution=p$pres*2, time_resolution=p$tres*2,
year.assessment=p$year.assessment,
variable_name="t.mean", tz="wAmerica/Halifax" )
}
save( logbook, file=fn, compress=T )
return ("Complete")
}
# -------------------------
if (DS %in% c("logbook.gridded", "logbook.gridded.redo" ) ) {
loc = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "gridded.fishery.data" )
dir.create( path=loc, recursive=T, showWarnings=F)
if (DS == "logbook.gridded") {
fn = file.path(loc, paste( "gridded.fishery", yrs, "rdata", sep=".") )
load(fn)
return(gridded.fishery.data)
}
yy = logbook.db(DS="logbook")
yrs = sort( unique( yy$year))
for ( y in yrs ) {
fn = file.path(loc, paste( "gridded.fishery", y, "rdata", sep=".") )
print (fn)
# load logbook info: global summary
fg = logbook.db( DS="fishing.grounds.global" ) # in dataframe fg
fg0 = regrid.lonlat(old=fg, res=p$fisheries.grid.resolution, vr.to.sum=c("total.landings", "total.effort", "total.visits"))
fg0$core.visits0 = ifelse( fg0$total.visits >= 5, 1, 0 )
fg0$total.cpue = log( fg0$total.landings / fg0$total.effort + 1)
fg0$total.landings = log( fg0$total.landings+1 )
fg0$total.effort = log( fg0$total.effort+1 )
fg0$total.visits = log( fg0$total.visits+1 )
fg0 = fg0[ , c( "gridid", "core.visits0", "total.effort", "total.cpue", "total.landings", "total.visits" ) ]
rm(fg)
# load logbook info: annual
fg = logbook.db( DS="fishing.grounds.annual" ) # in dataframe fg
fg = fg[ which(fg$yr==y),]
fg = regrid.lonlat(old=fg, res=p$fisheries.grid.resolution, vr.to.sum=c("total.landings", "total.effort", "total.visits") )
fg$core.visits = ifelse(fg$total.visits >= 3, 1, 0)
fg$core.visits = ifelse(fg$total.visits >= 3, 1, 0)
fg$core.landings = ifelse(fg$total.landings >= 5, 1, 0)
fg$core.effort = ifelse(fg$total.effort >= 100, 1, 0)
fg$cpue = log( fg$total.landings / fg$total.effort + 1)
fg$landings = log( fg$total.landings+1 )
fg$effort = log( fg$total.effort+1 )
fg$visits = log( fg$total.visits +1 )
fg = fg[ , c( "gridid", "core.visits", "core.landings", "core.effort", "cpue", "landings", "effort", "visits" ) ]
fg = fg[ is.finite(fg$cpue * fg$landings * fg$effort),]
fg = fg[ which(fg$core.visits==1) , ]
gridded.fishery.data = merge(fg0, fg, by="gridid", all.x=T, all.y=T, sort=F)
save( gridded.fishery.data, file=fn, compress=T)
}
} # end gridded fishieries data
}
jae0/bio.snowcrab documentation built on Nov. 6, 2024, 10:10 p.m.
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Defines functions logbook.db
logbook.db = function( DS, prorate=T, p=NULL, yrs=NULL, fn_root=project.datadirectory("bio.snowcrab") ) {
if (DS %in% c("rawdata.logbook", "rawdata.logbook.redo")) {
fn.loc = file.path( fn_root, "data", "logbook", "datadump" )
dir.create( fn.loc, recursive = TRUE, showWarnings = FALSE )
if (DS=="rawdata.logbook") {
out = NULL
for ( YR in yrs ) {
fny = file.path( fn.loc, paste( YR, "rdata", sep="."))
if (file.exists(fny)) {
load (fny)
out = rbind( out, logbook )
}
}
return (out)
}
con=ROracle::dbConnect(DBI::dbDriver("Oracle"),dbname=oracle.snowcrab.server , username=oracle.snowcrab.user, password=oracle.snowcrab.password, believeNRows=F)
for ( YR in yrs ) {
fny = file.path( fn.loc, paste( YR,"rdata", sep="."))
query = paste(
"SELECT * from marfissci.marfis_crab ",
"where target_spc=705",
"AND EXTRACT(YEAR from DATE_LANDED) = ", YR )
logbook = NULL
#in following line replaced sqlQuery (Rrawdata) with dbGetQuery (ROracle)
logbook = ROracle::dbGetQuery(con, query )
save( logbook, file=fny, compress=T)
gc() # garbage collection
print(YR)
}
ROracle::dbDisconnect(con)
return (yrs)
}
# -------------------------
if (DS %in% c("rawdata.licence.redo", "rawdata.licence" ) ) {
fn.loc = file.path( fn_root, "data", "logbook" )
dir.create( fn.loc, recursive = TRUE, showWarnings = FALSE )
filename.licence = file.path( fn.loc, "lic.datadump.rdata" )
if (DS=="rawdata.licence") {
load(filename.licence)
return (lic)
}
con=ROracle::dbConnect(DBI::dbDriver("Oracle"),dbname=oracle.snowcrab.server , username=oracle.snowcrab.user, password=oracle.snowcrab.password, believeNRows=F)
lic = ROracle::dbGetQuery(con, "select * from marfissci.licence_areas")
save(lic, file=filename.licence, compress=T)
ROracle::dbDisconnect(con)
}
if (DS %in% c("rawdata.areas.redo", "rawdata.areas" ) ) {
fn.loc = file.path( fn_root, "data", "logbook" )
dir.create( fn.loc, recursive = TRUE, showWarnings = FALSE )
filename.areas = file.path( fn.loc, "areas.datadump.rdata" )
if (DS=="rawdata.areas") {
load(filename.areas)
return (areas)
}
con=ROracle::dbConnect(DBI::dbDriver("Oracle"),dbname=oracle.snowcrab.server , username=oracle.snowcrab.user, password=oracle.snowcrab.password, believeNRows=F)
areas = ROracle::dbGetQuery(con, "select * from marfissci.areas")
save(areas, file=filename.areas, compress=T)
ROracle::dbDisconnect(con)
return ("Complete")
}
# -------
if (DS %in% c("logbook.filtered.positions", "logbook.filtered.positions.redo")) {
# exclude data that have positions that are incorrect
filename = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "logbook.filtered.positions.rdata" )
if (DS=="logbook.filtered.positions") {
load( filename )
return(lgbk)
}
lgbk = logbook.db( DS="logbook" )
h = which( !is.na( lgbk$lon + lgbk$lat ) )
lgbk = lgbk[h,]
i = polygon_inside( lgbk[, c("lon", "lat")], region="cfaall")
lgbk = lgbk[i,]
j = polygon_inside( lgbk[, c("lon", "lat")], region="isobath1000m")
lgbk = lgbk[j,]
# additional constraint ..
# remove data that are strange in location .. land
crs_lonlat = st_crs( projection_proj4string("lonlat_wgs84") )
mp = st_multipoint(cbind(p$corners$lon, p$corners$lat))
bbox = st_as_sfc(st_bbox( mp) )
st_crs(bbox) = crs_lonlat
coast = st_transform( st_as_sf(coastline_db( p=p )), crs=crs_lonlat )
coast = (
st_intersection( coast, bbox )
%>% st_buffer(0.01)
%>% st_union()
%>% st_cast("POLYGON" )
%>% st_union()
%>% st_make_valid()
)
inside = st_points_in_polygons(
pts =st_as_sf( lgbk[,c("lon", "lat")], coords=c("lon","lat"), crs=crs_lonlat ),
polys = coast
)
onland = which (is.finite(inside))
if (length(onland)>0) lgbk = lgbk[-onland, ]
# filter by depth ..
# use the match/map syntax in bathymetry and filter out shallow sets .. < 10 m? TODO
# keep those in the domain and deeper than depth=10 m
pL = aegis.bathymetry::bathymetry_parameters( project_class="stmv" )
LUT= aegis_survey_lookuptable( aegis_project="bathymetry",
project_class="core", DS="aggregated_data", pL=pL )
z = aegis_lookup( pL=pL,, LOCS=lgbk[, c("lon", "lat")], LUT=LUT,
output_format="points" ,
space_resolution=p$pres*2, variable_name="z.mean" ) # core=="rawdata"
aoi = which( z > 10 ) # negative = above land
lgbk = lgbk[ aoi,]
# only accept "correctly" positioned data within each subarea ... in case miscoded data have a large effect
icfa4x = polygon_inside( lgbk[, c("lon", "lat")], "cfa4x")
icfanorth = polygon_inside( lgbk[, c("lon", "lat")], "cfanorth")
icfa23 = polygon_inside( lgbk[, c("lon", "lat")], "cfa23")
icfa24 = polygon_inside( lgbk[, c("lon", "lat")], "cfa24")
gooddata = sort( unique( c(icfa4x, icfanorth, icfa23, icfa24 ) ) )
lgbk = lgbk[gooddata, ]
save( lgbk, file=filename, compress=T )
return(filename)
}
# -------
if (DS %in% c("logbook", "logbook.redo")) {
filename = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "logbook.rdata" )
if (DS=="logbook") {
load( filename )
return(logbook)
}
# stop(" MUST ADD EXTERNAL DATA -- landings in GULF ")
# logbooks from historical data tables (1996-2003; but 2002 and 2003 seem to be partial records)
lb.historical = logbook.db( DS="fisheries.historical" )
lb.historical$cfa = NA
lb.historical$date.fished = paste( lb.historical$date.fished, "01:00:00" )
#lb.historical$date.landed = as.POSIXct( lb.historical$date.landed )
# logbooks from marfissci tables
x = logbook.db( DS="rawdata.logbook", yrs=1996:(p$year.assessment + 1) ) # add one to catch 4X effort/landings in next year
names( x ) = tolower( names( x ) )
names( x ) = rename.bio.snowcrab.variables(names( x ))
to.char = c( "cfa", "licence_id_old", "licence", "date.fished",
"captain", "vessel", "doc_id", "doc_type")
for (i in to.char) x[,i] = as.character(x[,i])
iy = which(!is.finite(x$year))
if (length(iy) > 0) {
x$year[iy] = lubridate::year(x$date.landed) [iy]
iy = which(!is.finite(x$year))
if (length(iy) > 0) x = x[ -iy, ]
}
prorate=FALSE
# if (prorate) x = logbook.prorate( x ) # assume pro-rating not required for historical data as it was maintained manually by Moncton
x$soak.time = x$soak_days * 24 # make into hours
x$trap.type = "" # dummy value until this can be added to the views .. check with Alan
x$status = "" # "" "" ""
# datelanded = matrix(unlist(strsplit(x$date.landed, " ", fixed=T)), ncol=2, byrow=T)[,1]
# x$date.landed = lubridate::ymd( datelanded, tz="America/Halifax" )
x$date.landed = with_tz( x$date.landed, "UTC" )
x$landings = x$pro_rated_slip_wt_lbs * 0.45359 # convert to kg
x$cpue = x$landings / x$effort
x$depth = x$depth_fm*1.83
x$lat = round( as.numeric(substring(x$lat, 1,2)) + as.numeric(substring(x$lat, 3,6))/6000 ,6)
x$lon = - round((as.numeric(substring(x$lon, 1,2)) + as.numeric(substring(x$lon, 3,6))/6000), 6)
to.extract = c( "year","lat","lon","depth","landings","effort","soak.time",
"cpue","trap.type","cfv","status","licence",
"date.landed", "date.fished", "cfa" )
lb.marfis = x[, to.extract ]
# lb.historical$date.landed = as.POSIXct(lb.historical$date.landed)
a = lb.historical$date.fished
b = paste(substr(a, 1, 4), "/", substr(a, 5, 6), "/", substr(a, 7, 8), sep="")
lb.historical$date.fished = as.POSIXct(b)
x = NULL
x = rbind( lb.historical, lb.marfis )
# dups = which(duplicated(x))
# toremove = sort(unique(c(iy, dups)))
# if (length(toremove) > 0) x = x[-toremove,]
# known errors: manual fixes
ix = which( round(x$lat)==46 & round(x$lon)==-5930 )
if (length(ix) > 0) x$lon[ ix ] = x$lon[ ix ] / 100
x = logbook.determine.region(x) # using licence info and geographics
i.cfa4x = which( x$cfa == "cfa4x" )
i.offset = which( lubridate::month(x$date.landed) >= 1 & lubridate::month(x$date.landed) <= 6 )
to.offset = intersect( i.cfa4x, i.offset)
x$yr = x$year
x$yr[to.offset] = x$yr[to.offset] - 1
# x$yr[i.cfa4x] = x$yr[i.cfa4x] + 1 # ie:: fishery from 1999-2000 in 4X is now coded as 2000
message( "Fishing 'yr' for CFA 4X has been set to starting year:: 2001-2002 -> 2001, etc.")
a= x[which(x$cfa0=='cfa4x'),]
head(a)
# enforce bounds in effort and cpue
oo = which( x$cpue > 650 * 0.454 ) # 600 - 650 lbs / trap is a real/reasonable upper limit
if ( length(oo) > 0 ) x$cpue[oo] = NA
pp = which ( x$effort > 240 ) # small traps were used at times with large 240 trap compliments
if ( length(pp) > 0 ) x$effort[pp] = NA
x = lonlat2planar( x, proj.type=p$aegis_proj4string_planar_km )
logbook = x
save (logbook, file=filename, compress=T ) # this is for plotting maps, etc
return( "Complete" )
}
# ---------------------
if (DS %in% c( "fishing.grounds.annual", "fishing.grounds.global", "fishing.grounds.redo")) {
fn1 = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "fishing.grounds.global.rdata")
fn2 = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "fishing.grounds.annual.rdata")
if (DS=="fishing.grounds.global") {
load( fn1 )
return (fg)
}
if (DS=="fishing.grounds.annual") {
load( fn2 )
return (fg)
}
out = NULL
fg.res = p$fisheries.grid.resolution
x = logbook.db( DS="logbook.filtered.positions" )
grid = spatial_grid(p=p, DS="planar.coords")
x$plon = grid_internal( x$plon, grid$plon )
x$plat = grid_internal( x$plat, grid$plat )
yrs = c(T,F)
message ("The following warnings are ok: JC ... just a few NA's created which will be removed..")
for ( Y in yrs ) {
if (Y) {
fn = fn2
x$gridid = paste(x$plon%/%fg.res*fg.res, x$plat%/%fg.res*fg.res, x$year, sep="." )
ncols=3
} else {
fn = fn1
x$gridid = paste(x$plon%/%fg.res*fg.res, x$plat%/%fg.res*fg.res, sep="." )
ncols=2
}
v = "visits"
x$visits=1
w = x[is.finite(x[,v]),]
tmp = as.data.frame( xtabs( as.integer(x[,v]) ~ as.factor(x[,"gridid"]), exclude="" ) )
names(tmp) = c("gridid", "total.visits")
out = tmp
v = "landings"
w = x[is.finite(x[,v]),]
tmp = as.data.frame( xtabs( as.integer(x[,v]) ~ as.factor(x[,"gridid"]), exclude="" ) )
names(tmp) = c("gridid", "total.landings")
out = merge( out, tmp, by="gridid", all=T, sort=F)
v = "effort"
w = x[is.finite(x[,v]),]
tmp = as.data.frame( xtabs( as.integer(x[,v]) ~ as.factor(x[,"gridid"]), exclude="" ) )
names(tmp) = c("gridid", "total.effort")
out = merge( out, tmp, by="gridid", all=T, sort=F)
out$total.cpue = out$total.landings / out$total.effort
tmp = matrix(unlist(strsplit(as.character(out$gridid), ".", fixed=T)), ncol=ncols, byrow=T)
out$plat = as.numeric(tmp[,2])
out$plon = as.numeric(tmp[,1])
out$gridid = as.character( out$gridid )
if (Y) out$yr = as.numeric(tmp[,3])
fg = out[ which(is.finite(out$plat+out$plon)), ]
save( fg, file=fn, compress=T )
}
return( "Complete")
}
# -----------------------------
if (DS %in% c("fisheries.historical", "fisheries.historical.redo" )) {
fn = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "logbook.historical.rdata" )
if (DS=="fisheries.historical") {
logs = NULL
if (file.exists(fn)) load( fn)
return( logs )
}
historicaldataloc = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "archive")
files = c("logbooks1996.csv", "logbooks1997.csv", "logbooks1998.csv", "logbooks1999.csv", "logbooks2000.csv", "logbooks2001.csv")
out = NULL
for (g in files) {
f = file.path(historicaldataloc, g )
a = read.table(file=f, skip=1, as.is=T, strip.white=T, sep=";")
a = a[,c(1:14)]
names(a) = c("cfv", "areas", "status", "licence", "date.landed", "date.fished", "lat", "lon",
"landings.kg", "landings.lbs", "effort", "soak.time", "cpue", "trap.type" )
a$file = f
a$yr = as.numeric(gsub("[[:alpha:]]", "", f))
out = rbind(out, a)
}
f4x = read.table(file=file.path(historicaldataloc, "logbooks4x.csv"), skip=1, as.is=T, strip.white=T, sep=";")
names(f4x) = c("cfv", "areas", "date.landed", "date.fished", "lat", "lon",
"landings.kg", "landings.lbs", "effort", "soak.time", "cpue", "trap.type" )
f4x$areas="4X"
f4x$status = NA
f4x$licence = NA
f4x$file = "logbooks4x.csv"
f4x$yr = floor(f4x$date.landed/10000)
f4x = f4x[, names(out) ]
logs = rbind (out, f4x)
logs$lon = -logs$lon
logs$depth = NA
logs$year = logs$yr
logs$landings = logs$landings.kg
logs$cpue = logs$landings / logs$effort
i = which( nchar(logs$date.landed) <10 & !is.na(logs$date.landed) )
dt = logs[i, "date.landed"]
yr = substring(dt,1,4)
mon = substring(dt,5,6)
da = substring(dt,7,8)
logs[i, "date.landed"] = paste( mon, da, yr, sep="/")
logs$date.landed = lubridate::mdy( logs$date.landed, tz="America/Halifax" )
logs$date.landed = with_tz( logs$date.landed, "UTC" )
to.extract = c( "year","lat","lon","depth","landings","effort","soak.time",
"cpue","trap.type","cfv","status","licence",
"date.landed", "date.fished")
logs = logs[, to.extract]
logs = logs[ -which( !is.finite(logs$year) ), ]
save(logs, file=fn, compress=T)
return( "completed")
} # end if historical
# -------------------------
if (DS %in% c("fisheries.complete", "fisheries.complete.redo" )) {
fn = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "logbook.complete.rdata" )
if (DS=="fisheries.complete") {
load( fn)
return( logbook )
}
logbook = logbook.db(DS="logbook.filtered.positions")
nl0 = nrow( logbook )
grid = spatial_grid(p=p, DS="planar.coords")
logbook$plon = grid_internal( logbook$plon, grid$plon )
logbook$plat = grid_internal( logbook$plat, grid$plat )
logbook$timestamp = as.POSIXct( logbook$date.landed, tz="America/Halifax", origin=lubridate::origin )
logbook$timestamp = with_tz( logbook$timestamp, "UTC")
logbook$dyear = lubridate::decimal_date( logbook$timestamp ) - lubridate::year(logbook$timestamp )
logbook = logbook[which(logbook$yr<=p$year.assessment),]
# bring in time invariant features:: depth
logbook$z = logbook$depth
logbook$depth = NULL
oo = which( logbook$z < 10 | logbook$z > 500 ) # screen out large z's
if (length(oo) > 0 ) logbook$z[ oo ] = NA
ii = which(!is.finite(logbook$z))
if (length(ii)>0) {
pL = aegis.bathymetry::bathymetry_parameters( project_class="stmv" )
LUT= aegis_survey_lookuptable( aegis_project="bathymetry",
project_class="core", DS="aggregated_data", pL=pL )
logbook$z[ii] = aegis_lookup(
pL=pL, LOCS=logbook[ ii, c("lon", "lat")], LUT=LUT,
project_class="core", output_format="points",
space_resolution=p$pres*2, variable_name="z.mean" ) # core=="rawdata"
}
logbook$z = log( logbook$z )
ii = which( ! is.finite( logbook$z) )
if (length(ii)>0) logbook = logbook[ -ii, ]
# bring in time varing features:: temperature
ii = which(!is.finite(logbook$t))
if (length(ii)>0){
pL = aegis.temperature::temperature_parameters( project_class="core", yrs=p$yrs )
LUT= aegis_survey_lookuptable( aegis_project="temperature",
project_class="core", DS="aggregated_data", pL=pL )
logbook$t[ii] = aegis_lookup( pL=pL,
LOCS=logbook[ ii, c("lon", "lat", "timestamp")], LUT=LUT,
project_class="core", output_format="points",
space_resolution=p$pres*2, time_resolution=p$tres*2,
year.assessment=p$year.assessment,
variable_name="t.mean", tz="wAmerica/Halifax" )
}
save( logbook, file=fn, compress=T )
return ("Complete")
}
# -------------------------
if (DS %in% c("logbook.gridded", "logbook.gridded.redo" ) ) {
loc = file.path( project.datadirectory("bio.snowcrab"), "data", "logbook", "gridded.fishery.data" )
dir.create( path=loc, recursive=T, showWarnings=F)
if (DS == "logbook.gridded") {
fn = file.path(loc, paste( "gridded.fishery", yrs, "rdata", sep=".") )
load(fn)
return(gridded.fishery.data)
}
yy = logbook.db(DS="logbook")
yrs = sort( unique( yy$year))
for ( y in yrs ) {
fn = file.path(loc, paste( "gridded.fishery", y, "rdata", sep=".") )
print (fn)
# load logbook info: global summary
fg = logbook.db( DS="fishing.grounds.global" ) # in dataframe fg
fg0 = regrid.lonlat(old=fg, res=p$fisheries.grid.resolution, vr.to.sum=c("total.landings", "total.effort", "total.visits"))
fg0$core.visits0 = ifelse( fg0$total.visits >= 5, 1, 0 )
fg0$total.cpue = log( fg0$total.landings / fg0$total.effort + 1)
fg0$total.landings = log( fg0$total.landings+1 )
fg0$total.effort = log( fg0$total.effort+1 )
fg0$total.visits = log( fg0$total.visits+1 )
fg0 = fg0[ , c( "gridid", "core.visits0", "total.effort", "total.cpue", "total.landings", "total.visits" ) ]
rm(fg)
# load logbook info: annual
fg = logbook.db( DS="fishing.grounds.annual" ) # in dataframe fg
fg = fg[ which(fg$yr==y),]
fg = regrid.lonlat(old=fg, res=p$fisheries.grid.resolution, vr.to.sum=c("total.landings", "total.effort", "total.visits") )
fg$core.visits = ifelse(fg$total.visits >= 3, 1, 0)
fg$core.visits = ifelse(fg$total.visits >= 3, 1, 0)
fg$core.landings = ifelse(fg$total.landings >= 5, 1, 0)
fg$core.effort = ifelse(fg$total.effort >= 100, 1, 0)
fg$cpue = log( fg$total.landings / fg$total.effort + 1)
fg$landings = log( fg$total.landings+1 )
fg$effort = log( fg$total.effort+1 )
fg$visits = log( fg$total.visits +1 )
fg = fg[ , c( "gridid", "core.visits", "core.landings", "core.effort", "cpue", "landings", "effort", "visits" ) ]
fg = fg[ is.finite(fg$cpue * fg$landings * fg$effort),]
fg = fg[ which(fg$core.visits==1) , ]
gridded.fishery.data = merge(fg0, fg, by="gridid", all.x=T, all.y=T, sort=F)
save( gridded.fishery.data, file=fn, compress=T)
}
} # end gridded fishieries data
}
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