build/nss 2018/comparative/2018.verify.rvcomp.r
In TobieSurette/gulf.manage: Southern Gulf Data Management Functions
v <- list()
v$set <- Z$set
v$cat <- Z$cat
v$len <- Z$len
v$bio <- Z$bio
# Quick check - check keys
verify.key(v$set) #pass
verify.key(v$cat) #pass
verify.key(v$len) #pass
# VERIFY SET CARD
#view all points on map or a single point
xx = v$set[]
windows()
gulf.map(region = "gulf")
map.strata(region = "gulf", survey = "rv", label = TRUE) # Draw blocks.
points(xx$longitude.start, xx$latitude.start, pch=19)
# points(xx$longitude.end, xx$latitude.end, cex=0.5 ,pch=19, col="red")
lines(xx$longitude.start, xx$latitude.start)
text(xx$longitude.end, xx$latitude.end, paste("set=", xx$set.number), pos = 3, cex = 0.7)
verify.gulf.set(v$set,v$cat,temperature = FALSE)
# verify.gulf.set function by function
verify.key(v$set) #pass
verify.key(v$cat) #pass
verify.key(v$len) #pass
verify.format(v$set) #pass
verify.format(v$cat) #pass
verify.format(v$len) #pass
verify.format(v$bio) #pass
verify.coordinates(v$set) #pass
verify.distance(v$set,print=FALSE, tolerance = .15) #all verified with scanmar, could not identify errors
# PLOT distances
dist.obs= distance(v$set)
dist.latlon= distance(v$set, method="latlon")
dist.speed.duration= distance(v$set, method="speed-duration")
plot(dist.obs ,dist.latlon)
plot(dist.latlon, dist.speed.duration)
plot(dist.speed.duration, dist.obs)
text(dist.speed.duration, dist.obs, paste("set=", v$set$set.number), pos = 3, cex = 0.7)
verify.duration(v$set)
verify.depth(v$set) #scanmar data needed to confirm lat lons
#PLOT depth
plot(abs(depth(v$set, method="latlon")), depth(v$set))
text(abs(depth(v$set, method="latlon")), depth(v$set),paste("", v$set$set.number), pos = 3, cex = 0.7)
abline(0,1)
verify.speed(v$set) ##scanmar data needed to confirm lat lons
windows()
plot(distance(v$set), distance(v$set, method = "speed"))
plot(distance(v$set), distance(v$set, method = "latlon"))
plot(distance(v$set, method="speed"), distance(v$set, method = "latlon"))
text(distance(v$set, method="speed"), distance(v$set, method = "latlon"), paste("set=", v$set$set.number), pos = 3, cex = 0.7)
plot(depth(v$set, method="latlon")*-1, depth(v$set))
text(depth(v$set, method="latlon")*-1, depth(v$set), paste("set=", v$set$set.number), pos = 3, cex = 0.7)
verify.stratum(v$set) #scanmar data needed to confirm lat lons
verify.temperature(v$set) #waiting for temperature data
verify.time(v$set) #pass
verify.card.type(v$set) #pass
verify.card.type(v$cat) #pass
verify.card.type(v$len) #pass
verify.card.type(v$bio) #pass
verify.unit.area(v$set)
verify.species(v$cat,v$bio,v$len) #pass
verify.species.number(v$set, v$cat) #pass
verify.gulf.cat(v$cat, v$set, v$bio, v$len , format = FALSE,number.length = FALSE,number.caught = FALSE,number.sex = FALSE, weight.caught = FALSE , tolerance = 20)
# # coordinate verifcation. use scanmar data to double check on our data
# files <- scanmar.file.str(year = 2017)
# xx=subset(v$set, set.number= 1:5)
# xx = v$set
# scan <- read.scanmar(files[148:151])
# scan <- read.scanmar(files)
#
# match.scanmar()
# windows()
# start.color = "blue"
# end.color ="red"
# plot(scan$longitude, scan$latitude, col="grey")
# points(xx$longitude.start, xx$latitude.start, cex=1.0 ,pch=19, col = start.color,)
# points(xx$longitude.end, xx$latitude.end, cex=1.0 ,pch=19, col=end.color)
# text(xx$longitude.start, xx$latitude.start, paste("START - set =", xx$set.number), pos = 3, cex = 0.7, col=start.color)
# text(xx$longitude.end, xx$latitude.end, paste("End - set =", xx$set.number), pos = 3, cex = 0.7,col=end.color)
# #
# # windows()
# # plot(time(scan), scan$depth, ylim=c(60,80))
# # grid()
#VERIFY CATCH CARD
verify.number.caught(v$cat,v$len, tolerance = 10) #pass , 6 warnings come from Fish that had the number caught entered manually in the ESE
verify.number.sex.gulf.cat(v$cat, v$len, v$bio) #pass
#here we set our data set to only the main species
v$cat = subset(v$cat, species = species.we.like()[1:11])
v$len = subset(v$len, species = species.we.like()[1:11])
v$bio = subset(v$bio, species = species.we.like()[1:11])
verify.species(v$cat,v$bio, v$len) #pass
#this checks to see if any species that have been set to be sampled exist in either the len or bio card.
spec= unique(subset(v$cat, weight.sampled >0)$species)
temp = spec[!(spec %in% unique(v$bio$species) | spec %in% unique(v$len$species))]
#VERIFY LEN CARD
# VERIFY that RATIO in len card it not -0
# ratio == 0 need to be set to 1 at this point.. but if set in my correction file it generates some strange bugs....
verify.ratio(v$len) #pass
verify.number.caught(v$cat,v$len, tolerance = 100) #pass. one error but it's ok (set 39)
verify.number.sex.gulf.cat(v$cat, v$len, v$bio) #pass
# Check actual weight against calculated weight. Should produce a nice line at 45 degrees.
# look for values that wander significantly from this line
# had to hard code sex to 0 in order to get a pretty image of the overall catch (all sexes merged)
# list of main species: 10,12,40,41,42,43,60,62,64,30, 70,200, 201, 202,203,204
x=list()
x.set = read.card(year = 2015, card = "set", source = "ascii")
x.cat = read.card(year = 2015, card = "cat", source = "ascii")
x.len = read.card(year = 2015, card = "len", source = "ascii")
x.bio = read.card(year = 2015, card = "bio", source = "ascii")
species =204
year= 2017
# verify catch weight caught versus calculated weight from lenght card
x <- Z$set
y <- subset(Z$cat, species = species)
z <- subset(Z$len, species = species)
z$sex = 0
x <- merge.catch(x, y)
x <- merge(x, weight.caught(z, by = key(y)), by = key(x))
plot(log(x$weight.caught.x),log(x$weight.caught.y))
#text(log(x$weight.caught.x),log(x$weight.caught.y), paste("set=", x$set.number), pos = 4, cex = 0.7)
title(paste(year," - species:", species, " - sex:", sex), sep="")
#testing weights
#verify.gulf.cat(v$cat, v$set, v$bio, v$len , format = FALSE,number.length = FALSE,number.caught = FALSE,number.sex = FALSE, weight.caught = FALSE , tolerance = 20)
#vvcat = subset(v$cat, species =12, set.number = 43)
#vvset = subset(v$set, set.number = 43)
#vvlen = subset(v$len, species =12, set.number = 43)
#verify.gulf.cat(vvcat, vvset, vvlen, format = FALSE,number.length = FALSE,number.caught = FALSE,number.sex = FALSE, weight.caught = FALSE , tolerance = 20)
#return (c(10,12,40,41,42,43,60,61,62,30, 70,2526,2550))
# Quick basic check of common vars for odd data
table(v$bio$sex) #pass
table(v$bio$record.number) #pass
which(diff(Z$bio$fish.number) > 1 ) # should return nothing or positive numbers #pass
table(v$set$card.type)
table(v$set$vessel.code)
table(v$set$cruise.number)
table(v$set$stratum)
table(v$set$set.number)
diff(v$set$set.number)
table(v$set$year)
table(v$set$day)
table(v$set$unit.area)
table(v$set$experiment)
table(v$set$gear)
table(v$set$auxiliary)
table(v$set$speed)
table(v$set$speed.method)
table(v$set$latitude.start)
table(v$set$longitude.start)
table(v$set$latitude.end)
table(v$set$longitude.end)
table(v$set$depth.start)
table(v$set$depth.end)
table(v$set$distance)
table(v$set$distance.method)
table(v$set$wind.direction)
table(v$set$wind.force)
table(v$set$tide)
table(v$set$surface.temperature)
table(v$set$bottom.temperature)
table(v$set$bottom.salinity)
table(v$set$light)
table(v$set$btslide)
table(v$set$hydrostation)
table(v$set$bottom.type)
table(v$set$species.fish.number)
table(v$set$species.invertebrate.number)
table(v$set$catch.total.weight)
table(v$set$warp.out.port)
table(v$set$warp.out.starboard)
table(v$set$comment)
#check speed for NA or outliers
which(is.na(v$set$speed)) #should return NULL #pass
table(v$set$speed)
#check duration for NA or outliers
which(is.na(v$set$duration)) #should return NULL #pass
table(v$set$duration)
#these should not return NA's. if they do it means there's an invalid code
unique(speed.method.str(v$set$speed.method)) #pass
unique(gear.str(v$set$gear)) #pass
unique(auxiliary.str(v$set$auxiliary)) #pass
unique(distance.method.str(v$set$distance.method)) #pass
unique(wind.direction.str(v$set$wind.direction)) #pass
unique(wind.force.str(v$set$wind.force)) #pass
unique(tide.str(v$set$tide)) #pass
unique(bottom.type.str(v$set$bottom.type)) #pass
unique(Z$bio$card.type)
unique(Z$bio$vessel.code)
unique(Z$bio$cruise.number)
unique(Z$bio$stratum)
unique(Z$bio$set.number)
unique(Z$bio$year )
unique(Z$bio$month)
unique(Z$bio$day)
unique(Z$bio$unit.area)
unique(Z$bio$experiment)
unique(Z$bio$bottom.type)
unique(Z$bio$species )
unique(Z$bio$record.number)
unique(Z$bio$fish.number)
unique(Z$bio$length)
unique(Z$bio$sex)
unique(Z$bio$maturity)
unique(Z$bio$weight )
unique(Z$bio$stomach.type)
unique(Z$bio$stomach.weight)
unique(Z$bio$stomach.full)
unique(Z$bio$stomach.part)
unique(Z$bio$weight.gonad)
unique(Z$bio$age.material )
unique(Z$bio$annuli)
unique(Z$bio$edge.type)
unique(Z$bio$age.check)
unique(Z$bio$age)
unique(Z$bio$year.class)
unique(Z$bio$ager )
unique(Z$bio$parasite)
unique(Z$bio$field.definition)
unique(Z$bio$expedition.number)
unique(Z$bio$comment)
unique(Z$bio$shell.condition)
unique(Z$bio$egg.condition )
unique(Z$bio$chela)
unique(Z$bio$abdomen)
unique(Z$bio$block.number)
unique(Z$bio$station.number)
unique(Z$bio$missing.legs)
unique(Z$bio$disc.width )
unique(Z$bio$bobtail)
unique(Z$bio$specimen.number)
species.we.like <- function(){
return (c(10,12,40,41,42,43,60,61,62,30, 70,2526,2550,200:204))
}
TobieSurette/gulf.manage documentation built on Feb. 10, 2024, 10:51 p.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.
v <- list()
v$set <- Z$set
v$cat <- Z$cat
v$len <- Z$len
v$bio <- Z$bio
# Quick check - check keys
verify.key(v$set) #pass
verify.key(v$cat) #pass
verify.key(v$len) #pass
# VERIFY SET CARD
#view all points on map or a single point
xx = v$set[]
windows()
gulf.map(region = "gulf")
map.strata(region = "gulf", survey = "rv", label = TRUE) # Draw blocks.
points(xx$longitude.start, xx$latitude.start, pch=19)
# points(xx$longitude.end, xx$latitude.end, cex=0.5 ,pch=19, col="red")
lines(xx$longitude.start, xx$latitude.start)
text(xx$longitude.end, xx$latitude.end, paste("set=", xx$set.number), pos = 3, cex = 0.7)
verify.gulf.set(v$set,v$cat,temperature = FALSE)
# verify.gulf.set function by function
verify.key(v$set) #pass
verify.key(v$cat) #pass
verify.key(v$len) #pass
verify.format(v$set) #pass
verify.format(v$cat) #pass
verify.format(v$len) #pass
verify.format(v$bio) #pass
verify.coordinates(v$set) #pass
verify.distance(v$set,print=FALSE, tolerance = .15) #all verified with scanmar, could not identify errors
# PLOT distances
dist.obs= distance(v$set)
dist.latlon= distance(v$set, method="latlon")
dist.speed.duration= distance(v$set, method="speed-duration")
plot(dist.obs ,dist.latlon)
plot(dist.latlon, dist.speed.duration)
plot(dist.speed.duration, dist.obs)
text(dist.speed.duration, dist.obs, paste("set=", v$set$set.number), pos = 3, cex = 0.7)
verify.duration(v$set)
verify.depth(v$set) #scanmar data needed to confirm lat lons
#PLOT depth
plot(abs(depth(v$set, method="latlon")), depth(v$set))
text(abs(depth(v$set, method="latlon")), depth(v$set),paste("", v$set$set.number), pos = 3, cex = 0.7)
abline(0,1)
verify.speed(v$set) ##scanmar data needed to confirm lat lons
windows()
plot(distance(v$set), distance(v$set, method = "speed"))
plot(distance(v$set), distance(v$set, method = "latlon"))
plot(distance(v$set, method="speed"), distance(v$set, method = "latlon"))
text(distance(v$set, method="speed"), distance(v$set, method = "latlon"), paste("set=", v$set$set.number), pos = 3, cex = 0.7)
plot(depth(v$set, method="latlon")*-1, depth(v$set))
text(depth(v$set, method="latlon")*-1, depth(v$set), paste("set=", v$set$set.number), pos = 3, cex = 0.7)
verify.stratum(v$set) #scanmar data needed to confirm lat lons
verify.temperature(v$set) #waiting for temperature data
verify.time(v$set) #pass
verify.card.type(v$set) #pass
verify.card.type(v$cat) #pass
verify.card.type(v$len) #pass
verify.card.type(v$bio) #pass
verify.unit.area(v$set)
verify.species(v$cat,v$bio,v$len) #pass
verify.species.number(v$set, v$cat) #pass
verify.gulf.cat(v$cat, v$set, v$bio, v$len , format = FALSE,number.length = FALSE,number.caught = FALSE,number.sex = FALSE, weight.caught = FALSE , tolerance = 20)
# # coordinate verifcation. use scanmar data to double check on our data
# files <- scanmar.file.str(year = 2017)
# xx=subset(v$set, set.number= 1:5)
# xx = v$set
# scan <- read.scanmar(files[148:151])
# scan <- read.scanmar(files)
#
# match.scanmar()
# windows()
# start.color = "blue"
# end.color ="red"
# plot(scan$longitude, scan$latitude, col="grey")
# points(xx$longitude.start, xx$latitude.start, cex=1.0 ,pch=19, col = start.color,)
# points(xx$longitude.end, xx$latitude.end, cex=1.0 ,pch=19, col=end.color)
# text(xx$longitude.start, xx$latitude.start, paste("START - set =", xx$set.number), pos = 3, cex = 0.7, col=start.color)
# text(xx$longitude.end, xx$latitude.end, paste("End - set =", xx$set.number), pos = 3, cex = 0.7,col=end.color)
# #
# # windows()
# # plot(time(scan), scan$depth, ylim=c(60,80))
# # grid()
#VERIFY CATCH CARD
verify.number.caught(v$cat,v$len, tolerance = 10) #pass , 6 warnings come from Fish that had the number caught entered manually in the ESE
verify.number.sex.gulf.cat(v$cat, v$len, v$bio) #pass
#here we set our data set to only the main species
v$cat = subset(v$cat, species = species.we.like()[1:11])
v$len = subset(v$len, species = species.we.like()[1:11])
v$bio = subset(v$bio, species = species.we.like()[1:11])
verify.species(v$cat,v$bio, v$len) #pass
#this checks to see if any species that have been set to be sampled exist in either the len or bio card.
spec= unique(subset(v$cat, weight.sampled >0)$species)
temp = spec[!(spec %in% unique(v$bio$species) | spec %in% unique(v$len$species))]
#VERIFY LEN CARD
# VERIFY that RATIO in len card it not -0
# ratio == 0 need to be set to 1 at this point.. but if set in my correction file it generates some strange bugs....
verify.ratio(v$len) #pass
verify.number.caught(v$cat,v$len, tolerance = 100) #pass. one error but it's ok (set 39)
verify.number.sex.gulf.cat(v$cat, v$len, v$bio) #pass
# Check actual weight against calculated weight. Should produce a nice line at 45 degrees.
# look for values that wander significantly from this line
# had to hard code sex to 0 in order to get a pretty image of the overall catch (all sexes merged)
# list of main species: 10,12,40,41,42,43,60,62,64,30, 70,200, 201, 202,203,204
x=list()
x.set = read.card(year = 2015, card = "set", source = "ascii")
x.cat = read.card(year = 2015, card = "cat", source = "ascii")
x.len = read.card(year = 2015, card = "len", source = "ascii")
x.bio = read.card(year = 2015, card = "bio", source = "ascii")
species =204
year= 2017
# verify catch weight caught versus calculated weight from lenght card
x <- Z$set
y <- subset(Z$cat, species = species)
z <- subset(Z$len, species = species)
z$sex = 0
x <- merge.catch(x, y)
x <- merge(x, weight.caught(z, by = key(y)), by = key(x))
plot(log(x$weight.caught.x),log(x$weight.caught.y))
#text(log(x$weight.caught.x),log(x$weight.caught.y), paste("set=", x$set.number), pos = 4, cex = 0.7)
title(paste(year," - species:", species, " - sex:", sex), sep="")
#testing weights
#verify.gulf.cat(v$cat, v$set, v$bio, v$len , format = FALSE,number.length = FALSE,number.caught = FALSE,number.sex = FALSE, weight.caught = FALSE , tolerance = 20)
#vvcat = subset(v$cat, species =12, set.number = 43)
#vvset = subset(v$set, set.number = 43)
#vvlen = subset(v$len, species =12, set.number = 43)
#verify.gulf.cat(vvcat, vvset, vvlen, format = FALSE,number.length = FALSE,number.caught = FALSE,number.sex = FALSE, weight.caught = FALSE , tolerance = 20)
#return (c(10,12,40,41,42,43,60,61,62,30, 70,2526,2550))
# Quick basic check of common vars for odd data
table(v$bio$sex) #pass
table(v$bio$record.number) #pass
which(diff(Z$bio$fish.number) > 1 ) # should return nothing or positive numbers #pass
table(v$set$card.type)
table(v$set$vessel.code)
table(v$set$cruise.number)
table(v$set$stratum)
table(v$set$set.number)
diff(v$set$set.number)
table(v$set$year)
table(v$set$day)
table(v$set$unit.area)
table(v$set$experiment)
table(v$set$gear)
table(v$set$auxiliary)
table(v$set$speed)
table(v$set$speed.method)
table(v$set$latitude.start)
table(v$set$longitude.start)
table(v$set$latitude.end)
table(v$set$longitude.end)
table(v$set$depth.start)
table(v$set$depth.end)
table(v$set$distance)
table(v$set$distance.method)
table(v$set$wind.direction)
table(v$set$wind.force)
table(v$set$tide)
table(v$set$surface.temperature)
table(v$set$bottom.temperature)
table(v$set$bottom.salinity)
table(v$set$light)
table(v$set$btslide)
table(v$set$hydrostation)
table(v$set$bottom.type)
table(v$set$species.fish.number)
table(v$set$species.invertebrate.number)
table(v$set$catch.total.weight)
table(v$set$warp.out.port)
table(v$set$warp.out.starboard)
table(v$set$comment)
#check speed for NA or outliers
which(is.na(v$set$speed)) #should return NULL #pass
table(v$set$speed)
#check duration for NA or outliers
which(is.na(v$set$duration)) #should return NULL #pass
table(v$set$duration)
#these should not return NA's. if they do it means there's an invalid code
unique(speed.method.str(v$set$speed.method)) #pass
unique(gear.str(v$set$gear)) #pass
unique(auxiliary.str(v$set$auxiliary)) #pass
unique(distance.method.str(v$set$distance.method)) #pass
unique(wind.direction.str(v$set$wind.direction)) #pass
unique(wind.force.str(v$set$wind.force)) #pass
unique(tide.str(v$set$tide)) #pass
unique(bottom.type.str(v$set$bottom.type)) #pass
unique(Z$bio$card.type)
unique(Z$bio$vessel.code)
unique(Z$bio$cruise.number)
unique(Z$bio$stratum)
unique(Z$bio$set.number)
unique(Z$bio$year )
unique(Z$bio$month)
unique(Z$bio$day)
unique(Z$bio$unit.area)
unique(Z$bio$experiment)
unique(Z$bio$bottom.type)
unique(Z$bio$species )
unique(Z$bio$record.number)
unique(Z$bio$fish.number)
unique(Z$bio$length)
unique(Z$bio$sex)
unique(Z$bio$maturity)
unique(Z$bio$weight )
unique(Z$bio$stomach.type)
unique(Z$bio$stomach.weight)
unique(Z$bio$stomach.full)
unique(Z$bio$stomach.part)
unique(Z$bio$weight.gonad)
unique(Z$bio$age.material )
unique(Z$bio$annuli)
unique(Z$bio$edge.type)
unique(Z$bio$age.check)
unique(Z$bio$age)
unique(Z$bio$year.class)
unique(Z$bio$ager )
unique(Z$bio$parasite)
unique(Z$bio$field.definition)
unique(Z$bio$expedition.number)
unique(Z$bio$comment)
unique(Z$bio$shell.condition)
unique(Z$bio$egg.condition )
unique(Z$bio$chela)
unique(Z$bio$abdomen)
unique(Z$bio$block.number)
unique(Z$bio$station.number)
unique(Z$bio$missing.legs)
unique(Z$bio$disc.width )
unique(Z$bio$bobtail)
unique(Z$bio$specimen.number)
species.we.like <- function(){
return (c(10,12,40,41,42,43,60,61,62,30, 70,2526,2550,200:204))
}
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