R/tweaks.R
In PopulationEcologyDivision/andesmerge: andesmerge: Maritimes tools for getting data out of ANDES and into the Maritimes groundfish database
Defines functions
tweakLv1
tweakBasketsPostProcessing
tweakSets
tweakSpecimensRaw
tweakCatches
tweakBaskets
tweakUniversal
Documented in
tweakBaskets
tweakBasketsPostProcessing
tweakCatches
tweakLv1
tweakSets
tweakSpecimensRaw
tweakUniversal
#' @title tweakUniversal
#' @description This function will perform tweaks on data from Andes that exists in multiple
#' exported csv files
#' @param x default is \code{NULL}. This is a list of all of the objects from the csv files
#' @param mission default is \code{NULL}. This is the cleaned mission id (e.g. CAR2022102)
#' @return list
#' @family general_use
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
tweakUniversal <- function(x = NULL, mission=NULL){
theMsg <- NA
#get rid of text species name for overwritten spp, we will really entirely on the species codes
x$catch_data$species <- x$catch_data$species_id <- NULL
if (mission =="CAR2023011"){
#• Delete specimen_id 23286 from all tables. Setno 47, spec 11, length 1 (23286)
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==23286,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==23286,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==23286,]
# • Delete specimen_id 26437 from all tables. Setno 54, spec 23, length 1 (26437 )
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==26437,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==26437,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==26437,]
# • Delete specimen_id 999 from all tables. Setno 2, spec 60, length 0 (999 )
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==999,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==999,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==999,]
# • Delete specimen_id 26753 from all tables. Setno 54, spec 123, length 1 (26753)
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==26753,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==26753,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==26753,]
# • Delete specimen_id 31731 from all tables. Setno 68, spec 4321, length 0.31 (31731)
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==31731,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==31731,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==31731,]
# • Delete specimen_id 58696 from all tables. Setno 158, spec 40, length 1 (58696 )
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==58696,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==58696,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==58696,]
# • Delete specimen_id 68922 from all tables. Setno 190, spec 40, length 1
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==68922,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==68922,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==68922,]
# • Delete specimen_id 69568 from all tables. Setno 192, spec 40, length 1
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==69568,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==69568,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==69568,]
# • Delete specimen_id 69570 from all tables. Setno 192, spec 40, length 1
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==69570,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==69570,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==69570,]
# • Delete specimen_id 3670 from all tables. Setno 8, spec 40, length 0.1675. Incorrect length was entered and was the only individual for the basket. Change the basket (0.1155) to sampled = ‘N’
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==3670,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==3670,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==3670,]
x$basket_data[x$basket_data$set_number== 8 & x$basket_data$species_code == 40, "sampled"] <- "No"
# • Update car_ese_lv1_observations set data_value=1 where setno=236 and spec=14 and specimen_id=83667 and lv1_observation=’Weight’ and data_value=0.001;
x$specimensRaw[x$specimensRaw$id== 83667,]
x$specimen_data[x$specimen_data$id== 83667,]
x$observation_data[x$observation_data$specimen_id ==83667,]
}
if(mission == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemapping species in the catch_data\n")
x$catch_data[x$catch_data$species_code == 18411,"species_code"] <- 6102
x$catch_data[x$catch_data$species_code == 13519,"species_code"] <- 4213
x$catch_data[x$catch_data$species_code == 14878,"species_code"] <- 4508
x$catch_data[x$catch_data$species_code == 12161,"species_code"] <- 8216
x$catch_data[x$catch_data$species_code == 19218,"species_code"] <- 9331
x$catch_data[x$catch_data$species_code == 19950,"species_code"] <- 1510
x$catch_data[x$catch_data$species_code == 18680,"species_code"] <- 1821
x$catch_data[x$catch_data$species_code == 12157,"species_code"] <- 8382
x$catch_data[x$catch_data$species_code == 10854,"species_code"] <- 500
x$catch_data[x$catch_data$species_code == 12096,"species_code"] <- 8516
x$catch_data[x$catch_data$species_code == 9003,"species_code"] <- 1224
# x$catch_data[x$catch_data$species_code == 18495,"species_code"] <- 6105
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemapping species in the specimen_data\n")
x$specimen_data[x$specimen_data$species_code == 18411,"species_code"] <- 6102
x$specimen_data[x$specimen_data$species_code == 13519,"species_code"] <- 4213
x$specimen_data[x$specimen_data$species_code == 14878,"species_code"] <- 4508
x$specimen_data[x$specimen_data$species_code == 12161,"species_code"] <- 8216
x$specimen_data[x$specimen_data$species_code == 19218,"species_code"] <- 9331
x$specimen_data[x$specimen_data$species_code == 19950,"species_code"] <- 1510
x$specimen_data[x$specimen_data$species_code == 18680,"species_code"] <- 1821
x$specimen_data[x$specimen_data$species_code == 12157,"species_code"] <- 8382
x$specimen_data[x$specimen_data$species_code == 10854,"species_code"] <- 500
x$specimen_data[x$specimen_data$species_code == 12096,"species_code"] <- 8516
x$specimen_data[x$specimen_data$species_code == 9003,"species_code"] <- 1224
# x$specimen_data[x$specimen_data$species_code == 18495,"species_code"] <- 6105
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemapping species in the basket_data\n")
x$basket_data[x$basket_data$species_code == 18411,"species_code"] <- 6102
x$basket_data[x$basket_data$species_code == 13519,"species_code"] <- 4213
x$basket_data[x$basket_data$species_code == 14878,"species_code"] <- 4508
x$basket_data[x$basket_data$species_code == 12161,"species_code"] <- 8216
x$basket_data[x$basket_data$species_code == 19218,"species_code"] <- 9331
x$basket_data[x$basket_data$species_code == 19950,"species_code"] <- 1510
x$basket_data[x$basket_data$species_code == 18680,"species_code"] <- 1821
x$basket_data[x$basket_data$species_code == 12157,"species_code"] <- 8382
x$basket_data[x$basket_data$species_code == 10854,"species_code"] <- 500
x$basket_data[x$basket_data$species_code == 12096,"species_code"] <- 8516
x$basket_data[x$basket_data$species_code == 9003,"species_code"] <- 1224
# x$basket_data[x$basket_data$species_code == 18495,"species_code"] <- 6105
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tHandling 'spp 18495'. Basket 1 was spp 6102; Basket 2 was spp 6126 - need an additional catch record\n")
x$catch_data<- rbind(x$catch_data, x$catch_data[x$catch_data$species_code==18495,])
x$catch_data[x$catch_data$species_code==18495,"species_code"] <- c(6102,6126)
x$basket_data<-x$basket_data[order(x$basket_data$id),]
x$basket_data[x$basket_data$species_code==18495,"species_code"] <- c(6102,6126)
colnames(x$specimen_data)[colnames(x$specimen_data)=="species_code"] <- "SPEC"
colnames(x$catch_data)[colnames(x$catch_data)=="species_code"] <- "SPEC"
colnames(x$basket_data)[colnames(x$basket_data)=="species_code"] <- "SPEC"
}
if(mission == "TEL2022010"){
#changing time and coords here so they get appropriately converted by transmogrified
x$set_data[x$set_data$set_number == 148, c("start_latitude_DD", "start_latitude_MMmm", "start_longitude_DD", "start_longitude_MMmm")]<- as.data.frame(t(c(42,27.707,-64,51.821)))
x$set_data[x$set_data$set_number == 148, c("start_date")] <- "2022-08-03 13:43:00.000000+00:00"
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tConverting andes codes to Maritimes spp\n")
#mola mola was not in andes spp list
x$basket_data[x$basket_data$set_number == 69 & x$basket_data$SPEC == 9991,c("SPEC")] <- c(730)
x$specimen_data[x$specimen_data$set_number == 69 & x$specimen_data$SPEC == 9991,c("SPEC")] <- c(730)
x$catch_data[x$catch_data$set_number == 69 & x$catch_data$SPEC == 9991,c("SPEC")] <- c(730)
#andes used some codes not held by Gulf, so they get changed
x$basket_data[x$basket_data$SPEC==12161,"SPEC"] <- c(8216)
x$basket_data[x$basket_data$SPEC==12174,"SPEC"] <- c(8209)
x$basket_data[x$basket_data$SPEC==14878,"SPEC"] <- c(4508)
x$basket_data[x$basket_data$SPEC==16593,"SPEC"] <- c(2062)
x$basket_data[x$basket_data$SPEC==18411,"SPEC"] <- c(6126)
x$basket_data[x$basket_data$SPEC==18495,"SPEC"] <- c(6105)
x$basket_data[x$basket_data$SPEC==18515,"SPEC"] <- c(6107)
x$basket_data[x$basket_data$SPEC==18575,"SPEC"] <- c(6202)
x$basket_data[x$basket_data$SPEC==18792,"SPEC"] <- c(1812)
x$catch_data[x$catch_data$SPEC==12161,"SPEC"] <- c(8216)
x$catch_data[x$catch_data$SPEC==12174,"SPEC"] <- c(8209)
x$catch_data[x$catch_data$SPEC==14878,"SPEC"] <- c(4508)
x$catch_data[x$catch_data$SPEC==16593,"SPEC"] <- c(2062)
x$catch_data[x$catch_data$SPEC==18411,"SPEC"] <- c(6126)
x$catch_data[x$catch_data$SPEC==18495,"SPEC"] <- c(6105)
x$catch_data[x$catch_data$SPEC==18515,"SPEC"] <- c(6107)
x$catch_data[x$catch_data$SPEC==18575,"SPEC"] <- c(6202)
x$catch_data[x$catch_data$SPEC==18792,"SPEC"] <- c(1812)
x$specimen_data[x$specimen_data$SPEC==12161,"SPEC"] <- c(8216)
x$specimen_data[x$specimen_data$SPEC==12174,"SPEC"] <- c(8209)
x$specimen_data[x$specimen_data$SPEC==14878,"SPEC"] <- c(4508)
x$specimen_data[x$specimen_data$SPEC==16593,"SPEC"] <- c(2062)
x$specimen_data[x$specimen_data$SPEC==18411,"SPEC"] <- c(6126)
x$specimen_data[x$specimen_data$SPEC==18495,"SPEC"] <- c(6105)
x$specimen_data[x$specimen_data$SPEC==18515,"SPEC"] <- c(6107)
x$specimen_data[x$specimen_data$SPEC==18575,"SPEC"] <- c(6202)
x$specimen_data[x$specimen_data$SPEC==18792,"SPEC"] <- c(1812)
#all instances of mud star were actually pulvillus
x$basket_data[x$basket_data$SPEC==6115,"SPEC"] <- c(6126)
x$catch_data[x$catch_data$SPEC==6115,"SPEC"] <- c(6126)
x$specimen_data[x$specimen_data$SPEC==6115,"SPEC"] <- c(6126)
#andes used specified a level of detail different than what Mar has codes for
#J Emberley made these suggestions
x$basket_data[x$basket_data$SPEC==10244,"SPEC"] <- c(942)
x$basket_data[x$basket_data$SPEC==12676,"SPEC"] <- c(1900)
x$basket_data[x$basket_data$SPEC==12679,"SPEC"] <- c(1901)
x$basket_data[x$basket_data$SPEC==13090,"SPEC"] <- c(1930)
x$basket_data[x$basket_data$SPEC==14230,"SPEC"] <- c(4316)
x$basket_data[x$basket_data$SPEC==16592,"SPEC"] <- c(2990)
x$basket_data[x$basket_data$SPEC==18800,"SPEC"] <- c(7733)
x$basket_data[x$basket_data$SPEC==19220,"SPEC"] <- c(9303)
x$basket_data[x$basket_data$SPEC==13891,"SPEC"] <- c(4400)
x$basket_data[x$basket_data$SPEC==13908,"SPEC"] <- c(4400)
x$catch_data[x$catch_data$SPEC==10244,"SPEC"] <- c(942)
x$catch_data[x$catch_data$SPEC==12676,"SPEC"] <- c(1900)
x$catch_data[x$catch_data$SPEC==12679,"SPEC"] <- c(1901)
x$catch_data[x$catch_data$SPEC==13090,"SPEC"] <- c(1930)
x$catch_data[x$catch_data$SPEC==14230,"SPEC"] <- c(4316)
x$catch_data[x$catch_data$SPEC==16592,"SPEC"] <- c(2990)
x$catch_data[x$catch_data$SPEC==18800,"SPEC"] <- c(7733)
x$catch_data[x$catch_data$SPEC==19220,"SPEC"] <- c(9303)
x$catch_data[x$catch_data$SPEC==13891,"SPEC"] <- c(4400)
x$catch_data[x$catch_data$SPEC==13908,"SPEC"] <- c(4400)
x$specimen_data[x$specimen_data$SPEC==10244,"SPEC"] <- c(942)
x$specimen_data[x$specimen_data$SPEC==12676,"SPEC"] <- c(1900)
x$specimen_data[x$specimen_data$SPEC==12679,"SPEC"] <- c(1901)
x$specimen_data[x$specimen_data$SPEC==13090,"SPEC"] <- c(1930)
x$specimen_data[x$specimen_data$SPEC==14230,"SPEC"] <- c(4316)
x$specimen_data[x$specimen_data$SPEC==16592,"SPEC"] <- c(2990)
x$specimen_data[x$specimen_data$SPEC==18800,"SPEC"] <- c(7733)
x$specimen_data[x$specimen_data$SPEC==19220,"SPEC"] <- c(9303)
x$specimen_data[x$specimen_data$SPEC==13891,"SPEC"] <- c(4400)
x$specimen_data[x$specimen_data$SPEC==13908,"SPEC"] <- c(4400)
#Mar varies from Gulf
x$basket_data[x$basket_data$SPEC==7706,"SPEC"] <- c(8382)
x$basket_data[x$basket_data$SPEC==7712,"SPEC"] <- c(8367)
x$basket_data[x$basket_data$SPEC==7725,"SPEC"] <- c(3215)
x$basket_data[x$basket_data$SPEC==7733,"SPEC"] <- c(1811)
x$basket_data[x$basket_data$SPEC==7737,"SPEC"] <- c(708)
x$catch_data[x$catch_data$SPEC==7706,"SPEC"] <- c(8382)
x$catch_data[x$catch_data$SPEC==7712,"SPEC"] <- c(8367)
x$catch_data[x$catch_data$SPEC==7725,"SPEC"] <- c(3215)
x$catch_data[x$catch_data$SPEC==7733,"SPEC"] <- c(1811)
x$catch_data[x$catch_data$SPEC==7737,"SPEC"] <- c(708)
x$specimen_data[x$specimen_data$SPEC==7706,"SPEC"] <- c(8382)
x$specimen_data[x$specimen_data$SPEC==7712,"SPEC"] <- c(8367)
x$specimen_data[x$specimen_data$SPEC==7725,"SPEC"] <- c(3215)
x$specimen_data[x$specimen_data$SPEC==7733,"SPEC"] <- c(1811)
x$specimen_data[x$specimen_data$SPEC==7737,"SPEC"] <- c(708)
#tiny fish apparently marked as size class 12 instead of 2
x$basket_data[x$basket_data$set_number == 121 & x$basket_data$SPEC == 13 & x$basket_data$size_class ==12,"size_class"]<-2
x$specimen_data[x$specimen_data$set_number == 121 & x$specimen_data$SPEC == 13 & x$specimen_data$size_class ==12,"size_class"]<-2
}
if(mission == "CAB2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemapping species in the catch_, basket and speciment_ data\n")
#Mar varies from Gulf
x$basket_data[x$basket_data$SPEC==7706,"SPEC"] <- c(8382)
x$basket_data[x$basket_data$SPEC==7712,"SPEC"] <- c(8367)
x$basket_data[x$basket_data$SPEC==7725,"SPEC"] <- c(3215)
x$basket_data[x$basket_data$SPEC==7733,"SPEC"] <- c(1811)
x$catch_data[x$catch_data$SPEC==7706,"SPEC"] <- c(8382)
x$catch_data[x$catch_data$SPEC==7712,"SPEC"] <- c(8367)
x$catch_data[x$catch_data$SPEC==7725,"SPEC"] <- c(3215)
x$catch_data[x$catch_data$SPEC==7733,"SPEC"] <- c(1811)
x$specimen_data[x$specimen_data$SPEC==7706,"SPEC"] <- c(8382)
x$specimen_data[x$specimen_data$SPEC==7712,"SPEC"] <- c(8367)
x$specimen_data[x$specimen_data$SPEC==7725,"SPEC"] <- c(3215)
x$specimen_data[x$specimen_data$SPEC==7733,"SPEC"] <- c(1811)
#andes used some codes not held by Gulf, so they get changed
x$basket_data[x$basket_data$SPEC==12161,"SPEC"] <- c(8216)
x$basket_data[x$basket_data$SPEC==14878,"SPEC"] <- c(4508)
x$basket_data[x$basket_data$SPEC==16593,"SPEC"] <- c(2062)
x$basket_data[x$basket_data$SPEC==18114,"SPEC"] <- c(2217)
x$basket_data[x$basket_data$SPEC==18411,"SPEC"] <- c(6126)
x$basket_data[x$basket_data$SPEC==18495,"SPEC"] <- c(6105)
x$catch_data[x$catch_data$SPEC==12161,"SPEC"] <- c(8216)
x$catch_data[x$catch_data$SPEC==14878,"SPEC"] <- c(4508)
x$catch_data[x$catch_data$SPEC==16593,"SPEC"] <- c(2062)
x$catch_data[x$catch_data$SPEC==18114,"SPEC"] <- c(2217)
x$catch_data[x$catch_data$SPEC==18411,"SPEC"] <- c(6126)
x$catch_data[x$catch_data$SPEC==18495,"SPEC"] <- c(6105)
x$specimen_data[x$specimen_data$SPEC==12161,"SPEC"] <- c(8216)
x$specimen_data[x$specimen_data$SPEC==14878,"SPEC"] <- c(4508)
x$specimen_data[x$specimen_data$SPEC==16593,"SPEC"] <- c(2062)
x$specimen_data[x$specimen_data$SPEC==18114,"SPEC"] <- c(2217)
x$specimen_data[x$specimen_data$SPEC==18411,"SPEC"] <- c(6126)
x$specimen_data[x$specimen_data$SPEC==18495,"SPEC"] <- c(6105)
x$basket_data[x$basket_data$SPEC==11352,"SPEC"] <- c(8200) #Cnidarians
x$catch_data[x$catch_data$SPEC==11352,"SPEC"] <- c(8200) #Cnidarians
x$specimen_data[x$specimen_data$SPEC==11352,"SPEC"] <- c(8200) #Cnidarians
x$basket_data[x$basket_data$SPEC==13860,"SPEC"] <- c(4400) #Nudibranchs
x$catch_data[x$catch_data$SPEC==13860,"SPEC"] <- c(4400) #Nudibranchs
x$specimen_data[x$specimen_data$SPEC==13860,"SPEC"] <- c(4400) #Nudibranchs
x$basket_data[x$basket_data$SPEC==15053,"SPEC"] <- c(3100) #Polychaete
x$catch_data[x$catch_data$SPEC==15053,"SPEC"] <- c(3100) #Polychaete
x$specimen_data[x$specimen_data$SPEC==15053,"SPEC"] <- c(3100) #Polychaete
x$basket_data[x$basket_data$SPEC==19218,"SPEC"] <- c(9303) #Brown Seaweed
x$catch_data[x$catch_data$SPEC==19218,"SPEC"] <- c(9303) #Brown Seaweed
x$specimen_data[x$specimen_data$SPEC==19218,"SPEC"] <- c(9303) #Brown Seaweed
#these weren't necessarily global, but for specific sets
x$basket_data[x$basket_data$set_number == 8 & x$basket_data$SPEC == 6600,"SPEC"] <- 6615 #(stereoderma unisemita )
x$catch_data[x$catch_data$set_number == 8 & x$catch_data$SPEC == 6600,"SPEC"] <- 6615
x$specimen_data[x$specimen_data$set_number == 8 & x$specimen_data$SPEC == 6600,"SPEC"] <- 6615
x$basket_data[x$basket_data$set_number == 23 & x$basket_data$SPEC == 9300,"SPEC"] <- 1901 #("lemonweed")
x$catch_data[x$catch_data$set_number == 23 & x$catch_data$SPEC == 9300,"SPEC"] <- 1901
x$specimen_data[x$specimen_data$set_number == 23 & x$specimen_data$SPEC == 9300,"SPEC"] <- 1901
x$basket_data[x$basket_data$set_number == 30 & x$basket_data$SPEC == 1901,"SPEC"] <- 1901 #("lemonweed")
x$catch_data[x$catch_data$set_number == 30 & x$catch_data$SPEC == 1901,"SPEC"] <- 1901
x$specimen_data[x$specimen_data$set_number == 30 & x$specimen_data$SPEC == 1901,"SPEC"] <- 1901
x$basket_data[x$basket_data$set_number == 32 & x$basket_data$SPEC == 1901,"SPEC"] <- 1901 #("lemonweed")
x$catch_data[x$catch_data$set_number == 32 & x$catch_data$SPEC == 1901,"SPEC"] <- 1901
x$specimen_data[x$specimen_data$set_number == 32 & x$specimen_data$SPEC == 1901,"SPEC"] <- 1901
x$basket_data[x$basket_data$set_number == 44 & x$basket_data$SPEC == 1013,"SPEC"] <- 1270 #(Nezumia Aqualis)
x$catch_data[x$catch_data$set_number == 44 & x$catch_data$SPEC == 1013,"SPEC"] <- 1270
x$specimen_data[x$specimen_data$set_number == 44 & x$specimen_data$SPEC == 1013,"SPEC"] <- 1270
x$basket_data[x$basket_data$set_number == 46 & x$basket_data$SPEC == 410,"SPEC"] <- 410 #(?) (marlin spike grenadier)
x$catch_data[x$catch_data$set_number == 46 & x$catch_data$SPEC == 410,"SPEC"] <- 410
x$specimen_data[x$specimen_data$set_number == 46 & x$specimen_data$SPEC == 410,"SPEC"] <- 410
x$basket_data[x$basket_data$set_number == 47 & x$basket_data$SPEC == 6100,"SPEC"] <- 6139 #(Plutonaster agassizi)
x$catch_data[x$catch_data$set_number == 47 & x$catch_data$SPEC == 6100,"SPEC"] <- 6139
x$specimen_data[x$specimen_data$set_number == 47 & x$specimen_data$SPEC == 6100,"SPEC"] <- 6139
x$basket_data[x$basket_data$set_number == 47 & x$basket_data$SPEC == 8354,"SPEC"] <- 1283 #("Sergia robustus")
x$catch_data[x$catch_data$set_number == 47 & x$catch_data$SPEC == 8354,"SPEC"] <- 1283
x$specimen_data[x$specimen_data$set_number == 47 & x$specimen_data$SPEC == 8354,"SPEC"] <- 1283
x$basket_data[x$basket_data$set_number == 64 & x$basket_data$SPEC == 983,"SPEC"] <- 1071 #("chain cat shark")
x$catch_data[x$catch_data$set_number == 64 & x$catch_data$SPEC == 983,"SPEC"] <- 1071
x$specimen_data[x$specimen_data$set_number == 64 & x$specimen_data$SPEC == 983,"SPEC"] <- 1071
x$basket_data[x$basket_data$set_number == 73 & x$basket_data$SPEC == 8208,"SPEC"] <- 8383 #(Epizoanthus paguriphilus)
x$catch_data[x$catch_data$set_number == 73 & x$catch_data$SPEC == 8208,"SPEC"] <- 8383
x$specimen_data[x$specimen_data$set_number == 73 & x$specimen_data$SPEC == 8208,"SPEC"] <- 8383
x$basket_data[x$basket_data$set_number == 97 & x$basket_data$SPEC == 49,"SPEC"] <- 386 #( Etropus microstomus)
x$catch_data[x$catch_data$set_number == 97 & x$catch_data$SPEC == 49,"SPEC"] <- 386
x$specimen_data[x$specimen_data$set_number == 97 & x$specimen_data$SPEC == 49,"SPEC"] <- 386
x$basket_data[x$basket_data$set_number == 96 & x$basket_data$SPEC == 9992,"SPEC"] <- 785 #(silver-rag )
x$catch_data[x$catch_data$set_number == 96 & x$catch_data$SPEC == 9992,"SPEC"] <- 785
x$specimen_data[x$specimen_data$set_number == 96 & x$specimen_data$SPEC == 9992,"SPEC"] <- 785
x$basket_data[x$basket_data$set_number == 96 & x$basket_data$SPEC == 9991,"SPEC"] <- 530 #(red eyed gaper)
x$catch_data[x$catch_data$set_number == 96 & x$catch_data$SPEC == 9991,c("SPEC", "notes")] <- as.data.frame(t(c(530,"Red eye gaper (Chaunax stigmaeus)")))
x$specimen_data[x$specimen_data$set_number == 96 & x$specimen_data$SPEC == 9991,"SPEC"] <- 530
x$basket_data[x$basket_data$set_number == 105 & x$basket_data$SPEC == 9991,"SPEC"] <- 785 #(silver-rag )
x$catch_data[x$catch_data$set_number == 105 & x$catch_data$SPEC == 9991,"SPEC"] <- 785
x$specimen_data[x$specimen_data$set_number == 105 & x$specimen_data$SPEC == 9991,"SPEC"] <- 785
x$basket_data[x$basket_data$set_number == 64 & x$basket_data$SPEC == 9991,"SPEC"] <- 498 #(yellow fin bass )
x$catch_data[x$catch_data$set_number == 64 & x$catch_data$SPEC == 9991,"SPEC"] <- 498
x$specimen_data[x$specimen_data$set_number == 64 & x$specimen_data$SPEC == 9991,"SPEC"] <- 498
x$basket_data[x$basket_data$set_number == 85 & x$basket_data$SPEC == 9991,"SPEC"] <- 498 #(yellow fin bass )
x$catch_data[x$catch_data$set_number == 85 & x$catch_data$SPEC == 9991,"SPEC"] <- 498
x$specimen_data[x$specimen_data$set_number == 85 & x$specimen_data$SPEC == 9991,"SPEC"] <- 498
#note indicated that set 28, spec 9990 was actually all spec 2214 and was not sampled
#increase specimen_count with knowledge that 0.103kg was 67 shrimp, so .4535 was ~295 shrimp
# 67+295=362
x$catch_data[x$catch_data$set_number == 28 & x$catch_data$SPEC == 2214,c("specimen_count")] <- 362
x$basket_data[x$basket_data$set_number == 28 & x$basket_data$SPEC %in% c(2214),"basket_wt_kg"] <- 0.5565
#remove the catch and set recs for 9990 for this set, since they turned out to all be 2214 and are captured above)
x$catch_data <- x$catch_data[!(x$catch_data$set_number == 28 & x$catch_data$SPEC == 9990),]
x$basket_data <- x$basket_data[!(x$basket_data$set_number == 28 & x$basket_data$SPEC == 9990 & x$basket_data$basket_wt_kg == 0.1030),]
x$basket_data[x$basket_data$SPEC==400 & x$basket_data$set_number==40,"size_class"]<-1
x$specimen_data[x$specimen_data$SPEC==400 & x$specimen_data$set_number==40,"size_class"]<-1
x$basket_data[x$basket_data$SPEC==11 & x$basket_data$set_number==56,"size_class"]<-1
x$specimen_data[x$specimen_data$SPEC==11 & x$specimen_data$set_number==56,"size_class"]<-1
x$basket_data[x$basket_data$SPEC==11 & x$basket_data$set_number==57,"size_class"]<-1
x$specimen_data[x$specimen_data$SPEC==11 & x$specimen_data$set_number==57,"size_class"]<-1
#two brown algaes were entered with different andes codes:
#combine specimen count, delete one catch record, and reassign child basket to the retained catch record
x$catch_data[x$catch_data$id==1207,"specimen_count" ]<- sum(x$catch_data[x$catch_data$id==1207,"specimen_count" ], x$catch_data[x$catch_data$id==1223,"specimen_count" ])
x$catch_data<- x$catch_data[!(x$catch_data$id==1223),]
x$basket_data[x$basket_data$catch_id==1223,"catch_id"]<-1207
#two species of nudibranchs were entered with different andes codes but we only capture them as
#4400 - deleting one catch record, and reassigning its child basket to the retained catch record
x$catch_data[x$catch_data$id==2254,"specimen_count" ]<- sum(x$catch_data[x$catch_data$id==2254,"specimen_count" ], x$catch_data[x$catch_data$id==2255,"specimen_count" ])
x$catch_data<- x$catch_data[!(x$catch_data$id==2255),]
x$basket_data[x$basket_data$catch_id==2255,"catch_id"]<- 2254
x$set_data[x$set_data$set_number=="59",c("start_date")]<-"2022-07-31 07:07:00+00:00"
x$set_data[x$set_data$set_number=="59",c("start_latitude_DD")]<- 41
x$set_data[x$set_data$set_number=="59",c("start_latitude_MMmm")]<- 36.90
x$set_data[x$set_data$set_number=="59",c("start_longitude_DD")]<- -66
x$set_data[x$set_data$set_number=="59",c("start_longitude_MMmm")] <- 36.59
x$set_data[x$set_data$set_number=="84",c("start_date")]<-"2022-08-03 13:41:00.000000+00:00"
x$set_data[x$set_data$set_number=="84",c("start_latitude_DD")]<- 42
x$set_data[x$set_data$set_number=="84",c("start_latitude_MMmm")]<- 27.9
x$set_data[x$set_data$set_number=="84",c("start_longitude_DD")]<- -64
x$set_data[x$set_data$set_number=="84",c("start_longitude_MMmm")] <- 52.4
}
if(mission == "VEN2023001"){
#changes requested following Jamie Emberley's initial QC
x$basket_data[x$basket_data$SPEC == 314,"SPEC"] <- 303 #(Spatulate sculpin entries changed to Grubby Sculpins)
x$catch_data[x$catch_data$SPEC == 314,"SPEC"] <- 303
x$specimen_data[x$specimen_data$SPEC == 314,"SPEC"] <- 303
x$specimensRaw[x$specimensRaw$SPEC == 314,"SPEC"] <- 303
}
if (!is.na(theMsg)) message("Universal Tweaks: \n", theMsg)
return(x)
}
#' @title tweakBaskets
#' @description This function will perform tweaks to data coming from andes before
#' it is imported to Oracle.
#' @param x default is \code{NULL}. This is the ESE_BASKET data frame
#' @return a data frame for loading into
#' @family general_use
#' @author Pablo Vergara, \email{Pablo.Vergara@@dfo-mpo.gc.ca}
#' @export
tweakBaskets <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
if(x$MISSION[1] == "CAR2023011"){
#as requested by Jamie in "CAR2023011 Post Survey Processing.docx"
x[x$SETNO==56 & x$SPEC == 2555, "SAMPLED"] <- F
x[x$SETNO==54 & x$SPEC == 2214,"SAMPLED"] <- F
}
if(x$MISSION[1] == "TEL2023010"){
x[x$SETNO==32 & x$SPEC == 9331 & x$SIZE_CLASS== 2,"SIZE_CLASS"] <- 1
#remove this
# basket_wt_kg catch_id creation_date id last_modified_date mission_number sampled set_number size_class size_class_display species_aphia_id species_code species_en species_fr species_scientific species_uuid
# 0 824 2023-06-29 05:32:51 UTC 855 2023-06-29 05:32:51 UTC TEL-2023-010 No 1 1 1 158356 2214 Bristled longbeak shrimp Crevette - Dichelopandalus leptocerus Dichelopandalus leptocerus 0a120f9d-714f-48bc-925f-b39b246f8f17
toRemove <- x[x$SETNO == 1 & x$SPEC == 2214 & x$BASKET_WEIGHT == 0,]
x <- df.diff(x, toRemove)
}
if(x$MISSION[1] == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tCorrecting two baskets which were incorrectly flagged as being sampled\n")
x[x$SETNO == 13 & x$SPEC == 2100 & x$id == 630,"SAMPLED"]<-F
x[x$SETNO == 61 & x$SPEC == 8100 & x$id == 1918,"SAMPLED"]<-F
}
if(x$MISSION[1] == "TEL2022010"){
#nudibranchs had been broken into sp we don't track
x<- x[!(x$SETNO == 151 & x$SPEC == 4400),]
x<-rbind.data.frame(x,list("TEL2022010", 151, 4400, 1, 0.003, FALSE, NA, NA))
}
if(x$MISSION[1] == "CAB2022010"){
x[x$SETNO == 18 & x$SPEC == 150,"SAMPLED"]<-F
#remove a basket weight that was estimated from the unweighed baskets
x <- x[!(x$SETNO == 55 & x$SPEC == 2550 & x$basket_id == 2475),]
}
if(x$MISSION[1] == "CAR2023002"){
x[which(x$SETNO == 164 & x$SPEC == 4500),"SAMPLED"] <- FALSE
# SETNO 7, SPEC 2541
x[which(x$SETNO == 7 & x$SPEC == 2541),"SAMPLED"] <- FALSE
x[x$basket_id == 4484,"SIZE_CLASS"]<-1
x[x$basket_id == 4482,"SIZE_CLASS"]<-1
x[x$basket_id == 4480,"SIZE_CLASS"]<-2
x[x$basket_id == 1747,"SAMPLED"]<-TRUE
}
if(x$MISSION[1] == "VEN2023001"){
}
if (!is.na(theMsg)) message("Tweaking BASKET: \n", theMsg)
return(x)
}
#' @title tweakCatches
#' @description This function will perform tweaks to data coming from andes before
#' it is imported to Oracle.
#' @param x default is \code{NULL}. This is the ESE_CATCHES data frame
#' @return a data frame for loading into ESE_CATCHES
#' @family general_use
#' @author Pablo Vergara, \email{Pablo.Vergara@@dfo-mpo.gc.ca}
#' @export
tweakCatches <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
if(x$MISSION[1] == "CAR2023011"){
x[x$SETNO==5 & x$SPEC==8100,c( "UNWEIGHED_BASKETS", "NUMBER_CAUGHT")] <- as.data.frame(t(c(NA,10)))
}
if(x$MISSION[1] == "TEL2023010"){
#add this:
#MISSION SETNO SPEC catch_id UNWEIGHED_BASKETS NUMBER_CAUGHT is_parent parent_catch_id SIZE_CLASS
#TEL2023010 217 6211 6570 NA 235 FALSE 6568 1
# toAdd <- c(MISSION = "TEL2023010", SETNO=217,SPEC = 6211, NOTE = "", UNWEIGHED_BASKETS = NA, NUMBER_CAUGHT = 235, catch_id=NA, is_parent=F, parent_catch_id = 6568)
# .1905
# x <- rbind.data.frame(x, toAdd)
x[x$SETNO== 195 & x$SPEC==1510,"UNWEIGHED_BASKETS"] <- NA
}
if(x$MISSION[1] == "TEL2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tApplying fixes on the catch records\n")
x[x$SETNO==76 & x$SPEC == 2213,c("UNWEIGHED_BASKETS", "NUMBER_CAUGHT")] <- as.data.frame(t(c(NA,62)))
x[x$SETNO==133 & x$SPEC == 730,"NOTE"] <- "Caught dead. Hagfish inside. Weight was estimated. Fin to Fin measurement: 167cm. Weight estimated, not weighed. Measured on deck."
#nudibranchs had been broken into sp we don't track
x<- x[!(x$SETNO == 151 & x$SPEC == 4400),]
x<-rbind.data.frame(x,list("TEL2022010", 151, 4400, NA, NA, 6, NA, FALSE, NA))
}
if(x$MISSION[1] == "CAB2022010"){
x[x$SETNO==34 & x$SPEC == 243,"NOTE"] <- "basket weight is estimate only"
x[x$SETNO==50 & x$SPEC == 220,"NOTE"] <- "the large basket weight (858kg) was calculated at sea from a count of unweighed baskets"
x[x$SETNO==50 & x$SPEC == 204,"NOTE"] <- "the large basket weight (507kg) was calculated at sea from a count of unweighed baskets"
}
if (!is.na(theMsg)) message("Tweaking CATCH: ", theMsg)
return(x)
}
#' @title tweakSpecimensRaw
#' @description This function will perform tweaks to data coming from andes before
#' it is imported to Oracle. specimen_data gets converted into both ESE_SPECIMENS and
#' ESE_LV1_OBSERVATIONS, so many tweaks should be performed here to ensure that changes are
#' reflected in both output tables. Also, changing here will ensure sequential LV1_OBSERVATION_ID
#' values
#' @param x default is \code{NULL}. This is the raw "specimen_data" data frame
#' @return a data frame for loading into ESE_BASKETS
#' @family general_use
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
tweakSpecimensRaw <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
x$species_aphia_id <- NULL
# theMsg <- paste0(theMsg[!is.na(theMsg)], "\tBerried female crabs and lobsters recoded to 3\n")
x[which(x$sex==2 & (x$crab.female.eggs == 1 | x$lobster.female.eggs==1)), "sex"] <-3
if(nrow(x[which(x$sex==1 & (x$crab.female.eggs == 1 | x$lobster.female.eggs==1)), ]))warning("Berried Males detected")
if(x$MISSION[1] == "TEL2023010"){
x[x$id==4690,"weight"]<-0.5
x[x$id==4696,"weight"]<-0.5
x[x$id==4699,"weight"]<-0.5
x[x$id==22537,"weight"]<-13
x[x$id==24812,"length"]<-230
# • Setno 3, spec 610, specimen_id 4690 – update weight to 0.5
# • Setno 3, spec 610, specimen_id 4696 – update weight to 0.5
# • Setno 3, spec 610, specimen_id 4699 – update weight to 0.5
# • Setno 40, spec 14, specimen_id 22537 – update weight to 13
#• Setno 44, spec 60, specimen_id 24812 – update length to 230
x[x$id==75096,"gonad.weight"] <- 2
x[x$id==75846,"gonad.weight"] <- 2670
x[x$id==75846,"collect.gonads"] <- 1
# • Setno 214, spec 30, specimen_id 75096 – update gonad weight to 2
# • Setno 219, spec 30, specimen_id 75846 – update gonad weight to 2670, update collect gonads to 1 and data desc = collected
x[x$id==25131,"sex"]<-0
x[x$id==72792,"sex"]<-0
# • Setno 45, spec 2550, specimen_id 25131 – update sex to 0 (undetermined)
# • Setno 209, spec 41, specimen_id 72792 – update sex to 0 (undetermined)
}
if(x$MISSION[1] == "CAR2023002"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemoving Fish Numbers from Mackerel records\n")
# • Set 171, spec 11, specimen id 71795 – length entered as 0.30. Update length to 30
x[x$id==71795,"length"]<-30
# • Set 17 – spec 11, specimen id 5022, change weight to 217
x[x$id==5022,"weight"]<-217
# • Set 11 – spec 4511, specimen id 3709, remove the weight observation
x[x$id==3709,"weight"]<-NA
# • Set 104 – spec 303, specimen id 37264, change weight to 1.5
x[x$id==37264,"weight"]<-1.5
# • Set 65 – spec 303, specimen id 19640, Change weight to 0.5
x[x$id==19640,"weight"]<-0.5
# • Set 153 – spec 14, specimen id 63547, Change weight to 0.5
x[x$id==63547,"weight"]<-0.5
# • Set 69 – spec 150, specimen id 22031, change weight to 4
x[x$id==22031,"weight"]<-4
# • Set 189 – spec 340, specimen id 30865, change weight to 1.5
x[x$id==30865,"weight"]<-1.5
# • Set 167, spec 410, specimen id 70480, Change weight to 0.5
x[x$id==70480,"weight"]<-0.5
# • Set 166, spec 410, specimen id 70267, Change weight to 0.5
x[x$id==70267,"weight"]<-0.5
# • Set 166, spec 410, specimen id 70272, Change weight to 0.5
x[x$id==70272,"weight"]<-0.5
# • Set 166, spec 410, specimen id 70277, Change weight to 0.5
x[x$id==70277,"weight"]<-0.5
# • Set 166, spec 410, specimen id 70283, Change weight to 0.5
x[x$id==70283,"weight"]<-0.5
# • Set 167, spec 604, specimen id 70566, Change weight to 0.5
x[x$id==70566,"weight"]<-0.5
# • Set 7, spec 44, specimen id 1231, change weight from .5 to 0.5
x[x$id==1231,"weight"]<-0.5
# • Set 24, spec 143, specimen id 6483, change weight from .5 to 0.5
x[x$id==6483,"weight"]<-0.5
# • Set 47, spec 60, specimen id 11696, change length from 376 to 276
x[x$id==11696,"length"]<-276
#SET 29. SPEC 4321, SPECIMEN ID 7713
x <- x[-which(x$id == 7713),]
#SETNO 7, SPEC 2541, SPECIMEN ID 1094,
x <- x[-which(x$id == 1094),]
}
if(x$MISSION[1] == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemoving Fish Numbers from Mackerel records\n")
x[x$species_code == 70,"fish_number"] <- NA
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemoving comments created solely to generate labels\n")
commentsDrop <- c(".", "1", "edrftgujik", "fdgj", "fgjh", "rdfyg", "srdtfygvuh")
x[x$comment %in% commentsDrop,"comment"]<- NA
x[x$comments %in% commentsDrop,"comments"]<- NA
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 44/Spec 1191/Specimen id 14496: Removing incorrect length\n")
x[x$id == 14496,"length"] <- NA
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 26/Spec 14/Specimen id 9332: Weight corrected to grams\n")
x[x$id == 9332,"weight"] <- x[x$id == 9332,"weight"]*1000
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 49/Spec 11/Specimen id 16236: No useful info entered - deleted\n")
x <- x[-which(x$id == 16236),]
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSpec 60: Several sets list weight as less than <0.5g - the smallest precision available. Bump all of these up to 0.5g\n")
x[which(x$species_code == 60 & x$weight <0.5),"weight"] <- 0.5
}
if(x$MISSION[1] == "TEL2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 133 - removed a duplicate sunfish record")
x <- x[!x$id %in% 49411,]
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemoving some bad records")
x <- x[!x$id %in% 49475,]
x <- x[!x$id %in% 20427,]
x <- x[!x$id %in% 14656,]
}
if(x$MISSION[1] == "CAB2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 46 - The first 30 'silver hake' records are actually dogfish (fixed)")
x<- x[with(x,order(id)),]
x[x$set_number == 46 & x$SPEC == 14,][1:30,"SPEC"]<- 220
#remove specimens with length = 0
x <- x[!x$id==34724,]
x <- x[!x$id==34744,]
#certain 0cm lengths should be 10cm
x[x$id==35107,"length"]<-10
x[x$id==31275,"length"]<-10
x[x$id==47775,"length"]<-10
x[x$id==32839,"length"]<-10
x[x$id==27596,"length"]<-10
#likely typo - length should be 250 (not 25)
x[x$id==17577,"length"]<-250
#lobsters measured as less than 3mm are likely typos
x<-x[!(x$SPEC == 2550 & x$length <3),]
#some entries for the following spp had tiny lengths - almost certainly typos
x<-x[!(x$SPEC %in% c(11,13,14,23, 1191) & x$length <3),]
}
if(x$MISSION[1] == "VEN2023001"){
#changes requested following Jamie Emberley's initial QC
x <- x[!x$id==4098,]
x <- x[!x$id==14617,]
x <- x[!x$id==17226,]
x[x$id==3315,"weight"]<- 2 #0.002 to 2
x[x$id==9641,"weight"]<- 5 #0.0005 to 5
x[x$id==14872,"sex"] <- 0 #too small to have been sexed
x[x$id==20014,"weight"] <- 264 #likely typo in wgt
}
if (!is.na(theMsg)) message("Tweaking specimen_data: \n", theMsg)
return(x)
}
#' @title tweakSets
#' @description This function will perform tweaks to data coming from andes before
#' it is imported to Oracle.
#' @param x default is \code{NULL}. This is the ESE_SETS data frame.
#' @return a data frame for loading into ESE_SETS
#' @family general_use
#' @author Pablo Vergara, \email{Pablo.Vergara@@dfo-mpo.gc.ca}
#' @export
tweakSets <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
if(x$MISSION[1] == "CAR2023011"){
x[x$SETNO %in% c(1,216), "EXPERIMENT_TYPE_CODE"] <- 9
x[x$SETNO %in% c(1,216), "STATION"] <- NA
x[x$SETNO %in% c(1,216), "NOTE"] <- trimws(paste(x[x$SETNO %in% c(1,216), "NOTE"], "HFX HYD"))
x[x$EXPERIMENT_TYPE_CODE %in% c(1), "EXPERIMENT_TYPE_CODE"]<-5
}
if(x$MISSION[1] == "TEL2023010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tUsed manually recorded distance for sets 222 to 234\n")
x[x$SETNO %in% c(222:234),"DIST"]<- x[x$SETNO%in% c(222:234),"distance_towed"]
# x[x$SETNO%in% c(232),"START_TIME"] <- 2959
}
if(x$MISSION[1] == "CAR2023002"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRecoded GEAR from 23 to 15\n")
#NEST trawl is not 23, but 15 - change here; expect this will be corrected in the future
# Jamie created aux = 6 for the nest
x[x$GEAR==23,"GEAR"] <- 15
x[x$AUX==2,"AUX"] <- 6
#set 1
# • Set 1 – update Experiment type to 9
# • Set 1 – delete station 100, leave this field blank
# • Set 1 – delete Warpout, leave blank
# • Set 1 – add a Note for the set – HFX HYD
x[x$SETNO==1,"EXPERIMENT_TYPE_CODE"]<- 9
x[x$SETNO==1,"STATION"]<- NA
x[x$SETNO==1,"WARPOUT"]<- NA
x[x$SETNO==1,"NOTE"]<- "HFX HYD"
# set 129
# • Set 129 - update Experiment type to 9
# • Set 129 - delete station 100, leave this field blank
# • Set 129 - add a Note for the set – HFX HYD
x[x$SETNO==129,"EXPERIMENT_TYPE_CODE"]<- 9
x[x$SETNO==129,"STATION"]<- NA
x[x$SETNO==129,"NOTE"]<- "HFX HYD"
}
if(x$MISSION[1] == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRecoded GEAR from 23 to 15\n")
#NEST trawl is not 23, but 15 - change here; expect this will be corrected in the future
x[x$GEAR==23,"GEAR"] <- 15
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 16: Corrected DIST\n")
x[x$SETNO==16,"DIST"] <- 0.978
# Mission CAR2022102, Set 16 - DIST showing as -10.98, should be 0.98
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 16: Corrected START_DEPTH\n")
x[x$SETNO==16,"START_DEPTH"] <- 92
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 4: Corrected missing ELONG\n")
x[x$SETNO==4,"ELONG"] <- -6620.64599
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSets 9 & 41: Corrected ETIME\n")
x[x$SETNO==9,"END_TIME"] <- "1739"
x[x$SETNO==41,"END_TIME"] <- "0054"
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tManually added area for each set\n")
x[x$SETNO == "1", "AREA"] <- "523"
x[x$SETNO == "2", "AREA"] <- "524"
x[x$SETNO == "3", "AREA"] <- "524"
x[x$SETNO == "4", "AREA"] <- "524"
x[x$SETNO == "5", "AREA"] <- "524"
x[x$SETNO == "6", "AREA"] <- "524"
x[x$SETNO == "7", "AREA"] <- "524"
x[x$SETNO == "8", "AREA"] <- "524"
x[x$SETNO == "9", "AREA"] <- "524"
x[x$SETNO == "10", "AREA"] <- "524"
x[x$SETNO == "11", "AREA"] <- "523"
x[x$SETNO == "12", "AREA"] <- "523"
x[x$SETNO == "13", "AREA"] <- "523"
x[x$SETNO == "14", "AREA"] <- "523"
x[x$SETNO == "15", "AREA"] <- "523"
x[x$SETNO == "16", "AREA"] <- "523"
x[x$SETNO == "17", "AREA"] <- "523"
x[x$SETNO == "18", "AREA"] <- "523"
x[x$SETNO == "19", "AREA"] <- "523"
x[x$SETNO == "20", "AREA"] <- "523"
x[x$SETNO == "21", "AREA"] <- "523"
x[x$SETNO == "22", "AREA"] <- "523"
x[x$SETNO == "23", "AREA"] <- "523"
x[x$SETNO == "24", "AREA"] <- "523"
x[x$SETNO == "25", "AREA"] <- "523"
x[x$SETNO == "26", "AREA"] <- "523"
x[x$SETNO == "27", "AREA"] <- "523"
x[x$SETNO == "28", "AREA"] <- "523"
x[x$SETNO == "29", "AREA"] <- "523"
x[x$SETNO == "30", "AREA"] <- "523"
x[x$SETNO == "31", "AREA"] <- "523"
x[x$SETNO == "32", "AREA"] <- "524"
x[x$SETNO == "33", "AREA"] <- "524"
x[x$SETNO == "34", "AREA"] <- "524"
x[x$SETNO == "35", "AREA"] <- "524"
x[x$SETNO == "36", "AREA"] <- "524"
x[x$SETNO == "37", "AREA"] <- "524"
x[x$SETNO == "38", "AREA"] <- "524"
x[x$SETNO == "39", "AREA"] <- "524"
x[x$SETNO == "40", "AREA"] <- "524"
x[x$SETNO == "41", "AREA"] <- "524"
x[x$SETNO == "42", "AREA"] <- "524"
x[x$SETNO == "43", "AREA"] <- "524"
x[x$SETNO == "44", "AREA"] <- "523"
x[x$SETNO == "45", "AREA"] <- "524"
x[x$SETNO == "46", "AREA"] <- "524"
x[x$SETNO == "47", "AREA"] <- "524"
x[x$SETNO == "48", "AREA"] <- "524"
x[x$SETNO == "49", "AREA"] <- "524"
x[x$SETNO == "50", "AREA"] <- "523"
x[x$SETNO == "51", "AREA"] <- "523"
x[x$SETNO == "52", "AREA"] <- "523"
x[x$SETNO == "53", "AREA"] <- "523"
x[x$SETNO == "54", "AREA"] <- "523"
x[x$SETNO == "55", "AREA"] <- "523"
x[x$SETNO == "56", "AREA"] <- "523"
x[x$SETNO == "57", "AREA"] <- "524"
x[x$SETNO == "58", "AREA"] <- "524"
x[x$SETNO == "59", "AREA"] <- "524"
x[x$SETNO == "60", "AREA"] <- "524"
x[x$SETNO == "61", "AREA"] <- "524"
x[x$SETNO == "62", "AREA"] <- "524"
x[x$SETNO == "63", "AREA"] <- "524"
x[x$SETNO == "64", "AREA"] <- "524"
x[x$SETNO == "65", "AREA"] <- "524"
x[x$SETNO == "66", "AREA"] <- "524"
x[x$SETNO == "67", "AREA"] <- "524"
x[x$SETNO == "68", "AREA"] <- "523"
x[x$SETNO == "69", "AREA"] <- "523"
x[x$SETNO == "70", "AREA"] <- "523"
x[x$SETNO == "71", "AREA"] <- "523"
x[x$SETNO == "72", "AREA"] <- "467"
}
if(x$MISSION[1] == "TEL2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tModified exp type manually for several sets\n")
x[x$SETNO == "1", "EXPERIMENT_TYPE_CODE"] <- "9"
x[x$SETNO == "44", "EXPERIMENT_TYPE_CODE"] <- "9"
x[x$SETNO == "170", "EXPERIMENT_TYPE_CODE"] <- "9"
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tModified dist and speed manually for a set\n")
x[x$SETNO == "99", c("DIST", "SPEED")] <- as.data.frame(t(c(1.61,3.22)))
}
if (x$MISSION[1] == "CAB2022010"){
x[x$SETNO == "3", "DIST"] <- 0.95
#NEST trawl is not 23, but 15 - change here; expect this will be corrected in the future
x[x$GEAR==23,"GEAR"] <- 15
x[x$EXPERIMENT_TYPE_CODE==1, "EXPERIMENT_TYPE_CODE"]<- 5
}
if (x$MISSION[1] == "VEN2023001"){
x[x$SETNO == 32, "end_date"] <- "2023-02-11 23:13:04+00:00"
x[x$SETNO == 32, "END_TIME"] <- 1913
}
if (!is.na(theMsg)) message("Tweaking SETS: \n", theMsg)
return(x)
}
#' @title tweakBasketsPostProcessing
#' @description This function can do final changes to the basket data once all of the various basket/
#' catch handling and re-allocation of mixed catches is complete. This processing can include using
#' measured weights to change basket weights, so both basket and lv1 objects are necessary as
#' parameters.
#' @param basket default is \code{NULL}.
#' @param lv1 default is \code{NULL}.
#' @return an updated version of ESE_BASKETS
#' @family general_use
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
tweakBasketsPostProcessing <- function(basket=NULL, lv1 = NULL){
if(length(unique(basket$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
message("Tweaking final BASKET weights: \n")
badBasksSampled <- basket[which(basket$BASKET_WEIGHT<0.0005 & basket$SAMPLED),"basket_id"]
badBasksUnsampled <- basket[which(basket$BASKET_WEIGHT<0.0005 & !basket$SAMPLED),"basket_id"]
if (length(badBasksUnsampled)>0 | length(badBasksSampled)>0) message("\tMinimum measurable basket weight is 0.0005 kg\n")
if (length(badBasksUnsampled)>0){
message("\tUnsampled baskets reporting a weight lower than the minimum were bumped up to 0.0005 kg\n")
basket[which(basket$BASKET_WEIGHT<0.0005 & !basket$SAMPLED),"BASKET_WEIGHT"] <- 0.0005
}
if (length(badBasksSampled)>0){
message("\tOne or more sampled baskets reporting a weight lower than the minimum were bumped up using recorded speciment weights\n\n")
for (i in 1:length(badBasksSampled)){
thisBasketSampled <- basket[basket$basket_id %in% badBasksSampled[i],]
thisBasketSampledSpecimensWeight <- as.numeric(lv1[lv1$basket_id %in% badBasksSampled[i] & lv1$LV1_OBSERVATION == "Weight","DATA_VALUE"])
# message("\t\tHandling")
if (length(thisBasketSampledSpecimensWeight)>0){
#wts in lv1 are in grams, but baskets are kg, convert below
basket[basket$basket_id %in% thisBasketSampled$basket_id,"BASKET_WEIGHT"] <- sum(thisBasketSampledSpecimensWeight/1000)
# message("\t\t\t<done>")
}else{
basket[basket$basket_id %in% thisBasketSampled$basket_id,"BASKET_WEIGHT"] <- 0.0005
# message("\t\t\t<No sampled weights could be found - forcing 0.0005 kg>")
}
}
}
return(basket)
}
#' @title tweakLv1
#' @description This function will perform tweaks to the lv1_observations data coming from andes before
#' it is imported to Oracle.
#' @param x default is \code{NULL}. This is the ESE_LV1_OBSERVATIONS data frame
#' @return an updated version of ESE_LV1_OBSERVATIONS
#' @family general_use
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
tweakLv1 <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
if(x$MISSION[1] == "CAR2023011"){
x[x$SPECIMEN_ID == 83667 & x$LV1_OBSERVATION == "Weight","DATA_VALUE"]<-1
}
if(x$MISSION[1] == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tHerring otoliths taken post-survey - manually adding that information\n")
x[x$SPEC == 60 & x$LV1_OBSERVATION == "Collect Specimen" & x$DATA_VALUE =="1" ,c("LV1_OBSERVATION","DATA_DESC")] <- as.data.frame(t(as.matrix(c("Age Material Type","Otolith Taken"))))
}
if(x$MISSION[1] == "TEL2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSome records were recorded in kg instead of g (fixed)\n")
x[x$SPECIMEN_ID %in% c(24705,24707) & x$LV1_OBSERVATION == "Weight" & x$DATA_VALUE =="0.001" ,c("DATA_VALUE")] <- 1
x[x$SPECIMEN_ID == 178 & x$LV1_OBSERVATION == "Weight","DATA_VALUE"]<-1
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSome records had inncorrect lengths")
x[x$SPECIMEN_ID == 42542 & x$LV1_OBSERVATION == "Length","DATA_VALUE"]<-14
x[x$SPECIMEN_ID == 46991 & x$LV1_OBSERVATION == "Length","DATA_VALUE"]<-10
x[x$SPECIMEN_ID == 54423 & x$LV1_OBSERVATION == "Length","DATA_VALUE"]<-20
x[x$SPECIMEN_ID == 27478 & x$LV1_OBSERVATION == "Length","DATA_VALUE"]<-26
}
if (!is.na(theMsg)) message("Tweaking LV1_OBSERVATIONS: \n", theMsg)
return(x)
}
PopulationEcologyDivision/andesmerge documentation built on April 12, 2024, 6:28 a.m.
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Defines functions tweakLv1 tweakBasketsPostProcessing tweakSets tweakSpecimensRaw tweakCatches tweakBaskets tweakUniversal
Documented in tweakBaskets tweakBasketsPostProcessing tweakCatches tweakLv1 tweakSets tweakSpecimensRaw tweakUniversal
#' @title tweakUniversal
#' @description This function will perform tweaks on data from Andes that exists in multiple
#' exported csv files
#' @param x default is \code{NULL}. This is a list of all of the objects from the csv files
#' @param mission default is \code{NULL}. This is the cleaned mission id (e.g. CAR2022102)
#' @return list
#' @family general_use
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
tweakUniversal <- function(x = NULL, mission=NULL){
theMsg <- NA
#get rid of text species name for overwritten spp, we will really entirely on the species codes
x$catch_data$species <- x$catch_data$species_id <- NULL
if (mission =="CAR2023011"){
#• Delete specimen_id 23286 from all tables. Setno 47, spec 11, length 1 (23286)
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==23286,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==23286,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==23286,]
# • Delete specimen_id 26437 from all tables. Setno 54, spec 23, length 1 (26437 )
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==26437,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==26437,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==26437,]
# • Delete specimen_id 999 from all tables. Setno 2, spec 60, length 0 (999 )
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==999,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==999,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==999,]
# • Delete specimen_id 26753 from all tables. Setno 54, spec 123, length 1 (26753)
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==26753,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==26753,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==26753,]
# • Delete specimen_id 31731 from all tables. Setno 68, spec 4321, length 0.31 (31731)
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==31731,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==31731,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==31731,]
# • Delete specimen_id 58696 from all tables. Setno 158, spec 40, length 1 (58696 )
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==58696,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==58696,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==58696,]
# • Delete specimen_id 68922 from all tables. Setno 190, spec 40, length 1
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==68922,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==68922,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==68922,]
# • Delete specimen_id 69568 from all tables. Setno 192, spec 40, length 1
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==69568,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==69568,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==69568,]
# • Delete specimen_id 69570 from all tables. Setno 192, spec 40, length 1
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==69570,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==69570,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==69570,]
# • Delete specimen_id 3670 from all tables. Setno 8, spec 40, length 0.1675. Incorrect length was entered and was the only individual for the basket. Change the basket (0.1155) to sampled = ‘N’
x$specimensRaw <- x$specimensRaw[!x$specimensRaw$id ==3670,]
x$specimen_data <- x$specimen_data[!x$specimen_data$id ==3670,]
x$observation_data <- x$observation_data[!x$observation_data$specimen_id ==3670,]
x$basket_data[x$basket_data$set_number== 8 & x$basket_data$species_code == 40, "sampled"] <- "No"
# • Update car_ese_lv1_observations set data_value=1 where setno=236 and spec=14 and specimen_id=83667 and lv1_observation=’Weight’ and data_value=0.001;
x$specimensRaw[x$specimensRaw$id== 83667,]
x$specimen_data[x$specimen_data$id== 83667,]
x$observation_data[x$observation_data$specimen_id ==83667,]
}
if(mission == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemapping species in the catch_data\n")
x$catch_data[x$catch_data$species_code == 18411,"species_code"] <- 6102
x$catch_data[x$catch_data$species_code == 13519,"species_code"] <- 4213
x$catch_data[x$catch_data$species_code == 14878,"species_code"] <- 4508
x$catch_data[x$catch_data$species_code == 12161,"species_code"] <- 8216
x$catch_data[x$catch_data$species_code == 19218,"species_code"] <- 9331
x$catch_data[x$catch_data$species_code == 19950,"species_code"] <- 1510
x$catch_data[x$catch_data$species_code == 18680,"species_code"] <- 1821
x$catch_data[x$catch_data$species_code == 12157,"species_code"] <- 8382
x$catch_data[x$catch_data$species_code == 10854,"species_code"] <- 500
x$catch_data[x$catch_data$species_code == 12096,"species_code"] <- 8516
x$catch_data[x$catch_data$species_code == 9003,"species_code"] <- 1224
# x$catch_data[x$catch_data$species_code == 18495,"species_code"] <- 6105
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemapping species in the specimen_data\n")
x$specimen_data[x$specimen_data$species_code == 18411,"species_code"] <- 6102
x$specimen_data[x$specimen_data$species_code == 13519,"species_code"] <- 4213
x$specimen_data[x$specimen_data$species_code == 14878,"species_code"] <- 4508
x$specimen_data[x$specimen_data$species_code == 12161,"species_code"] <- 8216
x$specimen_data[x$specimen_data$species_code == 19218,"species_code"] <- 9331
x$specimen_data[x$specimen_data$species_code == 19950,"species_code"] <- 1510
x$specimen_data[x$specimen_data$species_code == 18680,"species_code"] <- 1821
x$specimen_data[x$specimen_data$species_code == 12157,"species_code"] <- 8382
x$specimen_data[x$specimen_data$species_code == 10854,"species_code"] <- 500
x$specimen_data[x$specimen_data$species_code == 12096,"species_code"] <- 8516
x$specimen_data[x$specimen_data$species_code == 9003,"species_code"] <- 1224
# x$specimen_data[x$specimen_data$species_code == 18495,"species_code"] <- 6105
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemapping species in the basket_data\n")
x$basket_data[x$basket_data$species_code == 18411,"species_code"] <- 6102
x$basket_data[x$basket_data$species_code == 13519,"species_code"] <- 4213
x$basket_data[x$basket_data$species_code == 14878,"species_code"] <- 4508
x$basket_data[x$basket_data$species_code == 12161,"species_code"] <- 8216
x$basket_data[x$basket_data$species_code == 19218,"species_code"] <- 9331
x$basket_data[x$basket_data$species_code == 19950,"species_code"] <- 1510
x$basket_data[x$basket_data$species_code == 18680,"species_code"] <- 1821
x$basket_data[x$basket_data$species_code == 12157,"species_code"] <- 8382
x$basket_data[x$basket_data$species_code == 10854,"species_code"] <- 500
x$basket_data[x$basket_data$species_code == 12096,"species_code"] <- 8516
x$basket_data[x$basket_data$species_code == 9003,"species_code"] <- 1224
# x$basket_data[x$basket_data$species_code == 18495,"species_code"] <- 6105
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tHandling 'spp 18495'. Basket 1 was spp 6102; Basket 2 was spp 6126 - need an additional catch record\n")
x$catch_data<- rbind(x$catch_data, x$catch_data[x$catch_data$species_code==18495,])
x$catch_data[x$catch_data$species_code==18495,"species_code"] <- c(6102,6126)
x$basket_data<-x$basket_data[order(x$basket_data$id),]
x$basket_data[x$basket_data$species_code==18495,"species_code"] <- c(6102,6126)
colnames(x$specimen_data)[colnames(x$specimen_data)=="species_code"] <- "SPEC"
colnames(x$catch_data)[colnames(x$catch_data)=="species_code"] <- "SPEC"
colnames(x$basket_data)[colnames(x$basket_data)=="species_code"] <- "SPEC"
}
if(mission == "TEL2022010"){
#changing time and coords here so they get appropriately converted by transmogrified
x$set_data[x$set_data$set_number == 148, c("start_latitude_DD", "start_latitude_MMmm", "start_longitude_DD", "start_longitude_MMmm")]<- as.data.frame(t(c(42,27.707,-64,51.821)))
x$set_data[x$set_data$set_number == 148, c("start_date")] <- "2022-08-03 13:43:00.000000+00:00"
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tConverting andes codes to Maritimes spp\n")
#mola mola was not in andes spp list
x$basket_data[x$basket_data$set_number == 69 & x$basket_data$SPEC == 9991,c("SPEC")] <- c(730)
x$specimen_data[x$specimen_data$set_number == 69 & x$specimen_data$SPEC == 9991,c("SPEC")] <- c(730)
x$catch_data[x$catch_data$set_number == 69 & x$catch_data$SPEC == 9991,c("SPEC")] <- c(730)
#andes used some codes not held by Gulf, so they get changed
x$basket_data[x$basket_data$SPEC==12161,"SPEC"] <- c(8216)
x$basket_data[x$basket_data$SPEC==12174,"SPEC"] <- c(8209)
x$basket_data[x$basket_data$SPEC==14878,"SPEC"] <- c(4508)
x$basket_data[x$basket_data$SPEC==16593,"SPEC"] <- c(2062)
x$basket_data[x$basket_data$SPEC==18411,"SPEC"] <- c(6126)
x$basket_data[x$basket_data$SPEC==18495,"SPEC"] <- c(6105)
x$basket_data[x$basket_data$SPEC==18515,"SPEC"] <- c(6107)
x$basket_data[x$basket_data$SPEC==18575,"SPEC"] <- c(6202)
x$basket_data[x$basket_data$SPEC==18792,"SPEC"] <- c(1812)
x$catch_data[x$catch_data$SPEC==12161,"SPEC"] <- c(8216)
x$catch_data[x$catch_data$SPEC==12174,"SPEC"] <- c(8209)
x$catch_data[x$catch_data$SPEC==14878,"SPEC"] <- c(4508)
x$catch_data[x$catch_data$SPEC==16593,"SPEC"] <- c(2062)
x$catch_data[x$catch_data$SPEC==18411,"SPEC"] <- c(6126)
x$catch_data[x$catch_data$SPEC==18495,"SPEC"] <- c(6105)
x$catch_data[x$catch_data$SPEC==18515,"SPEC"] <- c(6107)
x$catch_data[x$catch_data$SPEC==18575,"SPEC"] <- c(6202)
x$catch_data[x$catch_data$SPEC==18792,"SPEC"] <- c(1812)
x$specimen_data[x$specimen_data$SPEC==12161,"SPEC"] <- c(8216)
x$specimen_data[x$specimen_data$SPEC==12174,"SPEC"] <- c(8209)
x$specimen_data[x$specimen_data$SPEC==14878,"SPEC"] <- c(4508)
x$specimen_data[x$specimen_data$SPEC==16593,"SPEC"] <- c(2062)
x$specimen_data[x$specimen_data$SPEC==18411,"SPEC"] <- c(6126)
x$specimen_data[x$specimen_data$SPEC==18495,"SPEC"] <- c(6105)
x$specimen_data[x$specimen_data$SPEC==18515,"SPEC"] <- c(6107)
x$specimen_data[x$specimen_data$SPEC==18575,"SPEC"] <- c(6202)
x$specimen_data[x$specimen_data$SPEC==18792,"SPEC"] <- c(1812)
#all instances of mud star were actually pulvillus
x$basket_data[x$basket_data$SPEC==6115,"SPEC"] <- c(6126)
x$catch_data[x$catch_data$SPEC==6115,"SPEC"] <- c(6126)
x$specimen_data[x$specimen_data$SPEC==6115,"SPEC"] <- c(6126)
#andes used specified a level of detail different than what Mar has codes for
#J Emberley made these suggestions
x$basket_data[x$basket_data$SPEC==10244,"SPEC"] <- c(942)
x$basket_data[x$basket_data$SPEC==12676,"SPEC"] <- c(1900)
x$basket_data[x$basket_data$SPEC==12679,"SPEC"] <- c(1901)
x$basket_data[x$basket_data$SPEC==13090,"SPEC"] <- c(1930)
x$basket_data[x$basket_data$SPEC==14230,"SPEC"] <- c(4316)
x$basket_data[x$basket_data$SPEC==16592,"SPEC"] <- c(2990)
x$basket_data[x$basket_data$SPEC==18800,"SPEC"] <- c(7733)
x$basket_data[x$basket_data$SPEC==19220,"SPEC"] <- c(9303)
x$basket_data[x$basket_data$SPEC==13891,"SPEC"] <- c(4400)
x$basket_data[x$basket_data$SPEC==13908,"SPEC"] <- c(4400)
x$catch_data[x$catch_data$SPEC==10244,"SPEC"] <- c(942)
x$catch_data[x$catch_data$SPEC==12676,"SPEC"] <- c(1900)
x$catch_data[x$catch_data$SPEC==12679,"SPEC"] <- c(1901)
x$catch_data[x$catch_data$SPEC==13090,"SPEC"] <- c(1930)
x$catch_data[x$catch_data$SPEC==14230,"SPEC"] <- c(4316)
x$catch_data[x$catch_data$SPEC==16592,"SPEC"] <- c(2990)
x$catch_data[x$catch_data$SPEC==18800,"SPEC"] <- c(7733)
x$catch_data[x$catch_data$SPEC==19220,"SPEC"] <- c(9303)
x$catch_data[x$catch_data$SPEC==13891,"SPEC"] <- c(4400)
x$catch_data[x$catch_data$SPEC==13908,"SPEC"] <- c(4400)
x$specimen_data[x$specimen_data$SPEC==10244,"SPEC"] <- c(942)
x$specimen_data[x$specimen_data$SPEC==12676,"SPEC"] <- c(1900)
x$specimen_data[x$specimen_data$SPEC==12679,"SPEC"] <- c(1901)
x$specimen_data[x$specimen_data$SPEC==13090,"SPEC"] <- c(1930)
x$specimen_data[x$specimen_data$SPEC==14230,"SPEC"] <- c(4316)
x$specimen_data[x$specimen_data$SPEC==16592,"SPEC"] <- c(2990)
x$specimen_data[x$specimen_data$SPEC==18800,"SPEC"] <- c(7733)
x$specimen_data[x$specimen_data$SPEC==19220,"SPEC"] <- c(9303)
x$specimen_data[x$specimen_data$SPEC==13891,"SPEC"] <- c(4400)
x$specimen_data[x$specimen_data$SPEC==13908,"SPEC"] <- c(4400)
#Mar varies from Gulf
x$basket_data[x$basket_data$SPEC==7706,"SPEC"] <- c(8382)
x$basket_data[x$basket_data$SPEC==7712,"SPEC"] <- c(8367)
x$basket_data[x$basket_data$SPEC==7725,"SPEC"] <- c(3215)
x$basket_data[x$basket_data$SPEC==7733,"SPEC"] <- c(1811)
x$basket_data[x$basket_data$SPEC==7737,"SPEC"] <- c(708)
x$catch_data[x$catch_data$SPEC==7706,"SPEC"] <- c(8382)
x$catch_data[x$catch_data$SPEC==7712,"SPEC"] <- c(8367)
x$catch_data[x$catch_data$SPEC==7725,"SPEC"] <- c(3215)
x$catch_data[x$catch_data$SPEC==7733,"SPEC"] <- c(1811)
x$catch_data[x$catch_data$SPEC==7737,"SPEC"] <- c(708)
x$specimen_data[x$specimen_data$SPEC==7706,"SPEC"] <- c(8382)
x$specimen_data[x$specimen_data$SPEC==7712,"SPEC"] <- c(8367)
x$specimen_data[x$specimen_data$SPEC==7725,"SPEC"] <- c(3215)
x$specimen_data[x$specimen_data$SPEC==7733,"SPEC"] <- c(1811)
x$specimen_data[x$specimen_data$SPEC==7737,"SPEC"] <- c(708)
#tiny fish apparently marked as size class 12 instead of 2
x$basket_data[x$basket_data$set_number == 121 & x$basket_data$SPEC == 13 & x$basket_data$size_class ==12,"size_class"]<-2
x$specimen_data[x$specimen_data$set_number == 121 & x$specimen_data$SPEC == 13 & x$specimen_data$size_class ==12,"size_class"]<-2
}
if(mission == "CAB2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemapping species in the catch_, basket and speciment_ data\n")
#Mar varies from Gulf
x$basket_data[x$basket_data$SPEC==7706,"SPEC"] <- c(8382)
x$basket_data[x$basket_data$SPEC==7712,"SPEC"] <- c(8367)
x$basket_data[x$basket_data$SPEC==7725,"SPEC"] <- c(3215)
x$basket_data[x$basket_data$SPEC==7733,"SPEC"] <- c(1811)
x$catch_data[x$catch_data$SPEC==7706,"SPEC"] <- c(8382)
x$catch_data[x$catch_data$SPEC==7712,"SPEC"] <- c(8367)
x$catch_data[x$catch_data$SPEC==7725,"SPEC"] <- c(3215)
x$catch_data[x$catch_data$SPEC==7733,"SPEC"] <- c(1811)
x$specimen_data[x$specimen_data$SPEC==7706,"SPEC"] <- c(8382)
x$specimen_data[x$specimen_data$SPEC==7712,"SPEC"] <- c(8367)
x$specimen_data[x$specimen_data$SPEC==7725,"SPEC"] <- c(3215)
x$specimen_data[x$specimen_data$SPEC==7733,"SPEC"] <- c(1811)
#andes used some codes not held by Gulf, so they get changed
x$basket_data[x$basket_data$SPEC==12161,"SPEC"] <- c(8216)
x$basket_data[x$basket_data$SPEC==14878,"SPEC"] <- c(4508)
x$basket_data[x$basket_data$SPEC==16593,"SPEC"] <- c(2062)
x$basket_data[x$basket_data$SPEC==18114,"SPEC"] <- c(2217)
x$basket_data[x$basket_data$SPEC==18411,"SPEC"] <- c(6126)
x$basket_data[x$basket_data$SPEC==18495,"SPEC"] <- c(6105)
x$catch_data[x$catch_data$SPEC==12161,"SPEC"] <- c(8216)
x$catch_data[x$catch_data$SPEC==14878,"SPEC"] <- c(4508)
x$catch_data[x$catch_data$SPEC==16593,"SPEC"] <- c(2062)
x$catch_data[x$catch_data$SPEC==18114,"SPEC"] <- c(2217)
x$catch_data[x$catch_data$SPEC==18411,"SPEC"] <- c(6126)
x$catch_data[x$catch_data$SPEC==18495,"SPEC"] <- c(6105)
x$specimen_data[x$specimen_data$SPEC==12161,"SPEC"] <- c(8216)
x$specimen_data[x$specimen_data$SPEC==14878,"SPEC"] <- c(4508)
x$specimen_data[x$specimen_data$SPEC==16593,"SPEC"] <- c(2062)
x$specimen_data[x$specimen_data$SPEC==18114,"SPEC"] <- c(2217)
x$specimen_data[x$specimen_data$SPEC==18411,"SPEC"] <- c(6126)
x$specimen_data[x$specimen_data$SPEC==18495,"SPEC"] <- c(6105)
x$basket_data[x$basket_data$SPEC==11352,"SPEC"] <- c(8200) #Cnidarians
x$catch_data[x$catch_data$SPEC==11352,"SPEC"] <- c(8200) #Cnidarians
x$specimen_data[x$specimen_data$SPEC==11352,"SPEC"] <- c(8200) #Cnidarians
x$basket_data[x$basket_data$SPEC==13860,"SPEC"] <- c(4400) #Nudibranchs
x$catch_data[x$catch_data$SPEC==13860,"SPEC"] <- c(4400) #Nudibranchs
x$specimen_data[x$specimen_data$SPEC==13860,"SPEC"] <- c(4400) #Nudibranchs
x$basket_data[x$basket_data$SPEC==15053,"SPEC"] <- c(3100) #Polychaete
x$catch_data[x$catch_data$SPEC==15053,"SPEC"] <- c(3100) #Polychaete
x$specimen_data[x$specimen_data$SPEC==15053,"SPEC"] <- c(3100) #Polychaete
x$basket_data[x$basket_data$SPEC==19218,"SPEC"] <- c(9303) #Brown Seaweed
x$catch_data[x$catch_data$SPEC==19218,"SPEC"] <- c(9303) #Brown Seaweed
x$specimen_data[x$specimen_data$SPEC==19218,"SPEC"] <- c(9303) #Brown Seaweed
#these weren't necessarily global, but for specific sets
x$basket_data[x$basket_data$set_number == 8 & x$basket_data$SPEC == 6600,"SPEC"] <- 6615 #(stereoderma unisemita )
x$catch_data[x$catch_data$set_number == 8 & x$catch_data$SPEC == 6600,"SPEC"] <- 6615
x$specimen_data[x$specimen_data$set_number == 8 & x$specimen_data$SPEC == 6600,"SPEC"] <- 6615
x$basket_data[x$basket_data$set_number == 23 & x$basket_data$SPEC == 9300,"SPEC"] <- 1901 #("lemonweed")
x$catch_data[x$catch_data$set_number == 23 & x$catch_data$SPEC == 9300,"SPEC"] <- 1901
x$specimen_data[x$specimen_data$set_number == 23 & x$specimen_data$SPEC == 9300,"SPEC"] <- 1901
x$basket_data[x$basket_data$set_number == 30 & x$basket_data$SPEC == 1901,"SPEC"] <- 1901 #("lemonweed")
x$catch_data[x$catch_data$set_number == 30 & x$catch_data$SPEC == 1901,"SPEC"] <- 1901
x$specimen_data[x$specimen_data$set_number == 30 & x$specimen_data$SPEC == 1901,"SPEC"] <- 1901
x$basket_data[x$basket_data$set_number == 32 & x$basket_data$SPEC == 1901,"SPEC"] <- 1901 #("lemonweed")
x$catch_data[x$catch_data$set_number == 32 & x$catch_data$SPEC == 1901,"SPEC"] <- 1901
x$specimen_data[x$specimen_data$set_number == 32 & x$specimen_data$SPEC == 1901,"SPEC"] <- 1901
x$basket_data[x$basket_data$set_number == 44 & x$basket_data$SPEC == 1013,"SPEC"] <- 1270 #(Nezumia Aqualis)
x$catch_data[x$catch_data$set_number == 44 & x$catch_data$SPEC == 1013,"SPEC"] <- 1270
x$specimen_data[x$specimen_data$set_number == 44 & x$specimen_data$SPEC == 1013,"SPEC"] <- 1270
x$basket_data[x$basket_data$set_number == 46 & x$basket_data$SPEC == 410,"SPEC"] <- 410 #(?) (marlin spike grenadier)
x$catch_data[x$catch_data$set_number == 46 & x$catch_data$SPEC == 410,"SPEC"] <- 410
x$specimen_data[x$specimen_data$set_number == 46 & x$specimen_data$SPEC == 410,"SPEC"] <- 410
x$basket_data[x$basket_data$set_number == 47 & x$basket_data$SPEC == 6100,"SPEC"] <- 6139 #(Plutonaster agassizi)
x$catch_data[x$catch_data$set_number == 47 & x$catch_data$SPEC == 6100,"SPEC"] <- 6139
x$specimen_data[x$specimen_data$set_number == 47 & x$specimen_data$SPEC == 6100,"SPEC"] <- 6139
x$basket_data[x$basket_data$set_number == 47 & x$basket_data$SPEC == 8354,"SPEC"] <- 1283 #("Sergia robustus")
x$catch_data[x$catch_data$set_number == 47 & x$catch_data$SPEC == 8354,"SPEC"] <- 1283
x$specimen_data[x$specimen_data$set_number == 47 & x$specimen_data$SPEC == 8354,"SPEC"] <- 1283
x$basket_data[x$basket_data$set_number == 64 & x$basket_data$SPEC == 983,"SPEC"] <- 1071 #("chain cat shark")
x$catch_data[x$catch_data$set_number == 64 & x$catch_data$SPEC == 983,"SPEC"] <- 1071
x$specimen_data[x$specimen_data$set_number == 64 & x$specimen_data$SPEC == 983,"SPEC"] <- 1071
x$basket_data[x$basket_data$set_number == 73 & x$basket_data$SPEC == 8208,"SPEC"] <- 8383 #(Epizoanthus paguriphilus)
x$catch_data[x$catch_data$set_number == 73 & x$catch_data$SPEC == 8208,"SPEC"] <- 8383
x$specimen_data[x$specimen_data$set_number == 73 & x$specimen_data$SPEC == 8208,"SPEC"] <- 8383
x$basket_data[x$basket_data$set_number == 97 & x$basket_data$SPEC == 49,"SPEC"] <- 386 #( Etropus microstomus)
x$catch_data[x$catch_data$set_number == 97 & x$catch_data$SPEC == 49,"SPEC"] <- 386
x$specimen_data[x$specimen_data$set_number == 97 & x$specimen_data$SPEC == 49,"SPEC"] <- 386
x$basket_data[x$basket_data$set_number == 96 & x$basket_data$SPEC == 9992,"SPEC"] <- 785 #(silver-rag )
x$catch_data[x$catch_data$set_number == 96 & x$catch_data$SPEC == 9992,"SPEC"] <- 785
x$specimen_data[x$specimen_data$set_number == 96 & x$specimen_data$SPEC == 9992,"SPEC"] <- 785
x$basket_data[x$basket_data$set_number == 96 & x$basket_data$SPEC == 9991,"SPEC"] <- 530 #(red eyed gaper)
x$catch_data[x$catch_data$set_number == 96 & x$catch_data$SPEC == 9991,c("SPEC", "notes")] <- as.data.frame(t(c(530,"Red eye gaper (Chaunax stigmaeus)")))
x$specimen_data[x$specimen_data$set_number == 96 & x$specimen_data$SPEC == 9991,"SPEC"] <- 530
x$basket_data[x$basket_data$set_number == 105 & x$basket_data$SPEC == 9991,"SPEC"] <- 785 #(silver-rag )
x$catch_data[x$catch_data$set_number == 105 & x$catch_data$SPEC == 9991,"SPEC"] <- 785
x$specimen_data[x$specimen_data$set_number == 105 & x$specimen_data$SPEC == 9991,"SPEC"] <- 785
x$basket_data[x$basket_data$set_number == 64 & x$basket_data$SPEC == 9991,"SPEC"] <- 498 #(yellow fin bass )
x$catch_data[x$catch_data$set_number == 64 & x$catch_data$SPEC == 9991,"SPEC"] <- 498
x$specimen_data[x$specimen_data$set_number == 64 & x$specimen_data$SPEC == 9991,"SPEC"] <- 498
x$basket_data[x$basket_data$set_number == 85 & x$basket_data$SPEC == 9991,"SPEC"] <- 498 #(yellow fin bass )
x$catch_data[x$catch_data$set_number == 85 & x$catch_data$SPEC == 9991,"SPEC"] <- 498
x$specimen_data[x$specimen_data$set_number == 85 & x$specimen_data$SPEC == 9991,"SPEC"] <- 498
#note indicated that set 28, spec 9990 was actually all spec 2214 and was not sampled
#increase specimen_count with knowledge that 0.103kg was 67 shrimp, so .4535 was ~295 shrimp
# 67+295=362
x$catch_data[x$catch_data$set_number == 28 & x$catch_data$SPEC == 2214,c("specimen_count")] <- 362
x$basket_data[x$basket_data$set_number == 28 & x$basket_data$SPEC %in% c(2214),"basket_wt_kg"] <- 0.5565
#remove the catch and set recs for 9990 for this set, since they turned out to all be 2214 and are captured above)
x$catch_data <- x$catch_data[!(x$catch_data$set_number == 28 & x$catch_data$SPEC == 9990),]
x$basket_data <- x$basket_data[!(x$basket_data$set_number == 28 & x$basket_data$SPEC == 9990 & x$basket_data$basket_wt_kg == 0.1030),]
x$basket_data[x$basket_data$SPEC==400 & x$basket_data$set_number==40,"size_class"]<-1
x$specimen_data[x$specimen_data$SPEC==400 & x$specimen_data$set_number==40,"size_class"]<-1
x$basket_data[x$basket_data$SPEC==11 & x$basket_data$set_number==56,"size_class"]<-1
x$specimen_data[x$specimen_data$SPEC==11 & x$specimen_data$set_number==56,"size_class"]<-1
x$basket_data[x$basket_data$SPEC==11 & x$basket_data$set_number==57,"size_class"]<-1
x$specimen_data[x$specimen_data$SPEC==11 & x$specimen_data$set_number==57,"size_class"]<-1
#two brown algaes were entered with different andes codes:
#combine specimen count, delete one catch record, and reassign child basket to the retained catch record
x$catch_data[x$catch_data$id==1207,"specimen_count" ]<- sum(x$catch_data[x$catch_data$id==1207,"specimen_count" ], x$catch_data[x$catch_data$id==1223,"specimen_count" ])
x$catch_data<- x$catch_data[!(x$catch_data$id==1223),]
x$basket_data[x$basket_data$catch_id==1223,"catch_id"]<-1207
#two species of nudibranchs were entered with different andes codes but we only capture them as
#4400 - deleting one catch record, and reassigning its child basket to the retained catch record
x$catch_data[x$catch_data$id==2254,"specimen_count" ]<- sum(x$catch_data[x$catch_data$id==2254,"specimen_count" ], x$catch_data[x$catch_data$id==2255,"specimen_count" ])
x$catch_data<- x$catch_data[!(x$catch_data$id==2255),]
x$basket_data[x$basket_data$catch_id==2255,"catch_id"]<- 2254
x$set_data[x$set_data$set_number=="59",c("start_date")]<-"2022-07-31 07:07:00+00:00"
x$set_data[x$set_data$set_number=="59",c("start_latitude_DD")]<- 41
x$set_data[x$set_data$set_number=="59",c("start_latitude_MMmm")]<- 36.90
x$set_data[x$set_data$set_number=="59",c("start_longitude_DD")]<- -66
x$set_data[x$set_data$set_number=="59",c("start_longitude_MMmm")] <- 36.59
x$set_data[x$set_data$set_number=="84",c("start_date")]<-"2022-08-03 13:41:00.000000+00:00"
x$set_data[x$set_data$set_number=="84",c("start_latitude_DD")]<- 42
x$set_data[x$set_data$set_number=="84",c("start_latitude_MMmm")]<- 27.9
x$set_data[x$set_data$set_number=="84",c("start_longitude_DD")]<- -64
x$set_data[x$set_data$set_number=="84",c("start_longitude_MMmm")] <- 52.4
}
if(mission == "VEN2023001"){
#changes requested following Jamie Emberley's initial QC
x$basket_data[x$basket_data$SPEC == 314,"SPEC"] <- 303 #(Spatulate sculpin entries changed to Grubby Sculpins)
x$catch_data[x$catch_data$SPEC == 314,"SPEC"] <- 303
x$specimen_data[x$specimen_data$SPEC == 314,"SPEC"] <- 303
x$specimensRaw[x$specimensRaw$SPEC == 314,"SPEC"] <- 303
}
if (!is.na(theMsg)) message("Universal Tweaks: \n", theMsg)
return(x)
}
#' @title tweakBaskets
#' @description This function will perform tweaks to data coming from andes before
#' it is imported to Oracle.
#' @param x default is \code{NULL}. This is the ESE_BASKET data frame
#' @return a data frame for loading into
#' @family general_use
#' @author Pablo Vergara, \email{Pablo.Vergara@@dfo-mpo.gc.ca}
#' @export
tweakBaskets <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
if(x$MISSION[1] == "CAR2023011"){
#as requested by Jamie in "CAR2023011 Post Survey Processing.docx"
x[x$SETNO==56 & x$SPEC == 2555, "SAMPLED"] <- F
x[x$SETNO==54 & x$SPEC == 2214,"SAMPLED"] <- F
}
if(x$MISSION[1] == "TEL2023010"){
x[x$SETNO==32 & x$SPEC == 9331 & x$SIZE_CLASS== 2,"SIZE_CLASS"] <- 1
#remove this
# basket_wt_kg catch_id creation_date id last_modified_date mission_number sampled set_number size_class size_class_display species_aphia_id species_code species_en species_fr species_scientific species_uuid
# 0 824 2023-06-29 05:32:51 UTC 855 2023-06-29 05:32:51 UTC TEL-2023-010 No 1 1 1 158356 2214 Bristled longbeak shrimp Crevette - Dichelopandalus leptocerus Dichelopandalus leptocerus 0a120f9d-714f-48bc-925f-b39b246f8f17
toRemove <- x[x$SETNO == 1 & x$SPEC == 2214 & x$BASKET_WEIGHT == 0,]
x <- df.diff(x, toRemove)
}
if(x$MISSION[1] == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tCorrecting two baskets which were incorrectly flagged as being sampled\n")
x[x$SETNO == 13 & x$SPEC == 2100 & x$id == 630,"SAMPLED"]<-F
x[x$SETNO == 61 & x$SPEC == 8100 & x$id == 1918,"SAMPLED"]<-F
}
if(x$MISSION[1] == "TEL2022010"){
#nudibranchs had been broken into sp we don't track
x<- x[!(x$SETNO == 151 & x$SPEC == 4400),]
x<-rbind.data.frame(x,list("TEL2022010", 151, 4400, 1, 0.003, FALSE, NA, NA))
}
if(x$MISSION[1] == "CAB2022010"){
x[x$SETNO == 18 & x$SPEC == 150,"SAMPLED"]<-F
#remove a basket weight that was estimated from the unweighed baskets
x <- x[!(x$SETNO == 55 & x$SPEC == 2550 & x$basket_id == 2475),]
}
if(x$MISSION[1] == "CAR2023002"){
x[which(x$SETNO == 164 & x$SPEC == 4500),"SAMPLED"] <- FALSE
# SETNO 7, SPEC 2541
x[which(x$SETNO == 7 & x$SPEC == 2541),"SAMPLED"] <- FALSE
x[x$basket_id == 4484,"SIZE_CLASS"]<-1
x[x$basket_id == 4482,"SIZE_CLASS"]<-1
x[x$basket_id == 4480,"SIZE_CLASS"]<-2
x[x$basket_id == 1747,"SAMPLED"]<-TRUE
}
if(x$MISSION[1] == "VEN2023001"){
}
if (!is.na(theMsg)) message("Tweaking BASKET: \n", theMsg)
return(x)
}
#' @title tweakCatches
#' @description This function will perform tweaks to data coming from andes before
#' it is imported to Oracle.
#' @param x default is \code{NULL}. This is the ESE_CATCHES data frame
#' @return a data frame for loading into ESE_CATCHES
#' @family general_use
#' @author Pablo Vergara, \email{Pablo.Vergara@@dfo-mpo.gc.ca}
#' @export
tweakCatches <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
if(x$MISSION[1] == "CAR2023011"){
x[x$SETNO==5 & x$SPEC==8100,c( "UNWEIGHED_BASKETS", "NUMBER_CAUGHT")] <- as.data.frame(t(c(NA,10)))
}
if(x$MISSION[1] == "TEL2023010"){
#add this:
#MISSION SETNO SPEC catch_id UNWEIGHED_BASKETS NUMBER_CAUGHT is_parent parent_catch_id SIZE_CLASS
#TEL2023010 217 6211 6570 NA 235 FALSE 6568 1
# toAdd <- c(MISSION = "TEL2023010", SETNO=217,SPEC = 6211, NOTE = "", UNWEIGHED_BASKETS = NA, NUMBER_CAUGHT = 235, catch_id=NA, is_parent=F, parent_catch_id = 6568)
# .1905
# x <- rbind.data.frame(x, toAdd)
x[x$SETNO== 195 & x$SPEC==1510,"UNWEIGHED_BASKETS"] <- NA
}
if(x$MISSION[1] == "TEL2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tApplying fixes on the catch records\n")
x[x$SETNO==76 & x$SPEC == 2213,c("UNWEIGHED_BASKETS", "NUMBER_CAUGHT")] <- as.data.frame(t(c(NA,62)))
x[x$SETNO==133 & x$SPEC == 730,"NOTE"] <- "Caught dead. Hagfish inside. Weight was estimated. Fin to Fin measurement: 167cm. Weight estimated, not weighed. Measured on deck."
#nudibranchs had been broken into sp we don't track
x<- x[!(x$SETNO == 151 & x$SPEC == 4400),]
x<-rbind.data.frame(x,list("TEL2022010", 151, 4400, NA, NA, 6, NA, FALSE, NA))
}
if(x$MISSION[1] == "CAB2022010"){
x[x$SETNO==34 & x$SPEC == 243,"NOTE"] <- "basket weight is estimate only"
x[x$SETNO==50 & x$SPEC == 220,"NOTE"] <- "the large basket weight (858kg) was calculated at sea from a count of unweighed baskets"
x[x$SETNO==50 & x$SPEC == 204,"NOTE"] <- "the large basket weight (507kg) was calculated at sea from a count of unweighed baskets"
}
if (!is.na(theMsg)) message("Tweaking CATCH: ", theMsg)
return(x)
}
#' @title tweakSpecimensRaw
#' @description This function will perform tweaks to data coming from andes before
#' it is imported to Oracle. specimen_data gets converted into both ESE_SPECIMENS and
#' ESE_LV1_OBSERVATIONS, so many tweaks should be performed here to ensure that changes are
#' reflected in both output tables. Also, changing here will ensure sequential LV1_OBSERVATION_ID
#' values
#' @param x default is \code{NULL}. This is the raw "specimen_data" data frame
#' @return a data frame for loading into ESE_BASKETS
#' @family general_use
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
tweakSpecimensRaw <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
x$species_aphia_id <- NULL
# theMsg <- paste0(theMsg[!is.na(theMsg)], "\tBerried female crabs and lobsters recoded to 3\n")
x[which(x$sex==2 & (x$crab.female.eggs == 1 | x$lobster.female.eggs==1)), "sex"] <-3
if(nrow(x[which(x$sex==1 & (x$crab.female.eggs == 1 | x$lobster.female.eggs==1)), ]))warning("Berried Males detected")
if(x$MISSION[1] == "TEL2023010"){
x[x$id==4690,"weight"]<-0.5
x[x$id==4696,"weight"]<-0.5
x[x$id==4699,"weight"]<-0.5
x[x$id==22537,"weight"]<-13
x[x$id==24812,"length"]<-230
# • Setno 3, spec 610, specimen_id 4690 – update weight to 0.5
# • Setno 3, spec 610, specimen_id 4696 – update weight to 0.5
# • Setno 3, spec 610, specimen_id 4699 – update weight to 0.5
# • Setno 40, spec 14, specimen_id 22537 – update weight to 13
#• Setno 44, spec 60, specimen_id 24812 – update length to 230
x[x$id==75096,"gonad.weight"] <- 2
x[x$id==75846,"gonad.weight"] <- 2670
x[x$id==75846,"collect.gonads"] <- 1
# • Setno 214, spec 30, specimen_id 75096 – update gonad weight to 2
# • Setno 219, spec 30, specimen_id 75846 – update gonad weight to 2670, update collect gonads to 1 and data desc = collected
x[x$id==25131,"sex"]<-0
x[x$id==72792,"sex"]<-0
# • Setno 45, spec 2550, specimen_id 25131 – update sex to 0 (undetermined)
# • Setno 209, spec 41, specimen_id 72792 – update sex to 0 (undetermined)
}
if(x$MISSION[1] == "CAR2023002"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemoving Fish Numbers from Mackerel records\n")
# • Set 171, spec 11, specimen id 71795 – length entered as 0.30. Update length to 30
x[x$id==71795,"length"]<-30
# • Set 17 – spec 11, specimen id 5022, change weight to 217
x[x$id==5022,"weight"]<-217
# • Set 11 – spec 4511, specimen id 3709, remove the weight observation
x[x$id==3709,"weight"]<-NA
# • Set 104 – spec 303, specimen id 37264, change weight to 1.5
x[x$id==37264,"weight"]<-1.5
# • Set 65 – spec 303, specimen id 19640, Change weight to 0.5
x[x$id==19640,"weight"]<-0.5
# • Set 153 – spec 14, specimen id 63547, Change weight to 0.5
x[x$id==63547,"weight"]<-0.5
# • Set 69 – spec 150, specimen id 22031, change weight to 4
x[x$id==22031,"weight"]<-4
# • Set 189 – spec 340, specimen id 30865, change weight to 1.5
x[x$id==30865,"weight"]<-1.5
# • Set 167, spec 410, specimen id 70480, Change weight to 0.5
x[x$id==70480,"weight"]<-0.5
# • Set 166, spec 410, specimen id 70267, Change weight to 0.5
x[x$id==70267,"weight"]<-0.5
# • Set 166, spec 410, specimen id 70272, Change weight to 0.5
x[x$id==70272,"weight"]<-0.5
# • Set 166, spec 410, specimen id 70277, Change weight to 0.5
x[x$id==70277,"weight"]<-0.5
# • Set 166, spec 410, specimen id 70283, Change weight to 0.5
x[x$id==70283,"weight"]<-0.5
# • Set 167, spec 604, specimen id 70566, Change weight to 0.5
x[x$id==70566,"weight"]<-0.5
# • Set 7, spec 44, specimen id 1231, change weight from .5 to 0.5
x[x$id==1231,"weight"]<-0.5
# • Set 24, spec 143, specimen id 6483, change weight from .5 to 0.5
x[x$id==6483,"weight"]<-0.5
# • Set 47, spec 60, specimen id 11696, change length from 376 to 276
x[x$id==11696,"length"]<-276
#SET 29. SPEC 4321, SPECIMEN ID 7713
x <- x[-which(x$id == 7713),]
#SETNO 7, SPEC 2541, SPECIMEN ID 1094,
x <- x[-which(x$id == 1094),]
}
if(x$MISSION[1] == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemoving Fish Numbers from Mackerel records\n")
x[x$species_code == 70,"fish_number"] <- NA
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemoving comments created solely to generate labels\n")
commentsDrop <- c(".", "1", "edrftgujik", "fdgj", "fgjh", "rdfyg", "srdtfygvuh")
x[x$comment %in% commentsDrop,"comment"]<- NA
x[x$comments %in% commentsDrop,"comments"]<- NA
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 44/Spec 1191/Specimen id 14496: Removing incorrect length\n")
x[x$id == 14496,"length"] <- NA
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 26/Spec 14/Specimen id 9332: Weight corrected to grams\n")
x[x$id == 9332,"weight"] <- x[x$id == 9332,"weight"]*1000
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 49/Spec 11/Specimen id 16236: No useful info entered - deleted\n")
x <- x[-which(x$id == 16236),]
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSpec 60: Several sets list weight as less than <0.5g - the smallest precision available. Bump all of these up to 0.5g\n")
x[which(x$species_code == 60 & x$weight <0.5),"weight"] <- 0.5
}
if(x$MISSION[1] == "TEL2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 133 - removed a duplicate sunfish record")
x <- x[!x$id %in% 49411,]
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRemoving some bad records")
x <- x[!x$id %in% 49475,]
x <- x[!x$id %in% 20427,]
x <- x[!x$id %in% 14656,]
}
if(x$MISSION[1] == "CAB2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 46 - The first 30 'silver hake' records are actually dogfish (fixed)")
x<- x[with(x,order(id)),]
x[x$set_number == 46 & x$SPEC == 14,][1:30,"SPEC"]<- 220
#remove specimens with length = 0
x <- x[!x$id==34724,]
x <- x[!x$id==34744,]
#certain 0cm lengths should be 10cm
x[x$id==35107,"length"]<-10
x[x$id==31275,"length"]<-10
x[x$id==47775,"length"]<-10
x[x$id==32839,"length"]<-10
x[x$id==27596,"length"]<-10
#likely typo - length should be 250 (not 25)
x[x$id==17577,"length"]<-250
#lobsters measured as less than 3mm are likely typos
x<-x[!(x$SPEC == 2550 & x$length <3),]
#some entries for the following spp had tiny lengths - almost certainly typos
x<-x[!(x$SPEC %in% c(11,13,14,23, 1191) & x$length <3),]
}
if(x$MISSION[1] == "VEN2023001"){
#changes requested following Jamie Emberley's initial QC
x <- x[!x$id==4098,]
x <- x[!x$id==14617,]
x <- x[!x$id==17226,]
x[x$id==3315,"weight"]<- 2 #0.002 to 2
x[x$id==9641,"weight"]<- 5 #0.0005 to 5
x[x$id==14872,"sex"] <- 0 #too small to have been sexed
x[x$id==20014,"weight"] <- 264 #likely typo in wgt
}
if (!is.na(theMsg)) message("Tweaking specimen_data: \n", theMsg)
return(x)
}
#' @title tweakSets
#' @description This function will perform tweaks to data coming from andes before
#' it is imported to Oracle.
#' @param x default is \code{NULL}. This is the ESE_SETS data frame.
#' @return a data frame for loading into ESE_SETS
#' @family general_use
#' @author Pablo Vergara, \email{Pablo.Vergara@@dfo-mpo.gc.ca}
#' @export
tweakSets <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
if(x$MISSION[1] == "CAR2023011"){
x[x$SETNO %in% c(1,216), "EXPERIMENT_TYPE_CODE"] <- 9
x[x$SETNO %in% c(1,216), "STATION"] <- NA
x[x$SETNO %in% c(1,216), "NOTE"] <- trimws(paste(x[x$SETNO %in% c(1,216), "NOTE"], "HFX HYD"))
x[x$EXPERIMENT_TYPE_CODE %in% c(1), "EXPERIMENT_TYPE_CODE"]<-5
}
if(x$MISSION[1] == "TEL2023010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tUsed manually recorded distance for sets 222 to 234\n")
x[x$SETNO %in% c(222:234),"DIST"]<- x[x$SETNO%in% c(222:234),"distance_towed"]
# x[x$SETNO%in% c(232),"START_TIME"] <- 2959
}
if(x$MISSION[1] == "CAR2023002"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRecoded GEAR from 23 to 15\n")
#NEST trawl is not 23, but 15 - change here; expect this will be corrected in the future
# Jamie created aux = 6 for the nest
x[x$GEAR==23,"GEAR"] <- 15
x[x$AUX==2,"AUX"] <- 6
#set 1
# • Set 1 – update Experiment type to 9
# • Set 1 – delete station 100, leave this field blank
# • Set 1 – delete Warpout, leave blank
# • Set 1 – add a Note for the set – HFX HYD
x[x$SETNO==1,"EXPERIMENT_TYPE_CODE"]<- 9
x[x$SETNO==1,"STATION"]<- NA
x[x$SETNO==1,"WARPOUT"]<- NA
x[x$SETNO==1,"NOTE"]<- "HFX HYD"
# set 129
# • Set 129 - update Experiment type to 9
# • Set 129 - delete station 100, leave this field blank
# • Set 129 - add a Note for the set – HFX HYD
x[x$SETNO==129,"EXPERIMENT_TYPE_CODE"]<- 9
x[x$SETNO==129,"STATION"]<- NA
x[x$SETNO==129,"NOTE"]<- "HFX HYD"
}
if(x$MISSION[1] == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tRecoded GEAR from 23 to 15\n")
#NEST trawl is not 23, but 15 - change here; expect this will be corrected in the future
x[x$GEAR==23,"GEAR"] <- 15
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 16: Corrected DIST\n")
x[x$SETNO==16,"DIST"] <- 0.978
# Mission CAR2022102, Set 16 - DIST showing as -10.98, should be 0.98
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 16: Corrected START_DEPTH\n")
x[x$SETNO==16,"START_DEPTH"] <- 92
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSet 4: Corrected missing ELONG\n")
x[x$SETNO==4,"ELONG"] <- -6620.64599
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSets 9 & 41: Corrected ETIME\n")
x[x$SETNO==9,"END_TIME"] <- "1739"
x[x$SETNO==41,"END_TIME"] <- "0054"
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tManually added area for each set\n")
x[x$SETNO == "1", "AREA"] <- "523"
x[x$SETNO == "2", "AREA"] <- "524"
x[x$SETNO == "3", "AREA"] <- "524"
x[x$SETNO == "4", "AREA"] <- "524"
x[x$SETNO == "5", "AREA"] <- "524"
x[x$SETNO == "6", "AREA"] <- "524"
x[x$SETNO == "7", "AREA"] <- "524"
x[x$SETNO == "8", "AREA"] <- "524"
x[x$SETNO == "9", "AREA"] <- "524"
x[x$SETNO == "10", "AREA"] <- "524"
x[x$SETNO == "11", "AREA"] <- "523"
x[x$SETNO == "12", "AREA"] <- "523"
x[x$SETNO == "13", "AREA"] <- "523"
x[x$SETNO == "14", "AREA"] <- "523"
x[x$SETNO == "15", "AREA"] <- "523"
x[x$SETNO == "16", "AREA"] <- "523"
x[x$SETNO == "17", "AREA"] <- "523"
x[x$SETNO == "18", "AREA"] <- "523"
x[x$SETNO == "19", "AREA"] <- "523"
x[x$SETNO == "20", "AREA"] <- "523"
x[x$SETNO == "21", "AREA"] <- "523"
x[x$SETNO == "22", "AREA"] <- "523"
x[x$SETNO == "23", "AREA"] <- "523"
x[x$SETNO == "24", "AREA"] <- "523"
x[x$SETNO == "25", "AREA"] <- "523"
x[x$SETNO == "26", "AREA"] <- "523"
x[x$SETNO == "27", "AREA"] <- "523"
x[x$SETNO == "28", "AREA"] <- "523"
x[x$SETNO == "29", "AREA"] <- "523"
x[x$SETNO == "30", "AREA"] <- "523"
x[x$SETNO == "31", "AREA"] <- "523"
x[x$SETNO == "32", "AREA"] <- "524"
x[x$SETNO == "33", "AREA"] <- "524"
x[x$SETNO == "34", "AREA"] <- "524"
x[x$SETNO == "35", "AREA"] <- "524"
x[x$SETNO == "36", "AREA"] <- "524"
x[x$SETNO == "37", "AREA"] <- "524"
x[x$SETNO == "38", "AREA"] <- "524"
x[x$SETNO == "39", "AREA"] <- "524"
x[x$SETNO == "40", "AREA"] <- "524"
x[x$SETNO == "41", "AREA"] <- "524"
x[x$SETNO == "42", "AREA"] <- "524"
x[x$SETNO == "43", "AREA"] <- "524"
x[x$SETNO == "44", "AREA"] <- "523"
x[x$SETNO == "45", "AREA"] <- "524"
x[x$SETNO == "46", "AREA"] <- "524"
x[x$SETNO == "47", "AREA"] <- "524"
x[x$SETNO == "48", "AREA"] <- "524"
x[x$SETNO == "49", "AREA"] <- "524"
x[x$SETNO == "50", "AREA"] <- "523"
x[x$SETNO == "51", "AREA"] <- "523"
x[x$SETNO == "52", "AREA"] <- "523"
x[x$SETNO == "53", "AREA"] <- "523"
x[x$SETNO == "54", "AREA"] <- "523"
x[x$SETNO == "55", "AREA"] <- "523"
x[x$SETNO == "56", "AREA"] <- "523"
x[x$SETNO == "57", "AREA"] <- "524"
x[x$SETNO == "58", "AREA"] <- "524"
x[x$SETNO == "59", "AREA"] <- "524"
x[x$SETNO == "60", "AREA"] <- "524"
x[x$SETNO == "61", "AREA"] <- "524"
x[x$SETNO == "62", "AREA"] <- "524"
x[x$SETNO == "63", "AREA"] <- "524"
x[x$SETNO == "64", "AREA"] <- "524"
x[x$SETNO == "65", "AREA"] <- "524"
x[x$SETNO == "66", "AREA"] <- "524"
x[x$SETNO == "67", "AREA"] <- "524"
x[x$SETNO == "68", "AREA"] <- "523"
x[x$SETNO == "69", "AREA"] <- "523"
x[x$SETNO == "70", "AREA"] <- "523"
x[x$SETNO == "71", "AREA"] <- "523"
x[x$SETNO == "72", "AREA"] <- "467"
}
if(x$MISSION[1] == "TEL2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tModified exp type manually for several sets\n")
x[x$SETNO == "1", "EXPERIMENT_TYPE_CODE"] <- "9"
x[x$SETNO == "44", "EXPERIMENT_TYPE_CODE"] <- "9"
x[x$SETNO == "170", "EXPERIMENT_TYPE_CODE"] <- "9"
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tModified dist and speed manually for a set\n")
x[x$SETNO == "99", c("DIST", "SPEED")] <- as.data.frame(t(c(1.61,3.22)))
}
if (x$MISSION[1] == "CAB2022010"){
x[x$SETNO == "3", "DIST"] <- 0.95
#NEST trawl is not 23, but 15 - change here; expect this will be corrected in the future
x[x$GEAR==23,"GEAR"] <- 15
x[x$EXPERIMENT_TYPE_CODE==1, "EXPERIMENT_TYPE_CODE"]<- 5
}
if (x$MISSION[1] == "VEN2023001"){
x[x$SETNO == 32, "end_date"] <- "2023-02-11 23:13:04+00:00"
x[x$SETNO == 32, "END_TIME"] <- 1913
}
if (!is.na(theMsg)) message("Tweaking SETS: \n", theMsg)
return(x)
}
#' @title tweakBasketsPostProcessing
#' @description This function can do final changes to the basket data once all of the various basket/
#' catch handling and re-allocation of mixed catches is complete. This processing can include using
#' measured weights to change basket weights, so both basket and lv1 objects are necessary as
#' parameters.
#' @param basket default is \code{NULL}.
#' @param lv1 default is \code{NULL}.
#' @return an updated version of ESE_BASKETS
#' @family general_use
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
tweakBasketsPostProcessing <- function(basket=NULL, lv1 = NULL){
if(length(unique(basket$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
message("Tweaking final BASKET weights: \n")
badBasksSampled <- basket[which(basket$BASKET_WEIGHT<0.0005 & basket$SAMPLED),"basket_id"]
badBasksUnsampled <- basket[which(basket$BASKET_WEIGHT<0.0005 & !basket$SAMPLED),"basket_id"]
if (length(badBasksUnsampled)>0 | length(badBasksSampled)>0) message("\tMinimum measurable basket weight is 0.0005 kg\n")
if (length(badBasksUnsampled)>0){
message("\tUnsampled baskets reporting a weight lower than the minimum were bumped up to 0.0005 kg\n")
basket[which(basket$BASKET_WEIGHT<0.0005 & !basket$SAMPLED),"BASKET_WEIGHT"] <- 0.0005
}
if (length(badBasksSampled)>0){
message("\tOne or more sampled baskets reporting a weight lower than the minimum were bumped up using recorded speciment weights\n\n")
for (i in 1:length(badBasksSampled)){
thisBasketSampled <- basket[basket$basket_id %in% badBasksSampled[i],]
thisBasketSampledSpecimensWeight <- as.numeric(lv1[lv1$basket_id %in% badBasksSampled[i] & lv1$LV1_OBSERVATION == "Weight","DATA_VALUE"])
# message("\t\tHandling")
if (length(thisBasketSampledSpecimensWeight)>0){
#wts in lv1 are in grams, but baskets are kg, convert below
basket[basket$basket_id %in% thisBasketSampled$basket_id,"BASKET_WEIGHT"] <- sum(thisBasketSampledSpecimensWeight/1000)
# message("\t\t\t<done>")
}else{
basket[basket$basket_id %in% thisBasketSampled$basket_id,"BASKET_WEIGHT"] <- 0.0005
# message("\t\t\t<No sampled weights could be found - forcing 0.0005 kg>")
}
}
}
return(basket)
}
#' @title tweakLv1
#' @description This function will perform tweaks to the lv1_observations data coming from andes before
#' it is imported to Oracle.
#' @param x default is \code{NULL}. This is the ESE_LV1_OBSERVATIONS data frame
#' @return an updated version of ESE_LV1_OBSERVATIONS
#' @family general_use
#' @author Mike McMahon, \email{Mike.McMahon@@dfo-mpo.gc.ca}
#' @export
tweakLv1 <- function(x = NULL){
if(length(unique(x$MISSION)) > 1) stop("The object sent has more than one mission in it, abort")
theMsg <- NA
if(x$MISSION[1] == "CAR2023011"){
x[x$SPECIMEN_ID == 83667 & x$LV1_OBSERVATION == "Weight","DATA_VALUE"]<-1
}
if(x$MISSION[1] == "CAR2022102"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tHerring otoliths taken post-survey - manually adding that information\n")
x[x$SPEC == 60 & x$LV1_OBSERVATION == "Collect Specimen" & x$DATA_VALUE =="1" ,c("LV1_OBSERVATION","DATA_DESC")] <- as.data.frame(t(as.matrix(c("Age Material Type","Otolith Taken"))))
}
if(x$MISSION[1] == "TEL2022010"){
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSome records were recorded in kg instead of g (fixed)\n")
x[x$SPECIMEN_ID %in% c(24705,24707) & x$LV1_OBSERVATION == "Weight" & x$DATA_VALUE =="0.001" ,c("DATA_VALUE")] <- 1
x[x$SPECIMEN_ID == 178 & x$LV1_OBSERVATION == "Weight","DATA_VALUE"]<-1
theMsg <- paste0(theMsg[!is.na(theMsg)], "\tSome records had inncorrect lengths")
x[x$SPECIMEN_ID == 42542 & x$LV1_OBSERVATION == "Length","DATA_VALUE"]<-14
x[x$SPECIMEN_ID == 46991 & x$LV1_OBSERVATION == "Length","DATA_VALUE"]<-10
x[x$SPECIMEN_ID == 54423 & x$LV1_OBSERVATION == "Length","DATA_VALUE"]<-20
x[x$SPECIMEN_ID == 27478 & x$LV1_OBSERVATION == "Length","DATA_VALUE"]<-26
}
if (!is.na(theMsg)) message("Tweaking LV1_OBSERVATIONS: \n", theMsg)
return(x)
}
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