gistfile1.txt

rm(list = ls())
library(readxl)
library(caret)
library(dplyr)
library(readr)
library(DataExplorer)
library(skimr)
library(forecast)
library(lubridate)
library(xts)
library(tsbox)
library(TSstudio)
library(timetk)
library(tseries)
library(MLmetrics)
library(prophet)
library(xgboost)
library(tidymodels)
library(modeltime)
library(tidyverse)
library(hrbrthemes)
library(mgcv)
library(modelr)
library(knitr)
library(vars)
library(timelineR)
library(doParallel)
library(parallel)
library(data.table)
library(lme4)
library(sjPlot)
library(VCA)
library(MLtoolkit)
#### IMPORT DATA ####
arcraw <- read_excel("Fiskedatabase fra generasjon 05.xlsx", 
                     sheet = "Marc2", col_types = c("text", 
                                                   "text", "text", "date", "text", "text", 
                                                   "text", "text", "numeric", "text", 
                                                   "text", "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "numeric", 
                                                   "numeric", "numeric", "text", "numeric", 
                                                   "text", "text", "text")) 
dim(arcraw)
arc<-arcraw
##### DATA WRANGLING ####
### Make all column names lowercase 
names(arc)<-tolower(names(arc))
names(arcraw)<-tolower(names(arcraw))
### Fill in slaughter month, quarter, and year
arc$slaughtermonth<-format(arc$sampledate,'%m')
arc$slaughteryear<-format(arc$sampledate,'%Y')
arc$slaughterq<-quarters(arc$sampledate)
dim(arc)
table(arc$slaughteryear)
plot(table(arc$slaughteryear, arc$slaughtermonth))
heatmap(table(arc$slaughteryear, arc$slaughtermonth))
table(is.na(arc$slaughtermonth))
table(is.na(arc$slaughteryear))
table(is.na(arc$slaughterq))
table(is.na(arc$sampledate))
### Remove NA
arc<-arc[!(is.na(arc$rochefant) | arc$rochefant==""), ]
arc$strain<-car::recode(arc$strain, 
                             "c('(tom)', 'Bindalssmolt','Bolaks','Mowi','Rauma','Stofnfiskur')='REST'")
dim(arc)