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## Download OISST for NEUS
## From: https://cran.r-project.org/web/packages/heatwaveR/vignettes/OISST_preparation.html




# The packages we will need
# install.packages("dplyr")
# install.packages("lubridate")
# install.packages("ggplot2")

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  library(ggplot2)
  library(dplyr)
  library(patchwork)
  library(forcats)
  
  
  annualCondition <- read.csv("https://raw.githubusercontent.com/Laurels1/Condition/master/data/AnnualRelCond2018_GB.csv",
                              stringsAsFactors = FALSE)
  

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install.packages("fedregs")
library(fedregs)
library(dplyr)
library(ggplot2)
library(quanteda)
library(magick)

## For more info, check out the fedregs github repository:
## https://github.com/slarge/fedregs

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# devtools::install_github("tidyverse/ggplot2")
library(ggplot2)
# library(dplyr)
library(RCurl)
# library(rnaturalearth)
library(sf)
# library(purrr)
library(data.table)
# library(reshape2)
# library(formula.tools)

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## from https://eliocamp.github.io/codigo-r/2018/02/how-to-make-shaded-relief-in-r/

geom_relief <- function(mapping = NULL, data = NULL,
                        stat = "identity", position = "identity",
                        ...,
                        raster = TRUE,
                        interpolate = TRUE,
                        na.rm = FALSE,
                        show.legend = NA,
                        inherit.aes = TRUE) {

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## Print list of stocks for a year

#advice_year(2018)
advice_year <- function(year = 2018, path = "~/") {
  
  list_of_packages <- c("dplyr", "glue", "jsonlite", "flextable", "officer")
  new_packages <- list_of_packages[!(list_of_packages %in% installed.packages()[,"Package"])]
  if(length(new_packages)) install.packages(new_packages)
  
  library(dplyr)

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<?xml version="1.0" encoding="UTF-8"?>
<ns:Execute xmlns:ns="http://www.opengis.net/wps/1.0.0" service="WPS" version="1.0.0">
   <ns1:Identifier xmlns:ns1="http://www.opengis.net/ows/1.1">org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.VSURF</ns1:Identifier>
   <ns:DataInputs>
      <ns:Input>
         <ns1:Identifier xmlns:ns1="http://www.opengis.net/ows/1.1">x</ns1:Identifier>
         <ns:Reference xmlns:xlin="http://www.w3.org/1999/xlink" xlin:href="#XFILE#" mimeType="text/xml" />
      </ns:Input>
      <ns:Input>
         <ns1:Identifier xmlns:ns1="http://www.opengis.net/ows/1.1">y</ns1:Identifier>

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vsurf_bb <- function(file_x,
                     file_y,
                     ntree = 100,
                     mtry = 2,
                     nfor_thres = 50,
                     nmin = 1,
                     nfor_interp = 25,
                     nsd = 1,
                     nfor_pred = 25,
                     parallel = "true",

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## Exploring ICES advice ##

library(tabulizer)
library(glue)
library(dplyr)
library(stringr)
library(purrr)
library(httr)
library(jsonlite)

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library(icesSAG)
library(dplyr)

ref_list <- icesSAG::getSAG(stock = NULL, year = 2017, data = "refpts")

stock_list <- jsonlite::fromJSON("http://sd.ices.dk/services/odata3/StockListDWs3",
                                 simplifyDataFrame = TRUE)$value

all_msy <- ref_list %>% 
  filter(!is.na(FMSY) |