Test workflow

VMS-datacall/0_global.R

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+#-------------------------------------------------------------------------------
+#
+# Script to extract and process VMS and logbook data for ICES VMS data call
+#
+# By: Niels Hintzen, Katell Hamon, Marcel Machiels#
+# Code by: Niels Hintzen
+# Contact: [email protected]
+#
+# Date: 25-Jan-2017
+# Update Date: 29-Jan-2019 ; Updated by: Roi Martinez
+# Update Date: 04-Feb-2020 ; Updated by: Colin Millar
+# Update Date: 07-Feb 2020 ; Updated by: Neil Campbell
+# Client: ICES
+#-------------------------------------------------------------------------------
+
+#--------------------READ ME----------------------------------------------------
+# The following script is a proposed workflow example to processes the ICES
+# VMS datacall request. It is not an exact template to be applied to data from
+# every member state and needs to be adjusted according to the data availability
+# and needs of every member state.
+#-------------------------------------------------------------------------------
+
+
+#- Clear workspace
+rm(list=ls())
+
+library(vmstools) #- download from www.vmstools.org
+library(Matrix)   #- available on CRAN
+library(ggplot2)  #- available on CRAN
+library(dplyr)    #- available on CRAN
+library(sp)
+library(doBy)
+library(mixtools)
+library(tidyr)
+library(glue)
+library(gt)
+
+
+#- Settings paths
+codePath  <- "VMSdatacall/R"          #Location where you store R scripts
+dataPath  <- "VMSdatacall/Data"       #Location where you store tacsat (VMS) and eflalo (logbook) data
+outPath   <- "VMSdatacall/Results"    #Location where you want to store the results
+
+#- Setting specific thresholds
+spThres       <- 20   #Maximum speed threshold in analyses in nm
+intThres      <- 5    #Minimum difference in time interval in minutes to prevent pseudo duplicates
+intvThres     <- 240  #Maximum difference in time interval in minutes to prevent intervals being too large to be realistic
+lanThres      <- 1.5  #Maximum difference in log10-transformed sorted weights
+
+#- Re-run all years as we have new field for no. vessels
+yearsToSubmit <- sort(2009:2020)
+
+#- Set the gear names for which automatic fishing activity is wanted
+#  It is important to fill out the gears you want to apply auto detection for
+autoDetectionGears        <- c("TBB","OTB","OTT","SSC","SDN","DRB","PTB","HMD")
+
+#- Decide if you want to visualy analyse speed-histograms to identify fishing activity
+#  peaks or have prior knowledge and use the template provided around lines 380 below
+visualInspection          <- FALSE
+
+#- Specify how landings should be distributed over the VMS pings: By day, ICES rectangle, trip basis or otherwise
+linkEflaloTacsat          <- c("day","ICESrectangle","trip")
+# other options
+# linkEflaloTacsat          <- c("day","ICESrectangle","trip")
+# linkEflaloTacsat          <- c("ICESrectangle","trip")
+# linkEflaloTacsat          <- c("day","trip")
+# linkEflaloTacsat          <- c("trip")