report/knitr/Report_Sardara.R

In jsubei/IRDTunaAtlas: IRD (www.ird.fr) - UMR EME - Tuna atlas

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#####         BUILD THE UPDATE REPORT                     #####
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### LOAD libraries  ###
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library(ggplot2)
library(RColorBrewer)
library(knitr)
require(IRDTunaAtlas)

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### SOURCE PLOT FUNCTION for INDICATORS  ###
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#remove it if update IRDTunaAtlas package
source("/home/taha/R/monR-2013/esp_travail/IRDTunaAtlas/R_scripts/multiplot.R")
source("/home/taha/R/monR-2013/esp_travail/IRDTunaAtlas/R_scripts/Atlas_i1_SpeciesByOcean.R")
source("/home/taha/R/monR-2013/esp_travail/IRDTunaAtlas/R_scripts/Atlas_i2_SpeciesByGear.R")
source("/home/taha/R/monR-2013/esp_travail/IRDTunaAtlas/R_scripts/Atlas_i3_SpeciesYearByGearMonth.R")
source("/home/taha/R/monR-2013/esp_travail/IRDTunaAtlas/R_scripts/Atlas_i4_SpeciesMonthByOcean.R")
source("/home/taha/R/monR-2013/esp_travail/IRDTunaAtlas/R_scripts/Atlas_i9_RelativeSizeFrequenciesBySchoolType.R")
source("/home/taha/R/monR-2013/esp_travail/IRDTunaAtlas/R_scripts/Atlas_i10_RelativeSizeFrequenciesByDecade.R")


### SET INPUT PARAMETERS  ###
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i1_specie_name=c("YFT","BET","BFT","SKJ")
i1_scientific_specie_name=c("Thunnus albacares","Thunnus obesus","Thunnus Thynnus","Katsuwonus peianis")
i2_specie_name=c("YFT","BET","BFT","SKJ")
i2_scientific_specie_name=c("Thunnus albacares","Thunnus obesus","Thunnus Thynnus","Katsuwonus peianis")
i3_specie_name=c("YFT","BET","BFT","SKJ")
i3_scientific_specie_name=c("Thunnus albacares","Thunnus obesus","Thunnus Thynnus","Katsuwonus peianis")
i3_year = c("2000")
i4_specie_name=c("YFT","BET","BFT","SKJ")
i4_scientific_specie_name=c("Thunnus albacares","Thunnus obesus","Thunnus Thynnus","Katsuwonus peianis")
i4_year = "2000"
i9_specie_name=c("YFT","BET","BFT","SKJ")
i9_scientific_specie_name=c("Thunnus albacares","Thunnus obesus","Thunnus Thynnus","Katsuwonus peianis")
i9_year = "2000"
i10_specie_name=c("YFT","BET","BFT","SKJ")
i10_scientific_specie_name=c("Thunnus albacares","Thunnus obesus","Thunnus Thynnus","Katsuwonus peianis")
i10_period = c("1980","2005")
#####