clean scripts folder

00-scripts/sss.R

-###############################################################################
-## Librairies
-library("raster")
-library("rgdal")
-library("ncdf4")
-
-
-## load data
-coo=read.csv("01-sample_coords/all_coords.csv",sep="\t")
-coo=na.omit(coo)
-names(coo)=c("id","lat","lon")
-latlon = data.frame(lon=coo$lon,lat=coo$lat)
-coordinates(latlon) = c("lon", "lat")
-### indiquer que les lat/lon est en projection google map
-proj4string(latlon) = CRS("+init=epsg:4326")
-
-fichier="01-infos/salinity/MEDSEA_PHY_006_004_SSS_jan1987-nov2016_monthly.nc"
-br <- brick(fichier)
-##convertir les lat/lon dans la projection du raster "rp"
-latlon = spTransform(latlon,proj4string(br))
-
-buffer_distance=13000
-tt=extract(br,latlon, buffer=buffer_distance,fun=mean,normalizeWeights=FALSE,weigths=TRUE,factors=TRUE)
-
-january=tt[,seq(1,(359-10),12)]
-february=tt[,seq(2,(359-9),12)]
-march=tt[,seq(3,(359-8),12)]
-april=tt[,seq(4,(359-7),12)]
-may=tt[,seq(5,(359-6),12)]
-june=tt[,seq(6,(359-5),12)]
-july=tt[,seq(7,(359-4),12)]
-august=tt[,seq(8,(359-3),12)]
-september=tt[,seq(9,(359-2),12)]
-october=tt[,seq(10,(359-1),12)]
-november=tt[,seq(11,359,12)]
-december=tt[,seq(12,359-11,12)]
-
-year=list(january,february,march,april,may,june,july,august,september,october,november,december)
-
-
-
-monthlysalinity.frame <- as.data.frame(matrix(,ncol=(36),nrow=0))
-for(i in seq(1,dim(tt)[1])){
- yeartemp=c()
- for(mois in seq(1,12)) {
-  month_min=min(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
-  month_max=max(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
-  month_mean=mean(as.numeric(as.data.frame(year[mois])[i,]),na.rm=TRUE)
-  yeartemp=c(yeartemp,month_min,month_max,month_mean)
- }
- monthlysalinity.frame=rbind(monthlysalinity.frame,yeartemp) 
-}
-
-mois_nom=c("january","february","march","april","may","june","july","august","september","october","november","december")
-value_nom=c("min","max","mean")
-col_nom=c()
-for(m in mois_nom){
-	for(n in value_nom) {
-		mois_value=paste(m,n,sep="_")
-		nom_value=paste("SSS",as.character(mois_value),sep="_")
-		col_nom=c(col_nom,as.character(nom_value))
-	}
-}
-colnames(monthlysalinity.frame)=col_nom
-
-monthlysalinity.coo=cbind(coo,monthlysalinity.frame)
-
-write.table(monthlysalinity.coo, file="03-results/all_monthly_salinity.tsv",quote=F,sep="\t",col.names=T,row.names=F)
\ No newline at end of file

00-scripts/tricky_sss_sst.R

-###############################################################################
-## Librairies
-library("raster")
-library("rgdal")
-library("ncdf4")
-###############################################################################
-
-###############################################################################
-## load data
-
-##salinity
-fichier="01-infos/MEDSEA_REANALYSIS_PHYS_006_004_6Wto17E_0to210m_1m_vosaline_1987-2015.nc"
-fichier="01-infos/MEDSEA_REANALYSIS_PHYS_006_004_6Wto17E_0to210m_1m_votemper_1987-2015.nc"
-
-## coordinates
-coof="01-sample_coords/GeneticData_usedInAnalyses_adjustedGPS.txt"
-coo=read.table(coof,sep="\t",header=T,stringsAsFactors = FALSE)
-labels=as.character(coo[,1])
-
-latlon = data.frame(lon=as.numeric(coo$long_adjusted) ,lat=as.numeric(coo$lat_adjusted))
-## shit lattitude to get a grid point
-latlon[c(24:34,39, 40),]$lat=latlon[c(24:34,39, 40),]$lat-0.5
-coordinates(latlon) = c("lon", "lat")
-### indiquer que les lat/lon est en projection google map
-proj4string(latlon) = CRS("+init=epsg:4326")
-
-
-br <- nc_open(fichier)
-brdepth = ncvar_get(br, "depth")
-
-january=seq(1,(348-11),12)
-february=seq(2,(348-10),12)
-march=seq(3,(348-9),12)
-april=seq(4,(348-8),12)
-may=seq(5,(348-7),12)
-june=seq(6,(348-6),12)
-july=seq(7,(348-5),12)
-august=seq(8,(348-4),12)
-september=seq(9,(348-3),12)
-october=seq(10,(348-2),12)
-november=seq(11,348-1,12)
-december=seq(12,348,12)
-
-
-## salinities ALL
-repro_period=cbind(january,february,march,april,may,june,july,august,september,october,november,december)
-depth_range=which(brdepth <300)
-
-salinities=array(, dim=c(dim(latlon)[1],348,26))
-for(LVL in depth_range){ 
-	br <- brick(fichier,level=LVL)
-	LVL_ma_var=extract(br,latlon)
-	salinities[,,LVL]=LVL_ma_var[,repro_period]
-}
-temperatures=array(, dim=c(dim(latlon)[1],348,26))
-for(LVL in depth_range){ 
-	br <- brick(fichier,level=LVL)
-	LVL_ma_var=extract(br,latlon)
-	temperatures[,,LVL]=LVL_ma_var[,repro_period]
-}
-
-write.table(salt_temp, file="03-results/ADJUSTED_depth_repro_temperature_salinity.tsv",quote=F,sep="\t",col.names=T,row.names=F)