Commit 42fd0cf0 authored by peguerin's avatar peguerin
Browse files

latclass table

parent ca1956c1
......@@ -14,10 +14,36 @@
##
##########################################################################
## Libraries
library(plyr)
lib_vect <-c("plyr","SpatialPack", "raster","rgdal","rgeos")
sapply(lib_vect,library,character.only=TRUE)
##########################################################################
## functions
source("00-scripts/step5/figures/functions.R")
## attribute "polar", "tropical" and "temperate" according to lattitude
lat2class <- function(lat) {
if(lat < 24 && lat > -24) {
return("tropical")
} else if(lat > 66 | lat < -66) {
return("polar")
} else {
return("temperate")
}
}
##########################################################################
## load data
## load worldcoast shapefile
grid <- readOGR("01-infos/grid_equalarea200km","gridFish.b_260418")
##########################################################################
## read the table
dcT=read.table("09-all_descripteurs/total_data_genetic_diversity_with_all_descripteurs.tsv",header=T)
## keep entries with GD!=0
......@@ -41,22 +67,46 @@ dcF.1=dcF.1[which(!is.na(dcF.1$SST)),]
## remove freshwater data with no bathyval information
dcF.1=dcF.1[which(!is.na(dcF.1$bathyVal)),]
## add non transformed coordinates latitude
convertedCoords_M=convert_coordinates_into_epsg4326(dcM, dcM.1, grid)
convertedCoords_F=convert_coordinates_into_epsg4326(dcF, dcF.1, grid)
dcM.2=cbind(dcM.1,convertedCoords_M)
dcF.2=cbind(dcF.1,convertedCoords_F)
## load richness data
richness=read.csv("01-infos/equalarea_id_coordsCA_FWRS_MR_RS.csv")
Fr=merge(dcF.1,richness,by ="cell", all.x=F)
Fr=merge(dcF.2,richness,by ="cell", all.x=F)
Fr=Fr[which(Fr$RS_FW_FISH !=0),]
Fr_wCoords=Fr[,c(2,3,4,6,7,27)] #with coordinates
Fr=Fr[,c(1,4,6,7,27)]
Fr_wCoords=Fr[,c(2,3,4,6,7,24,29)] #with coordinates
Fr=Fr[,c(1,4,6,7,24,29)]
Fr=na.omit(Fr)
names(Fr)=c("cell","GD_mean","nb_species","nb_indv_mean","richness")
Mr=merge(dcM.1,richness,by ="cell", all.x=F)
names(Fr)=c("cell","GD_mean","nb_species","nb_indv_mean","latitude","richness")
Mr=merge(dcM.2,richness,by ="cell", all.x=F)
Mr=Mr[which(Mr$RS_MR_FISH !=0),]
Mr_wCoords=Mr[,c(2,3,4,6,7,28)] #with coordinates
Mr=Mr[,c(1,4,6,7,28)]
Mr_wCoords=Mr[,c(2,3,4,6,7,24,30)] #with coordinates
Mr=Mr[,c(1,4,6,7,24,30)]
Mr=na.omit(Mr)
names(Mr)=c("cell","GD_mean","nb_species","nb_indv_mean","richness")
names(Mr)=c("cell","GD_mean","nb_species","nb_indv_mean","latitude","richness")
Tr=rbind(Mr,Fr)
## add marine/freshwater info
is_marine_M=rep(1,dim(Mr)[1])
is_marine_F=rep(0,dim(Fr)[1])
is_marine=c(is_marine_M,is_marine_F)
Tr.1=cbind(Tr,is_marine)
## add latband info
latband=coords_to_latband(Tr.1$latitude)
Tr.2=cbind(Tr.1, latband)
## add class info latitude
latclass= apply(as.data.frame(Tr.2$latband),1, function(x) lat2class(x) )
Tr.3=cbind(Tr.2, latclass)
##write table with latband latclass and latitude
write.table(Tr.3,"14-tables/latclass.tsv",col.names=T,row.names=F,sep="\t")
......@@ -86,10 +136,15 @@ modified.ttest(Mr$GD_mean,Mr$richness,coordsM, nclass = 13)
coordsF = cbind(Fr$x,Fr$y)
modified.ttest(Fr$GD_mean,Fr$richness,coordsF, nclass = 13)
##########################################################################
###### between freshwater and marine genetic diversity
coordsM = cbind(Mr$x,Mr$y)
coordsF = cbind(Fr$x,Fr$y)
coordsT=rbind(coordsM,coordsF)
GD_meanT=data.frame(marine=Mr$GD_mean, freshwater= Fr$GD_mean)
###### table with 0/1 marine/freshwater, temperature and latitude as a qualitative variable
#coordsM = cbind(Mr$x,Mr$y)
#coordsF = cbind(Fr$x,Fr$y)
#coordsT=rbind(coordsM,coordsF)
#GD_meanT=data.frame(marine=Mr$GD_mean, freshwater= Fr$GD_mean)
#modified.ttest(GD_meanT$marine, GDmeanT$freshwater,coordsT, nclass = 13)
modified.ttest(GD_meanT$marine, GDmeanT$freshwater,coordsT, nclass = 13)
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