latclass table

00-scripts/step5/analysis/tests.R

@@ -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)