diff --git a/code/Trait-Environment-Relationships2.R b/code/Trait-Environment-Relationships2.R index 7905b6187405ac9ed8d04c717da685a620b68d0f..6ad4f3259eda6931784cb2d8665e33a0586580c8 100644 --- a/code/Trait-Environment-Relationships2.R +++ b/code/Trait-Environment-Relationships2.R @@ -109,6 +109,7 @@ str(backbone.splot.try3) ###### Harmonized plot data ###### DT <- read.csv("data/plots_without_unified_cover_scales_20160120a.csv") +DT <- read.csv("data/plots_without_unified_cover_scales_20160120a.csv") library(data.table) DT <- data.table(DT) colnames(DT) @@ -1182,7 +1183,8 @@ for (i in 1:18){ } write.csv(FD,file = "FD3.csv", row.names = T) -FD <- read.csv("C://Daten//iDiv2//splot2//FD3.csv") +#FD <- read.csv("C://Daten//iDiv2//splot2//FD3.csv") +FD <- read.csv("C://Daten//iDiv2//splot2//splot2.0//FD_TRY3.csv") str(FD) dimnames(FD)[[1]] <- FD$X FD <- FD[,-1] @@ -1195,12 +1197,12 @@ any(is.na(index12)) # F splot.header3 <- splot.header[index12,] str(FD) # num [1:1117898, 1:18] FD <- FD[!(is.na(splot.header3$Longitude)|is.na(splot.header3$Latitude)|is.na(FD[,"SLA.mean"])),] -str(FD) # num [1:1111307 , 1:18] -1111307 /1117898*100 # 99.41041 % of plots have traits, Long and Lat +str(FD) # num [1:1112287 , 1:18] +1112287 /1117898*100 # 99.49808 % of plots have traits, Long and Lat any(is.na(FD)) #F # match header again index13 <- match(dimnames(FD)[[1]],splot.header$PlotObservationID) -length(index13) #1111307 +length(index13) #1112287 any(is.na(index13)) # F splot.header3 <- splot.header[index13,] # now in the same sequence as FD @@ -1232,13 +1234,14 @@ write.csv(data.frame(names(splot.bioclim)[4:49],FD.bioclim[,,5]),file = "FD2_bio library(vegan) FD.pca1 <- rda(FD,scale=T) FD.pca1 -'Eigenvalues for unconstrained axes: -PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 -8.597 1.876 1.378 0.886 0.790 0.780 0.583 0.551 +' +Eigenvalues for unconstrained axes: + PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 +8.703 1.758 1.122 0.974 0.732 0.643 0.590 0.540 (Showed only 8 of all 18 unconstrained eigenvalues) ' plot(FD.pca1) -summary(FD.pca1) +head(summary(FD.pca1)) #text(summary(FD.pca1)$species[,c(1,2)],dimnames(summary(FD.pca1)$species)[[1]]) traitnames <- dimnames(summary(FD.pca1)$species)[[1]] traitnames <- substr(traitnames,1,nchar(traitnames)-5)