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During startup - Warning message:
Setting LC_CTYPE failed, using "C" 
> #setwd("/Users/new_user/Documents/For_Work/2021/Drought_Thay_Tan")
> library(ncdf4)
> library(ggplot2)
> #library(reshape2)
> library(factoextra)
Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
> library(cluster)
> library(NbClust)
> library(corrplot)
corrplot 0.92 loaded
> library(maps)

Attaching package: 'maps'

The following object is masked from 'package:cluster':

    votes.repub

> library(mapdata);library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(mapproj)
> library(viridis)
Loading required package: viridisLite

Attaching package: 'viridis'

The following object is masked from 'package:maps':

    unemp

> library(ggthemes)
> #library(RColorBrewer)
> 
> # Input/output Dir:
> Indir <- "" #"/home/tanpv/Progs/2021/NC/"
> Outtxt <- "" #"/home/tanpv/Progs/2021/NC/"
> Outpdf <-""  #"/home/tanpv/Progs/2021/PDF/"
> 
> # read input data
> in.file <- paste(Indir,"HWday.nc",sep="")
> innc <- nc_open(in.file)
> ivar.name <- "hwday"
> idat <- ncvar_get(innc,ivar.name)
> lon <- round(ncvar_get(innc,"lon"),digits = 4)
> nlon <- dim(lon)
> lat <- round(ncvar_get(innc,"lat"),digits = 4)
> nlat <- dim(lat)
> 
> max.clus <- 7 # so cum lon nhat
> cluster <- array(NA,dim=c(nlon,1))
> 
> # for k-means clustering
> 
> r2dat.new <- idat
> for (iclus in seq(max.clus)) {
+      km.res <- kmeans(r2dat.new, iclus, nstart = 25)
+      sta.data <- seq(nrow(r2dat.new))
+      dd <- cbind(sta.data,lon,lat,cluster = km.res$cluster)
+  
+      # write to ncdf file
+      write.table(dd, file=paste(Outtxt,"cluster_",iclus,"groups.txt",sep=""),col.names = T, row.names = F,sep="\t")
+  
+      # for draw
+      map('world',col="white", fill=TRUE, bg="white", lwd=0.05,boundary = TRUE,
+          mar=rep(0,4),border=1.2, ylim=c(8,25),xlim = c(100,115))
+      
+      
+      # Get the world polygon and extract UK
+      library(maps)
+      VN <- map_data("world") %>% filter(region=="Vietnam")
+      data <- world.cities %>% filter(country.etc=="Vietnam")
+      dd <- as.data.frame(dd)
+      p <- ggplot() +
+        geom_polygon(data = VN, aes(x=long, y = lat, group = group), fill="grey", alpha=1,color="black") +
+        geom_point(data=dd, aes(x=lon, y=lat,shape=as.factor(cluster),col=cluster)) +
+        xlab("")+ylab("")+
+        #scale_shape_manual(values=c(25, 21, 24))+
+        scale_size_continuous(range=c(1.5,3.2)) +coord_map() +
+        scale_x_continuous(breaks=seq(102,116,2),limits = c(102,116))+
+        scale_y_continuous(breaks=seq(8,24,2))+
+        guides(shape = FALSE,size=FALSE)+ ggtitle(paste("cluster",iclus,sep=""))
+      pdf(paste("Fig_kmeans_",iclus,"group.pdf",sep=""), width = 4, height = 5)
+      print(p)
+      dev.off()    
+ }
Warning messages:
1: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
2: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
3: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
4: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
5: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
6: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
7: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead. 
8: The shape palette can deal with a maximum of 6 discrete values because
more than 6 becomes difficult to discriminate; you have 7. Consider
specifying shapes manually if you must have them. 
9: Removed 13 rows containing missing values (geom_point). 
> 
> idata <- r2dat.new
> p <- fviz_nbclust(idata, kmeans, method = "wss") +
+ #  geom_vline(xintercept = 4, linetype = 2)+
+ #  geom_vline(xintercept = 6, linetype = 2)+
+   labs(subtitle = "Elbow method")+
+   theme(legend.title=element_text(size = 22, face = "bold"))
> 
> 
> pdf(paste(Outpdf,"new_optimal_k_Elbow_method.pdf",sep=""),height = 4, width = 4)
> print(p)
> dev.off()
pdf 
  2 
> 
> 
> p <- fviz_nbclust(idata, kmeans, method = "silhouette") +
+ #  geom_vline(xintercept = 4, linetype = 2)+
+   labs(subtitle = "Silhouette method")
> pdf(paste(Outpdf,"optimal_k_Silhouette_method.pdf",sep=""),height = 4, width = 4)
> print(p)
> dev.off()
pdf 
  2 
> 
> p <- fviz_nbclust(idata, kmeans, nstart = 25,  method = "gap_stat", nboot = 25)+
+   labs(subtitle = "Gap statistic method")
> pdf(paste(Outpdf,"optimal_k_gap_stat_method.pdf",sep=""),height = 4, width = 4)
> print(p)
> dev.off()
pdf 
  2 
> 
> 
> proc.time()
   user  system elapsed 
  7.246   3.966   7.216