 library(maptools)
 FileName<-"japan_jdg"#パスは任意に指定してください。
 jpn<-read.shape(FileName)
 jpn_poly<-Map2poly(jpn)
 jpn_df<-jpn$att.data
 japan_poly<-subset(jpn_poly,jpn_df$JCODE!=0)
 japan_df<-subset(jpn_df,jpn_df$JCODE!=0)
 japan_poly2<-subset(japan_poly,japan_df$JCODE!=1999)
 japan_df2<-subset(japan_df,japan_df$JCODE!=1999)
 japan_df2$CITY2<-ifelse(is.na(japan_df2$CITY2),"",as.character(japan_df2$CITY2))
 japan_df2$CITY1<-ifelse(is.na(japan_df2$CITY1),"",as.character(japan_df2$CITY1))
 japan_df2$TOWN1<-ifelse(is.na(japan_df2$TOWN1),"",as.character(japan_df2$TOWN1))
 japan_df2$TOWN2<-ifelse(is.na(japan_df2$TOWN2),"",as.character(japan_df2$TOWN2))
 write.polylistShape(japan_poly2,japan_df2,FileName)