1
|
################## Data preparation for interpolation #######################################
|
2
|
############################ Extraction of station data ##########################################
|
3
|
#This script perform queries on the Postgres database ghcn for stations matching the #
|
4
|
#interpolation area. It requires the following inputs: #
|
5
|
# 1)the text file ofGHCND stations from NCDC matching the database version release #
|
6
|
# 2)a shape file of the study area with geographic coordinates: lonlat WGS84 # #
|
7
|
# 3)a new coordinate system can be provided as an argument #
|
8
|
# 4)the variable of interest: "TMAX","TMIN" or "PRCP" #
|
9
|
# #
|
10
|
#The outputs are text files and a shape file of a time subset of the database #
|
11
|
#AUTHOR: Benoit Parmentier #
|
12
|
#DATE: 06/02/212 #
|
13
|
#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363-- #
|
14
|
##################################################################################################
|
15
|
|
16
|
###Loading R library and packages
|
17
|
library(RPostgreSQL)
|
18
|
library(sp) # Spatial pacakge with class definition by Bivand et al.
|
19
|
library(spdep) # Spatial pacakge with methods and spatial stat. by Bivand et al.
|
20
|
library(rgdal) # GDAL wrapper for R, spatial utilities
|
21
|
|
22
|
### Parameters and arguments
|
23
|
|
24
|
db.name <- "ghcn" #name of the Postgres database
|
25
|
var <- "TMAX" #name of the variables to keep: TMIN, TMAX or PRCP
|
26
|
year_start<-"2010" #starting year for the query (included)
|
27
|
year_end<-"2011" #end year for the query (excluded)
|
28
|
infile1<- "ORWGS84_state_outline.shp" #This is the shape file of outline of the study area.
|
29
|
infile2<-"ghcnd-stations.txt" #This is the textfile of station locations from GHCND
|
30
|
new_proj<-"+proj=lcc +lat_1=43 +lat_2=45.5 +lat_0=41.75 +lon_0=-120.5 +x_0=400000 +y_0=0 +ellps=GRS80 +units=m +no_defs";
|
31
|
|
32
|
path<-"/home/parmentier/Data/IPLANT_project/data_Oregon_stations/" #Jupiter LOCATION on EOS/Atlas
|
33
|
#path<-"H:/Data/IPLANT_project/data_Oregon_stations" #Jupiter Location on XANDERS
|
34
|
setwd(path)
|
35
|
out_prefix<-"y2010_2010_OR_0626012" #User defined output prefix
|
36
|
|
37
|
### Functions used in the script
|
38
|
|
39
|
format_s <-function(s_ID){
|
40
|
#Format station ID in a vector format/tuple that is used in a psql query.
|
41
|
# Argument 1: vector of station ID
|
42
|
# Return: character of station ID
|
43
|
tx2<-s_ID
|
44
|
tx2<-as.character(tx2)
|
45
|
stat_list<-tx2
|
46
|
temp<-shQuote(stat_list)
|
47
|
t<-paste(temp, collapse= " ")
|
48
|
t1<-gsub(" ", ",",t)
|
49
|
sf_ID<-paste("(",t1,")",sep="") #vector containing the station ID to query
|
50
|
return(sf_ID)
|
51
|
}
|
52
|
|
53
|
############ START OF THE SCRIPT #################
|
54
|
|
55
|
##### STEP 1: Select station in the study area
|
56
|
|
57
|
infile1<- "ORWGS84_state_outline.shp" #This is the shape file of outline of the study area.
|
58
|
filename<-sub(".shp","",infile1) #Removing the extension from file.
|
59
|
interp_area <- readOGR(".",filename)
|
60
|
CRS_interp<-proj4string(interp_area) #Storing the coordinate information: geographic coordinates longlat WGS84
|
61
|
|
62
|
dat_stat <- read.fwf("ghcnd-stations.txt", widths = c(11,9,10,7,3,31,4,4,6),fill=TRUE)
|
63
|
colnames(dat_stat)<-c("STAT_ID","lat","lon","elev","state","name","GSNF","HCNF","WMOID")
|
64
|
coords<- dat_stat[,c('lon','lat')]
|
65
|
coordinates(dat_stat)<-coords
|
66
|
locs_coord<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0")
|
67
|
#proj4string(dat_stat)<-locs_coord
|
68
|
proj4string(dat_stat)<-CRS_interp
|
69
|
|
70
|
# Spatial query to find relevant stations
|
71
|
inside <- !is.na(over(dat_stat, as(interp_area, "SpatialPolygons"))) #Finding stations contained in the current interpolation area
|
72
|
stat_OR<-dat_stat[inside,] #Finding stations contained in the current interpolation area
|
73
|
|
74
|
#Quick visualization of station locations
|
75
|
plot(interp_area, axes =TRUE)
|
76
|
plot(stat_OR, pch=1, col="red", cex= 0.7, add=TRUE)
|
77
|
#legend("topleft", pch=1,col="red",bty="n",title= "Stations",cex=1.6)
|
78
|
|
79
|
#### STEP 2: Connecting to the database and query for relevant data
|
80
|
|
81
|
drv <- dbDriver("PostgreSQL")
|
82
|
db <- dbConnect(drv, dbname=db.name)
|
83
|
|
84
|
time1<-proc.time() #Start stop watch
|
85
|
list_s<-format_s(stat_OR$STAT_ID)
|
86
|
data2<-dbGetQuery(db, paste("SELECT *
|
87
|
FROM ghcn
|
88
|
WHERE element=",shQuote(var),
|
89
|
"AND year>=",year_start,
|
90
|
"AND year<",year_end,
|
91
|
"AND station IN ",list_s,";",sep="")) #Selecting station using a SQL query
|
92
|
time_duration<-proc.time()-time1 #Time for the query may be long given the size of the database
|
93
|
time_minutes<-time_duration[3]/60
|
94
|
|
95
|
data_table<-merge(data2,stat_OR, by.x = "station", by.y = "STAT_ID")
|
96
|
|
97
|
#Transform the subset data frame in a spatial data frame and reproject
|
98
|
data3<-data_table #Make a copy of the data frame
|
99
|
coords<- data3[c('lon.1','lat.1')] #Define coordinates in a data frame
|
100
|
coordinates(data3)<-coords #Assign coordinates to the data frame
|
101
|
proj4string(data3)<-CRS_interp #Assign coordinates reference system in PROJ4 format
|
102
|
data_proj<-spTransform(data3,CRS(new_proj)) #Project from WGS84 to new coord. system
|
103
|
|
104
|
### STEP 3: Save results and outuput in textfile and a shape file
|
105
|
|
106
|
#Save a textfile of the locations of meteorological stations in the study area
|
107
|
write.table(as.data.frame(stat_OR), file=paste(path,"/","location_study_area",out_prefix,".txt",sep=""),sep=",")
|
108
|
|
109
|
#Save a textfile and shape file of all the subset data
|
110
|
write.table(data_table, file= paste(path,"/","ghcn_data_",var,out_prefix,".txt",sep=""), sep=",")
|
111
|
#outfile<-paste(path,"ghcn_data_",var,out_prefix,sep="") #Removing extension if it is present
|
112
|
outfile<-paste("ghcn_data_",var,out_prefix,sep="") #Name of the file
|
113
|
writeOGR(data_proj, paste(outfile, "shp", sep="."), outfile, driver ="ESRI Shapefile") #Note that the layer name is the file name without extension
|
114
|
|
115
|
##### END OF SCRIPT ##########
|