| 1 |
4ef959c2
|
Adam M. Wilson
|
#! /bin/R
|
| 2 |
|
|
### Script to download and process the NDP-026D station cloud dataset
|
| 3 |
710f7456
|
Adam M. Wilson
|
setwd("~/acrobates/adamw/projects/interp/data/NDP026D")
|
| 4 |
|
|
|
| 5 |
|
|
library(multicore)
|
| 6 |
|
|
library(latticeExtra)
|
| 7 |
|
|
library(doMC)
|
| 8 |
ddd9a810
|
Adam M. Wilson
|
library(rasterVis)
|
| 9 |
710f7456
|
Adam M. Wilson
|
library(rgdal)
|
| 10 |
9a19743f
|
Adam M. Wilson
|
library(reshape)
|
| 11 |
|
|
library(hexbin)
|
| 12 |
710f7456
|
Adam M. Wilson
|
## register parallel processing
|
| 13 |
2bca6aaa
|
Adam M. Wilson
|
registerDoMC(10)
|
| 14 |
710f7456
|
Adam M. Wilson
|
|
| 15 |
4ef959c2
|
Adam M. Wilson
|
|
| 16 |
|
|
## available here http://cdiac.ornl.gov/epubs/ndp/ndp026d/ndp026d.html
|
| 17 |
|
|
|
| 18 |
|
|
## Get station locations
|
| 19 |
a6d44f2d
|
Adam M. Wilson
|
system("wget -N -nd http://cdiac.ornl.gov/ftp/ndp026d/cat01/01_STID -P data/")
|
| 20 |
4ef959c2
|
Adam M. Wilson
|
st=read.table("data/01_STID",skip=1)
|
| 21 |
|
|
colnames(st)=c("StaID","LAT","LON","ELEV","ny1","fy1","ly1","ny7","fy7","ly7","SDC","b5c")
|
| 22 |
|
|
st$lat=st$LAT/100
|
| 23 |
|
|
st$lon=st$LON/100
|
| 24 |
|
|
st$lon[st$lon>180]=st$lon[st$lon>180]-360
|
| 25 |
9a19743f
|
Adam M. Wilson
|
st=st[,c("StaID","ELEV","lat","lon")]
|
| 26 |
|
|
colnames(st)=c("id","elev","lat","lon")
|
| 27 |
|
|
write.csv(st,"stations.csv",row.names=F)
|
| 28 |
4ef959c2
|
Adam M. Wilson
|
|
| 29 |
710f7456
|
Adam M. Wilson
|
## download data
|
| 30 |
4ef959c2
|
Adam M. Wilson
|
system("wget -N -nd ftp://cdiac.ornl.gov/pub/ndp026d/cat67_78/* -A '.tc.Z' -P data/")
|
| 31 |
|
|
|
| 32 |
9a19743f
|
Adam M. Wilson
|
system("gunzip data/*.Z")
|
| 33 |
710f7456
|
Adam M. Wilson
|
|
| 34 |
|
|
## define FWF widths
|
| 35 |
|
|
f162=c(5,5,4,7,7,7,4) #format 162
|
| 36 |
4ef959c2
|
Adam M. Wilson
|
c162=c("StaID","YR","Nobs","Amt","Fq","AWP","NC")
|
| 37 |
|
|
|
| 38 |
710f7456
|
Adam M. Wilson
|
## use monthly timeseries
|
| 39 |
|
|
cld=do.call(rbind.data.frame,mclapply(sprintf("%02d",1:12),function(m) {
|
| 40 |
4ef959c2
|
Adam M. Wilson
|
d=read.fwf(list.files("data",pattern=paste("MNYDC.",m,".tc",sep=""),full=T),skip=1,widths=f162)
|
| 41 |
|
|
colnames(d)=c162
|
| 42 |
|
|
d$month=as.numeric(m)
|
| 43 |
710f7456
|
Adam M. Wilson
|
print(m)
|
| 44 |
4ef959c2
|
Adam M. Wilson
|
return(d)}
|
| 45 |
|
|
))
|
| 46 |
|
|
|
| 47 |
710f7456
|
Adam M. Wilson
|
## add lat/lon
|
| 48 |
|
|
cld[,c("lat","lon")]=st[match(cld$StaID,st$StaID),c("lat","lon")]
|
| 49 |
4ef959c2
|
Adam M. Wilson
|
|
| 50 |
a6d44f2d
|
Adam M. Wilson
|
## drop missing values
|
| 51 |
4ef959c2
|
Adam M. Wilson
|
cld$Amt[cld$Amt<0]=NA
|
| 52 |
|
|
cld$Fq[cld$Fq<0]=NA
|
| 53 |
|
|
cld$AWP[cld$AWP<0]=NA
|
| 54 |
|
|
cld$NC[cld$NC<0]=NA
|
| 55 |
710f7456
|
Adam M. Wilson
|
cld=cld[cld$Nobs>0,]
|
| 56 |
4ef959c2
|
Adam M. Wilson
|
|
| 57 |
710f7456
|
Adam M. Wilson
|
## calculate means and sds
|
| 58 |
a6d44f2d
|
Adam M. Wilson
|
cldm=do.call(rbind.data.frame,by(cld,list(month=as.factor(cld$month),StaID=as.factor(cld$StaID)),function(x){
|
| 59 |
710f7456
|
Adam M. Wilson
|
data.frame(
|
| 60 |
|
|
month=x$month[1],
|
| 61 |
|
|
StaID=x$StaID[1],
|
| 62 |
|
|
cld=mean(x$Amt[x$Nobs>10]/100,na.rm=T),
|
| 63 |
|
|
cldsd=sd(x$Amt[x$Nobs>10]/100,na.rm=T))}))
|
| 64 |
|
|
cldm[,c("lat","lon")]=st[match(cldm$StaID,st$StaID),c("lat","lon")]
|
| 65 |
|
|
|
| 66 |
99b3508d
|
Adam M. Wilson
|
## means by year
|
| 67 |
|
|
cldy=do.call(rbind.data.frame,by(cld,list(year=as.factor(cld$YR),StaID=as.factor(cld$StaID)),function(x){
|
| 68 |
|
|
data.frame(
|
| 69 |
|
|
year=x$YR[1],
|
| 70 |
|
|
StaID=x$StaID[1],
|
| 71 |
|
|
cld=mean(x$Amt[x$Nobs>10]/100,na.rm=T),
|
| 72 |
|
|
cldsd=sd(x$Amt[x$Nobs>10]/100,na.rm=T))}))
|
| 73 |
|
|
cldy[,c("lat","lon")]=st[match(cldy$StaID,st$StaID),c("lat","lon")]
|
| 74 |
|
|
|
| 75 |
9a19743f
|
Adam M. Wilson
|
## add the MOD09 data to cld
|
| 76 |
|
|
#### Evaluate MOD35 Cloud data
|
| 77 |
|
|
mod09=brick("~/acrobates/adamw/projects/cloud/data/mod09.nc")
|
| 78 |
99b3508d
|
Adam M. Wilson
|
|
| 79 |
9a19743f
|
Adam M. Wilson
|
## overlay the data with 5km radius buffer
|
| 80 |
|
|
mod09st=extract(mod09,st,buffer=5000,fun=mean,na.rm=T,df=T)
|
| 81 |
|
|
mod09st$id=st$id
|
| 82 |
|
|
mod09stl=melt(mod09st[,-1],id.vars="id")
|
| 83 |
|
|
mod09stl[,c("year","month")]=do.call(rbind,strsplit(sub("X","",mod09stl$variable),"[.]"))[,1:2]
|
| 84 |
|
|
## add it to cld
|
| 85 |
|
|
cld$mod09=mod09stl$value[match(paste(cld$StaID,cld$YR,cld$month),paste(mod09stl$id,mod09stl$year,as.numeric(mod09stl$month)))]
|
| 86 |
a6d44f2d
|
Adam M. Wilson
|
|
| 87 |
99b3508d
|
Adam M. Wilson
|
## write out the tables
|
| 88 |
9a19743f
|
Adam M. Wilson
|
write.csv(cld,file="cld.csv",row.names=F)
|
| 89 |
99b3508d
|
Adam M. Wilson
|
write.csv(cldy,file="cldy.csv")
|
| 90 |
a6d44f2d
|
Adam M. Wilson
|
write.csv(cldm,file="cldm.csv")
|
| 91 |
|
|
|
| 92 |
555815c9
|
Adam M. Wilson
|
#########################################################################
|
| 93 |
a6d44f2d
|
Adam M. Wilson
|
##################
|
| 94 |
|
|
###
|
| 95 |
9a19743f
|
Adam M. Wilson
|
cld=read.csv("cld.csv")
|
| 96 |
a6d44f2d
|
Adam M. Wilson
|
cldm=read.csv("cldm.csv")
|
| 97 |
99b3508d
|
Adam M. Wilson
|
cldy=read.csv("cldy.csv")
|
| 98 |
9a19743f
|
Adam M. Wilson
|
st=read.csv("stations.csv")
|
| 99 |
a6d44f2d
|
Adam M. Wilson
|
|
| 100 |
9a19743f
|
Adam M. Wilson
|
coordinates(st)=c("lon","lat")
|
| 101 |
|
|
projection(st)=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
|
| 102 |
4ef959c2
|
Adam M. Wilson
|
|
| 103 |
710f7456
|
Adam M. Wilson
|
##make spatial object
|
| 104 |
|
|
cldms=cldm
|
| 105 |
|
|
coordinates(cldms)=c("lon","lat")
|
| 106 |
|
|
projection(cldms)=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
|
| 107 |
|
|
|
| 108 |
ddd9a810
|
Adam M. Wilson
|
##make spatial object
|
| 109 |
|
|
cldys=cldy
|
| 110 |
|
|
coordinates(cldys)=c("lon","lat")
|
| 111 |
|
|
projection(cldys)=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
|
| 112 |
|
|
|
| 113 |
710f7456
|
Adam M. Wilson
|
#### Evaluate MOD35 Cloud data
|
| 114 |
9a19743f
|
Adam M. Wilson
|
mod09=brick("~/acrobates/adamw/projects/cloud/data/mod09.nc")
|
| 115 |
99b3508d
|
Adam M. Wilson
|
|
| 116 |
|
|
|
| 117 |
ddd9a810
|
Adam M. Wilson
|
## LULC
|
| 118 |
2bca6aaa
|
Adam M. Wilson
|
#system(paste("gdalwarp -r near -co \"COMPRESS=LZW\" -tr ",paste(res(mod09),collapse=" ",sep=""),
|
| 119 |
|
|
# "-tap -multi -t_srs \"", projection(mod09),"\" /mnt/data/jetzlab/Data/environ/global/landcover/MODIS/MCD12Q1_IGBP_2005_v51.tif ../modis/mod12/MCD12Q1_IGBP_2005_v51.tif"))
|
| 120 |
ddd9a810
|
Adam M. Wilson
|
lulc=raster("../modis/mod12/MCD12Q1_IGBP_2005_v51.tif")
|
| 121 |
9a19743f
|
Adam M. Wilson
|
#lulc=ratify(lulc)
|
| 122 |
ddd9a810
|
Adam M. Wilson
|
require(plotKML); data(worldgrids_pal) #load IGBP palette
|
| 123 |
|
|
IGBP=data.frame(ID=0:16,col=worldgrids_pal$IGBP[-c(18,19)],stringsAsFactors=F)
|
| 124 |
|
|
IGBP$class=rownames(IGBP);rownames(IGBP)=1:nrow(IGBP)
|
| 125 |
|
|
levels(lulc)=list(IGBP)
|
| 126 |
9a19743f
|
Adam M. Wilson
|
#lulc=crop(lulc,mod09)
|
| 127 |
ddd9a810
|
Adam M. Wilson
|
|
| 128 |
99b3508d
|
Adam M. Wilson
|
n=100
|
| 129 |
|
|
at=seq(0,100,length=n)
|
| 130 |
|
|
colr=colorRampPalette(c("black","green","red"))
|
| 131 |
|
|
cols=colr(n)
|
| 132 |
|
|
|
| 133 |
|
|
|
| 134 |
9a19743f
|
Adam M. Wilson
|
hexbinplot(Amt/100~mod09,data=cld[cld$Nobs>100,])+
|
| 135 |
|
|
layer(panel.abline(lm(y~x),col="blue"))+
|
| 136 |
|
|
layer(panel.abline(0,1,col="red"))
|
| 137 |
a6d44f2d
|
Adam M. Wilson
|
|
| 138 |
9a19743f
|
Adam M. Wilson
|
xyplot(Amt/100~mod09,grpups="month",data=cld[cld$Nobs>75,],cex=.2,pch=16)+
|
| 139 |
|
|
layer(panel.abline(lm(y~x),col="blue"))+
|
| 140 |
|
|
# layer(panel.lines(x,predict(lm(y~x),type="prediction")))+
|
| 141 |
|
|
layer(panel.abline(0,1,col="red"))
|
| 142 |
710f7456
|
Adam M. Wilson
|
|
| 143 |
9a19743f
|
Adam M. Wilson
|
xyplot(Amt/100~mod09|month,data=cld[cld$Nobs>75,],cex=.2,pch=16)+
|
| 144 |
|
|
layer(panel.abline(lm(y~x),col="blue"))+
|
| 145 |
|
|
# layer(panel.lines(x,predict(lm(y~x),type="prediction")))+
|
| 146 |
|
|
layer(panel.abline(0,1,col="red"))
|
| 147 |
710f7456
|
Adam M. Wilson
|
|
| 148 |
ddd9a810
|
Adam M. Wilson
|
|
| 149 |
|
|
d$lulc=unlist(extract(lulc,d))
|
| 150 |
|
|
d$lulc_10=unlist(extract(lulc,d,buffer=10000,fun=mode,na.rm=T))
|
| 151 |
|
|
d$lulc=factor(d$lulc,labels=IGBP$class)
|
| 152 |
|
|
|
| 153 |
|
|
save(d,file="annualsummary.Rdata")
|
| 154 |
|
|
|
| 155 |
9a19743f
|
Adam M. Wilson
|
|
| 156 |
|
|
|
| 157 |
|
|
load("annualsummary.Rdata")
|
| 158 |
|
|
|
| 159 |
ddd9a810
|
Adam M. Wilson
|
## quick model to explore fit
|
| 160 |
9a19743f
|
Adam M. Wilson
|
xyplot(cld~mod35c5_10,groups=lulc,data=d@data)
|
| 161 |
|
|
summary(lm(cld~mod35c5_10+as.factor(lulc),data=d@data))
|
| 162 |
|
|
summary(lm(Amt~mod09,data=cld))
|
| 163 |
ddd9a810
|
Adam M. Wilson
|
summary(lm(cld~mod09_10+as.factor(lulc),data=d))
|
| 164 |
|
|
summary(lm(cld~mod09_10+as.factor(lulc),data=d))
|
| 165 |
|
|
|
| 166 |
|
|
### exploratory plots
|
| 167 |
|
|
xyplot(cld~mod09_10,groups=lulc,data=d@data,pch=16,cex=.5)+layer(panel.abline(0,1,col="red"))
|
| 168 |
2bca6aaa
|
Adam M. Wilson
|
xyplot(cld~mod09_10+mod35c5_10|as.factor(lulc),data=d@data,type=c("p","r"),pch=16,cex=.25,auto.key=T)+layer(panel.abline(0,1,col="green"))
|
| 169 |
ddd9a810
|
Adam M. Wilson
|
xyplot(cld~mod35_10|as.factor(lulc),data=d@data,pch=16,cex=.5)+layer(panel.abline(0,1,col="red"))
|
| 170 |
|
|
xyplot(mod35_10~mod09_10|as.factor(lulc),data=d@data,pch=16,cex=.5)+layer(panel.abline(0,1,col="red"))
|
| 171 |
|
|
|
| 172 |
|
|
densityplot(stack(mod35,mod09))
|
| 173 |
|
|
boxplot(mod35,lulc)
|
| 174 |
|
|
|
| 175 |
|
|
bwplot(mod09~mod35|cut(y,5),data=stack(mod09,mod35))
|
| 176 |
|
|
|
| 177 |
710f7456
|
Adam M. Wilson
|
## month factors
|
| 178 |
|
|
cldm$month2=factor(cldm$month,labels=month.name)
|
| 179 |
|
|
## add a color key
|
| 180 |
|
|
breaks=seq(0,100,by=25)
|
| 181 |
|
|
cldm$cut=cut(cldm$cld,breaks)
|
| 182 |
|
|
cp=colorRampPalette(c("blue","orange","red"))
|
| 183 |
|
|
cols=cp(length(at))
|
| 184 |
|
|
|
| 185 |
|
|
## read in global coasts for nice plotting
|
| 186 |
|
|
library(maptools)
|
| 187 |
|
|
|
| 188 |
|
|
data(wrld_simpl)
|
| 189 |
|
|
coast <- unionSpatialPolygons(wrld_simpl, rep("land",nrow(wrld_simpl)), threshold=5)
|
| 190 |
|
|
coast=as(coast,"SpatialLines")
|
| 191 |
|
|
#coast=spTransform(coast,CRS(projection(mod35)))
|
| 192 |
|
|
|
| 193 |
|
|
|
| 194 |
|
|
## write a pdf
|
| 195 |
|
|
#dir.create("output")
|
| 196 |
|
|
pdf("output/NDP026d.pdf",width=11,height=8.5)
|
| 197 |
|
|
|
| 198 |
|
|
## map of stations
|
| 199 |
|
|
xyplot(lat~lon,data=st,pch=16,cex=.5,col="black",auto.key=T,
|
| 200 |
|
|
main="NDP-026D Cloud Climatology Stations",ylab="Latitude",xlab="Longitude")+
|
| 201 |
|
|
layer(sp.lines(coast,col="grey"),under=T)
|
| 202 |
|
|
|
| 203 |
|
|
xyplot(lat~lon|month2,groups=cut,data=cldm,pch=".",cex=.2,auto.key=T,
|
| 204 |
|
|
main="Mean Monthly Cloud Coverage",ylab="Latitude",xlab="Longitude",
|
| 205 |
|
|
par.settings = list(superpose.symbol= list(pch=16,col=c("blue","green","yellow","red"))))+
|
| 206 |
|
|
layer(sp.lines(coast,col="grey"),under=T)
|
| 207 |
|
|
|
| 208 |
|
|
|
| 209 |
|
|
## Validation
|
| 210 |
|
|
m=10
|
| 211 |
|
|
zlim=c(40,100)
|
| 212 |
|
|
dr=subset(mod35,subset=m);projection(dr)=projection(mod35)
|
| 213 |
|
|
ds=cldms[cldms$month==m,]
|
| 214 |
|
|
plot(dr,col=cp(100),zlim=zlim,main="Comparison of MOD35 Cloud Frequency and NDP-026D Station Cloud Climatologies",
|
| 215 |
|
|
ylab="Northing (m)",xlab="Easting (m)",sub="MOD35 is proportion of cloudy days, while NDP-026D is Mean Cloud Coverage")
|
| 216 |
|
|
plot(ds,add=T,pch=21,cex=3,lwd=2,fg="black",bg=as.character(cut(ds$cld,breaks=seq(zlim[1],zlim[2],len=5),labels=cp(4))))
|
| 217 |
|
|
#legend("topright",legend=seq(zlim[1],zlim[2],len=5),pch=16,col=cp(length(breaks)))
|
| 218 |
|
|
|
| 219 |
|
|
|
| 220 |
|
|
xyplot(mod35~cld,data=mod35v,subscripts=T,auto.key=T,panel=function(x,y,subscripts){
|
| 221 |
|
|
td=mod35v[subscripts,]
|
| 222 |
|
|
# panel.segments(x-td$cldsd[subscripts],y,x+td$cldsd[subscripts],y,subscripts=subscripts)
|
| 223 |
|
|
panel.xyplot(x,y,subscripts=subscripts,type=c("p","smooth"),pch=16,col="black")
|
| 224 |
|
|
# panel.segments(x-td$cldsd[subscripts],y,x+td$cldsd[subscripts],y,subscripts=subscripts)
|
| 225 |
|
|
},ylab="MOD35 Proportion Cloudy Days",xlab="NDP-026D Mean Monthly Cloud Amount",
|
| 226 |
|
|
main="Comparison of MOD35 Cloud Mask and Station Cloud Climatologies")
|
| 227 |
|
|
|
| 228 |
|
|
#xyplot(mod35~cld|month,data=mod35v,subscripts=T,auto.key=T,panel=function(x,y,subscripts){
|
| 229 |
|
|
# td=mod35v[subscripts,]
|
| 230 |
|
|
# panel.segments(x-td$cldsd[subscripts],y,x+td$cldsd[subscripts],y,subscripts=subscripts)
|
| 231 |
|
|
# panel.xyplot(x,y,subscripts=subscripts,type=c("p","smooth"),pch=16,col="black")
|
| 232 |
|
|
# panel.segments(x-td$cldsd[subscripts],y,x+td$cldsd[subscripts],y,subscripts=subscripts)
|
| 233 |
|
|
# },ylab="MOD35 Proportion Cloudy Days",xlab="NDP-026D Mean Monthly Cloud Amount",
|
| 234 |
|
|
# main="Comparison of MOD35 Cloud Mask and Station Cloud Climatologies")
|
| 235 |
|
|
|
| 236 |
|
|
|
| 237 |
|
|
dev.off()
|
| 238 |
|
|
|
| 239 |
|
|
graphics.off()
|
