Revision e9998467
Added by Benoit Parmentier about 12 years ago
| climate/research/oregon/interpolation/methods_comparison_assessment_part5.R | ||
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##################################### METHODS COMPARISON part 5 ########################################## |
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#################################### Spatial Analysis ############################################ |
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#This script utilizes the R ojbects created during the interpolation phase. # |
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#At this stage the script produces figures of various accuracy metrics and compare methods: # |
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#This scripts focuses on a detailed studay of differences in the predictions of CAI_kr and FUsion_Kr # |
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#This scripts focuses on a detailed study of differences in the predictions of CAI_kr and FUsion_Kr |
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#Differences are examined through: |
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#1) per land cover classes |
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#2) per elevation classes |
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#3) through spiatial transects |
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# |
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#Note this code is for exploratory analyses so some sections are not succinct and |
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#can be improve for repeatability and clarity. |
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#AUTHOR: Benoit Parmentier # |
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#DATE: 11/23/2012 #
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#DATE: 12/04/2012 #
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#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#491 -- # |
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################################################################################################### |
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| ... | ... | |
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infile6<-"OR83M_state_outline.shp" |
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#stat_loc<-read.table(paste(path,"/","location_study_area_OR_0602012.txt",sep=""),sep=",", header=TRUE) |
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out_prefix<-"methods_11292012_"
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out_prefix<-"methods_comp5_12042012_"
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nb_transect<-4 |
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##### LOAD USEFUL DATA |
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#obj_list<-"list_obj_08262012.txt" #Results of fusion from the run on ATLAS |
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path<-"/home/parmentier/Data/IPLANT_project/methods_interpolation_comparison_10242012" #Jupiter LOCATION on Atlas for kriging #Jupiter Location on XANDERS |
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path_wd<-"/home/parmentier/Data/IPLANT_project/methods_interpolation_comparison_10242012" #Jupiter LOCATION on Atlas for kriging #Jupiter Location on XANDERS
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#path<-"/Users/benoitparmentier/Dropbox/Data/NCEAS/Oregon_covariates/" #Local dropbox folder on Benoit's laptop |
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setwd(path) |
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setwd(path_wd) |
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path_data_cai<-"/home/parmentier/Data/IPLANT_project/data_Oregon_stations_10242012_CAI" #Change to constant |
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path_data_fus<-"/home/parmentier/Data/IPLANT_project/data_Oregon_stations_10242012_GAM" |
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#list files that contain model objects and ratingin-testing information for CAI and Fusion |
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obj_mod_fus_name<-"results_mod_obj__365d_GAM_fusion_const_all_lstd_11022012.RData" |
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obj_mod_cai_name<-"results_mod_obj__365d_GAM_CAI2_const_all_10312012.RData" |
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gam_fus<-load_obj(file.path(path_data_fus,obj_mod_fus_name)) |
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gam_cai<-load_obj(file.path(path_data_cai,obj_mod_cai_name)) #This contains all the info |
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sampling_date_list<-gam_fus$sampling_obj$sampling_dat$date |
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### Projection for the current region |
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proj_str="+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"; |
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#User defined output prefix |
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### MAKE THIS A FUNCTION TO LOAD STACK AND DEFINE VALID RANGE... |
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#CRS<-proj4string(ghcn) #Storing projection information (ellipsoid, datum,etc.) |
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lines<-read.table(paste(path,"/",inlistf,sep=""), sep="") #Column 1 contains the names of raster files |
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inlistvar<-lines[,1] |
| ... | ... | |
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avg_elev_rec_forest<-zonal(rast_diff,zones=elev_rec_forest,stat="mean",na.rm=TRUE) |
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std_elev_rec_forest<-zonal(rast_diff,zones=elev_rec_forest,stat="sd",na.rm=TRUE) |
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## CREATE plots |
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X11() |
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plot(avg_elev_rec[,1],avg_elev_rec[,2],type="b",ylim=c(-10,1), |
| ... | ... | |
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} |
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################################################################### |
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################ TRANSECT THROUGH THE IMAGE: #################### |
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################ SPATIAL TRANSECT THROUGH THE IMAGE: ####################
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#select date |
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dates<-c("20100103","20100901")
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j=1
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#j=2
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for (j in 1:length(dates)){
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#Read predicted tmax raster surface and modeling information |
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date_selected<-dates[j] |
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oldpath<-getwd() |
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setwd(path_data_cai) |
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file_pat<-glob2rx(paste("*tmax_predicted*",date_selected,"*_365d_GAM_CAI2_const_all_10312012.rst",sep="")) #Search for files in relation to fusion
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| ... | ... | |
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rast_fus_pred<-raster(rast_fus1c,1) |
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rast_cai_pred<-raster(rast_cai2c,1) |
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rast_diff_fc<-rast_fus_pred-rast_cai_pred |
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#Read in data_s and data_v |
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k<-match(date_selected,sampling_date_list) |
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names(gam_fus$gam_fus_mod[[k]]) #Show the name structure of the object/list |
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#Extract the training and testing information for the given date... |
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data_sf<-gam_fus$gam_fus_mod[[k]]$data_s #object for the first date...20100103 #Make this a function?? |
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data_vf<-gam_fus$gam_fus_mod[[k]]$data_v #object for the first date...20100103 |
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data_sc<-gam_cai$gam_CAI_mod[[k]]$data_s #object for the first date...20100103 |
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data_vc<-gam_cai$gam_CAI_mod[[k]]$data_v #object for the first date...20100103 |
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### CREATE A NEW TRANSECT BASED ON LOCATION OF SPECIFIED STATIONS |
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| ... | ... | |
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data_vf$training<-rep(0,nrow(data_vf)) |
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data_sf$training<-rep(1,nrow(data_sf)) |
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data_stat<-rbind(data_vf[,c("id","training")],data_sf[,c("id","training")])
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data_stat<-rbind(data_vf[,c("id","training")],data_sf[,c("id","training")]) #bringing together data_v and data_s
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m<-match(selected_stations,data_stat$id) |
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m<-as.integer(na.omit(m)) |
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trans4_stations<-transect_from_spdf(data_stat,m) |
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point4_stations<-data_stat[m,] |
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#tmp<-as.data.frame(data_stat[1,]) |
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#row.names(tmp)<-rep("X",1)
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#test<-SpatialLinesDataFrame(trans4_stations,data=tmp) |
| ... | ... | |
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list_transect2[[1]]<-c("t1_line.shp",paste("figure_13_tmax_elevation_transect1_OR",date_selected,out_prefix,sep="_"))
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list_transect2[[2]]<-c("t2_line.shp",paste("figure_14_tmax_elevation_transect2_OR",date_selected,out_prefix,sep="_"))
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list_transect2[[3]]<-c("t3_line.shp",paste("figure_15_tmax_elevation_transect3_OR",date_selected,out_prefix,sep="_"))
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list_transect2[[4]]<-c("t4_line.shp",paste("figure_16_tmax_elevation_transect3_OR",date_selected,out_prefix,sep="_"))
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list_transect2[[4]]<-c("t4_line.shp",paste("figure_16_tmax_elevation_transect4_OR",date_selected,out_prefix,sep="_"))
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names(list_transect2)<-c("transect_OR1","transect_OR2","transect_OR3","transect_OR4")
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| ... | ... | |
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trans_data2<-plot_transect_m(list_transect2,rast_pred2,title_plot2,disp=TRUE,m_layers_sc) |
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dev.off() |
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### PLOT LOCATIONS OF STATION ON FIGURES |
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X11(width=18,height=9) |
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trans_elev<-vector("list",nb_transect)
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for (k in 1:nb_transect){
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trans_file<-list_transect[[k]] |
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filename<-sub(".shp","",trans_file) #Removing the extension from file.
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transect<-readOGR(".", filename) #reading shapefile
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trans_elev[[k]]<-extract(ELEV_SRTM,transect) |
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y<-as.numeric(trans_elev[[k]][[1]]) |
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elev_y<-y |
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x<-1:length(y) |
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plot(x,y,type="l", ylab="Elevation (in meters)",xlab="Transect position (in km)") |
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data_y<-(trans_data[[k]][[1]]) # data for the first transect |
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#as.data.frame(data_y) |
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par(new=TRUE) # key: ask for new plot without erasing old |
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y<-data_y[,1] |
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x <- 1:length(y) |
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fus_y<-y |
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plot(x,y,type="l",col="red",axes=F) #plotting fusion profile |
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axis(4,xlab="",ylab="tmax (in degree C)") |
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y<-data_y[,2] |
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cai_y<-y |
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lines(x,y,col="green") |
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#title(title_plot[i])) |
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legend("topleft",legend=c("elev","fus","CAI"),
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cex=1.2, col=c("black","red","green"),
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data_stat<-rbind(data_vf[,c("id","training")],data_sf[,c("id","training")]) #bringing together data_v and data_s
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m<-match(selected_stations,data_stat$id) |
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m<-as.integer(na.omit(m)) |
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trans4_stations<-transect_from_spdf(data_stat,m) |
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point4_stations<-data_stat[m,] |
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pos<-match(c("x_OR83M","y_OR83M"),layerNames(s_raster)) #Find column with name "value"
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xy_stack<-subset(s_raster,pos) #Select multiple layers from the stack |
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r_stack<-stack(xy_stack, rast_pred2) |
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trans4_data<-extract(r_stack,trans4_stations,cellnumbers=TRUE) #This extracts a list |
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trans4_data<-as.data.frame(trans4_data[[1]]) |
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point4_cellID<-cellFromXY(r_stack,coordinates(point4_stations)) #This contains the cell ID the points |
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pos<-match(point4_cellID,trans4_data$cell) |
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#Plots lines where there are stations... |
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X11(width=18,height=9) |
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y<-trans4_data$fus |
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x <- 1:length(y) |
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plot(x,y,type="l",col="red", #plotting fusion profile |
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,xlab="",ylab="tmax (in degree C)") |
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y<-trans4_data$CAI |
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lines(x,y,col="green") |
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abline(v=pos)#addlines whtere the stations area... |
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#plot(elev) |
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#title(title_plot[i])) |
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legend("topleft",legend=c("fus","CAI"),
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cex=1.2, col=c("red","green"),
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lty=1) |
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savePlot(paste("fig17_transect_path_tmax_diff_CAI_fusion_",date_selected,out_prefix,".png", sep=""), type="png")
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y<-trans4_data$fus[1:150] |
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x <- 1:150 |
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plot(x,y,type="l",col="red", #plotting fusion profile |
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,xlab="",ylab="tmax (in degree C)") |
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y<-trans4_data$CAI[1:150] |
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lines(x,y,col="green") |
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abline(v=pos)#addlines whtere the stations area... |
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#plot(elev) |
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#title(title_plot[i])) |
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legend("topleft",legend=c("fus","CAI"),
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cex=1.2, col=c("red","green"),
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lty=1) |
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savePlot(file=paste(list_transect[[k]][2],".png",sep=""),type="png") |
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cor(fus_y,elev_y) |
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cor(cai_y,elev_y) |
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cor(fus_y,cai_y) |
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} |
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dev.off |
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savePlot(paste("fig18a_transect_path_tmax_diff_CAI_fusion_",date_selected,out_prefix,".png", sep=""), type="png")
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y<-trans4_data$fus[151:300] |
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x <- 151:300 |
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plot(x,y,type="l",col="red", #plotting fusion profile |
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,xlab="",ylab="tmax (in degree C)") |
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y<-trans4_data$CAI[151:300] |
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lines(x,y,col="green") |
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abline(v=pos)#addlines whtere the stations area... |
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#plot(elev) |
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#title(title_plot[i])) |
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legend("topleft",legend=c("fus","CAI"),
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cex=1.2, col=c("red","green"),
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lty=1) |
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savePlot(paste("fig18b_transect_path_tmax_diff_CAI_fusion_",date_selected,out_prefix,".png", sep=""), type="png")
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dev.off() |
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#cor(fus_y,elev_y) |
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#cor(cai_y,elev_y) |
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#cor(fus_y,cai_y) |
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} |
Also available in: Unified diff
Methods comp part5-task#491- residuals analyses, spatial transect through stations with diff and elevation