Revision 2ba35352
Added by Benoit Parmentier over 11 years ago
| climate/research/oregon/interpolation/results_covariates_database_stations_output_analyses.R | ||
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#Part 1: Script produces summary information about stations used in the interpolation |
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#Part 2: Script produces plots of input covariates for study region |
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#AUTHOR: Benoit Parmentier |
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#DATE: 03/27/2013
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#DATE: 04/01/2013
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#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#???-- |
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#5) monthly_query_ghcn_data: ghcn daily data from monthly query before application of quality flag |
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#6) monthly_covar_ghcn_data: ghcn monthly averaged data with covariates for the year range of interpolation (locally projected) |
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#7) var |
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#8) range_years |
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#9) range_years_clim |
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#8) infile_covariate: s_raster brick file |
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#9) covar_names: variable mames |
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#10) raster_prediction |
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#12) region_outline |
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#13) out_prefix |
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#list_param <-list_outfiles$loc_stations |
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#list_param <-list_outfiles$loc_stations_ghcn |
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#list_param <-list_outfiles$loc_stations_ghcn_data |
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#list_param <-list_outfiles$loc_stations |
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#list_param <-list_outfiles$loc_stations |
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## Functions used in the script |
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load_obj <- function(f) |
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} |
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extract_number_obs<-function(list_param){
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#Function to extract the number of observations used in modeling |
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method_mod_obj<-list_param$method_mod_obj |
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#Change to results_mod_obj[[i]]$data_s to make it less specific |
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lapply(1:length(method_obj),function(k) nrow(method_mod_obj[[k]]$data_s)) |
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lapply(1:length(method_obj),function(k) nrow(method_mod_obj[[k]]$data_v)) |
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lapply(1:length(clim_obj),function(k) nrow(method_mod_obj[[k]]$data_month)) |
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#Change to results_mod_obj[[i]]$data_s to make it less specific!!!! |
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#number of observations |
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list_nrow_data_s<-lapply(1:length(method_obj),function(k) nrow(method_mod_obj[[k]]$data_s)) |
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list_nrow_data_v<-lapply(1:length(method_obj),function(k) nrow(method_mod_obj[[k]]$data_v)) |
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#lapply(1:length(clim_obj),function(k) nrow(method_mod_obj[[k]]$data_month)) |
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list_nrow_data_month<-lapply(1:length(gamclim_fus_mod),function(k) nrow(gamclim_fus_mod[[k]]$data_month)) |
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#number of valid observations |
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list_nrow_valid_data_s<-lapply(1:length(method_obj),function(k) length(method_mod_obj[[k]]$data_s$[[y_var_name]]) |
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list_nrow_data_v<-lapply(1:length(method_obj),function(k) length(method_mod_obj[[k]]$data_v$[[y_var_name]]) |
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list_nrow_valid_data_month<-lapply(1:length(gamclim_fus_mod),function(k) length(gamclim_fus_mod[[k]]$data_month$y_var)) |
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c1<-do.call(rbind,list_nrow_data_s) |
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c2<-do.call(rbind,list_nrow_data_v) |
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c3<-do.call(rbind,list_nrow_data_month) |
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return() |
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c1v<-do.call(rbind,list_valid_nrow_data_s) |
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c2v<-do.call(rbind,list_valid_nrow_data_v) |
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c3v<-do.call(rbind,list_valid_nrow_data_month) |
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n_data_s<-cbdind(c1,c1v) |
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n_data_v<-cbdind(c2,c2v) |
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n_data_month<-cbdind(c3,c3vv) |
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list_observations<-list(n_data_s,n_data_v,n_data_month) |
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return(list_observations) |
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} |
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########################################################################### |
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########################## BEGIN SCRIPT/FUNCTION ########################## |
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######################################## |
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#### STEP 1: read in data |
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#Stations in the processing region/study area |
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stat_reg <- readOGR(dsn=dirname(list_outfiles$loc_stations),sub(".shp","",basename(list_outfiles$loc_stations)))
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data_reg <- readOGR(dsn=dirname(list_outfiles$loc_stations_ghcn),sub(".shp","",basename(list_outfiles$loc_stations_ghcn)))
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#Stations available before screening the data query: ghcn daily data for the year range of interpolation |
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data_d <- readOGR(dsn=dirname(list_outfiles$loc_stations_ghcn),sub(".shp","",basename(list_outfiles$loc_stations_ghcn)))
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#Stations available after screening the data query: ghcn daily data for the year range of interpolation |
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data_reg <- readOGR(dsn=dirname(list_outfiles$daily_query_ghcn_data),sub(".shp","",basename(list_outfiles$daily_query_ghcn_data)))
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#Covariates data available after screening:ghcn daily data with covariates for the year range of interpolation |
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data_RST_SDF <-readOGR(dsn=dirname(list_outfiles$daily_covar_ghcn_data),sub(".shp","",basename(list_outfiles$daily_covar_ghcn_data)))
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#Stations before screening monthly_query_ghcn_data: ghcn daily data from monthly query before application of quality flag |
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data_m <- readOGR(dsn=dirname(list_outfiles$monthly_query_ghcn_data),sub(".shp","",basename(list_outfiles$monthly_query_ghcn_data)))
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#Stations after screening monthly_query_ghcn_data, extraction of covariates and monthly averages |
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dst<-readOGR(dsn=dirname(list_outfiles$monthly_covar_ghcn_data),sub(".shp","",basename(list_outfiles$monthly_covar_ghcn_data)))
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### Load data used in fitting the model at monthly scale... |
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data_month<-gamclim_fus_mod[[1]]$data_month |
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list_data_month<-lapply(1:length(gamclim_fus_mod),function(k) gamclim_fus_mod[[k]]$data_month) |
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#Loading covariates raster images |
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s_raster<-brick(infile_covariates) |
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names(s_raster)<-covar_names |
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rast_ref<-subset(s_raster,"mm_01") # mean month for January |
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######## PART I |
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names(raster_prediction_obj) |
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var<-list_param$var |
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raster_prediction_obj<-load_obj(list_param$raster_prediction_obj) |
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#method_mod_obj<-raster_prediction_obj$method_mod_obj |
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method_mod_obj<-raster_prediction_obj$gam_fus_mod #change later for any model type |
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#validation_obj<-raster_prediction_obj$validation_obj |
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validation_obj<-raster_prediction_obj$gam_fus_validation_mod #change later for any model type |
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#clim_obj<-raster_prediction_obj$clim_obj |
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clim_obj<-raster_prediction_obj$gamclim_fus_mod #change later for any model type |
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names(raster_prediction_obj$method_obj[[1]]) |
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data_s<-validation_obj[[1]]$data_s |
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summary_data_v<-validation_obj[[1]]$summary_data_v |
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names(validation_obj[[1]]) |
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################################################################### |
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######## PART I: Script produces summary information about stations used in the interpolation ######## |
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### Figue 1: stations in the study area/processing tile |
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png(paste("Total_number_of_stations_in_study_area_",out_prefix,".png", sep=""))
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plot(rast_ref) |
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plot(stat_reg,add=TRUE) |
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nb_point1<-paste("n_station=",length(stat_reg$STAT_ID))
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#Add the number of data points on the plot |
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title("Stations located in the study area")
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legend("topleft",legend=c(nb_point1),bty="n",cex=1.2)
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dev.off() |
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#add number of stations+ name of region |
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#title() |
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### Figue 2: stations in the study area/processing tile: from query without flag screening |
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png(paste("Studay_area_",out_prefix,".png", sep=""))
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png(paste("Stations_for_range_",range_years[1],"_",range_years[2],"_no_screening",out_prefix,".png", sep=""))
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plot(rast_ref) |
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plot(data_d, add=TRUE) |
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nb_point<-paste("ns=",length(data_d$TMax),sep="")
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nb_point2<-paste("ns_obs=",length(data_s$TMax)-sum(is.na(data_s[[y_var_name]])),sep="")
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nb_point3<-paste("n_month=",length(data_month$TMax),sep="")
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nb_point<-paste("nrow=",nrow(data_d),sep="")
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nb_point2<-paste("ns_stations=",length(unique(data_d$station)),sep="")
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#Add the number of data points on the plot |
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legend("topleft",legend=c(nb_point,nb_point2,nb_point3),bty="n",cex=0.8)
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legend("topleft",legend=c(nb_point,nb_point2),bty="n",cex=1)
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title(paste("Stations available for year ",range_years[1],sep=""))
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dev.off() |
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### Figue 3: stations in the study area/processing tile: after screening |
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### Figue 3: stations in the study area/processing tile: after screening |
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png(paste("Stations_for_range_",range_years[1],"_",range_years[2],"_after_screening",out_prefix,".png", sep=""))
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plot(rast_ref) |
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plot(data_reg,add=TRUE) |
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nb_point<-paste("nrow=",nrow(data_reg),sep="")
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nb_point2<-paste("ns_stations=",length(unique(data_reg$station)),sep="")
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#Add the number of data points on the plot |
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legend("topleft",legend=c(nb_point,nb_point2),bty="n",cex=1)
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title(paste("Stations available for year ",range_years[1]," after screening",sep=""))
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#Add the number of data points on the plot |
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dev.off() |
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### Figue 4: stations in the study area/processing tile: from monthly climatology query without flag screening |
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### Figue 4: stations in the study area/processing tile: after screening and covar extraction |
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png(paste("Stations_for_range_",range_years[1],"_",range_years[2],"_after_screening",out_prefix,".png", sep=""))
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plot(rast_ref) |
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plot(data_RST_SDF,add=TRUE) |
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### Figue 5: stations in the study area/processing tile: after screening |
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nb_point<-paste("nrow=",nrow(data_RST_SDF),sep="")
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nb_point2<-paste("ns_stations=",length(unique(data_RST_SDF$station)),sep="")
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#Add the number of data points on the plot |
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legend("topleft",legend=c(nb_point,nb_point2),bty="n",cex=1)
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title(paste("Stations year ",range_years[1]," after screening and covar extraction",sep=""))
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#Add the number of data points on the plot |
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dev.off() |
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### Figue 5: stations in the study area/processing tile: monthly query for specified range of years before screening |
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png(paste("Stations_monthly_for_range_",range_years[1],"_",range_years[2],"_before_screening",out_prefix,".png", sep=""))
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plot(rast_ref) |
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plot(data_m,add=TRUE) |
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nb_point<-paste("nrow=",nrow(data_m),sep="")
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nb_point2<-paste("ns_stations=",length(unique(data_m$station)),sep="")
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#Add the number of data points on the plot |
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legend("topleft",legend=c(nb_point,nb_point2),bty="n",cex=1)
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title(paste("Stations ",range_years[1],"-",range_years[2]," after screening and covar extraction",sep=""))
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#Add the number of data points on the plot |
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dev.off() |
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### Figue 6: histogram |
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#plot(dst) |
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#dst$nobs_station |
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png(paste("Stations_data_month_modeled_for_range_",range_years_clim[1],"_",range_years_clim[2],out_prefix,".png", sep=""))
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dst$nobs_station<-dst$nbs_stt |
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hist(dst$nobs_station) |
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dev.off() |
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### Figue 7: LST and TMax |
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### Figure 7: data month |
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png(paste("Stations_data_month_modeled_for_range_",range_years_clim[1],"_",range_years_clim[2],out_prefix,".png", sep=""))
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par(mfrow=c(3,4)) |
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for (j in 1:12){
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data_month<-list_data_month[[j]] |
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plot(rast_ref) |
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plot(data_month,add=TRUE) |
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nb_point<-paste("nrow=",nrow(data_month),sep="")
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nb_point2<-paste("ns_stations=",length(unique(data_month$station)),sep="")
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nb_point3<-paste("ns_non_na_stations=",length(unique(data_month$y_var)),sep="")
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#Add the number of data points on the plot |
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legend("topleft",legend=c(nb_point,nb_point2,nb_point3),bty="n",cex=0.9)
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title(paste("Stations ",range_years_clim[1],"-",range_years_clim[2]," used for modeling on ",sep=""))
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#data_NA<-subset(data=data_month,is.na(data_month$y_var)) |
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data_NA<-data_month[is.na(data_month$y_var),] |
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plot(data_NA,add=TRUE,pch=2,col=c("red"))
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legend("topright",legend=c("NA value"),pch=2,col=c("red"),bty="n",cex=0.9)
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} |
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dev.off() |
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### Figue 8: LST and TMax |
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names_tmp<-c("mm_01","mm_02","mm_03","mm_04","mm_05","mm_06","mm_07","mm_08","mm_09","mm_10","mm_11","mm_12")
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LST_s<-subset(s_raster,names_tmp) |
| ... | ... | |
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names_tmp<-c("nobs_01","nobs_02","nobs_03","nobs_04","nobs_05","nobs_06","nobs_07","nobs_08",
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"nobs_09","nobs_10","nobs_11","nobs_12") |
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LST_nobs<-subset(s_raster,names_tmp) |
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## Function...note differnces in patternin agricultural areas |
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list_statistic_values_LST_s<-mclapply(c("min","max","mean","sd"),FUN=cellStats,x=LST_s,mc.preschedule=FALSE,mc.cores = 4)
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list_statistic_values_LST_nobs<-mclapply(c("min","max","mean","sd"),FUN=cellStats,x=LST_nobs,mc.preschedule=FALSE,mc.cores = 4)
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LSTnobs_stat_data<-as.data.frame(statistics_LSTnobs_s) |
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names(LSTnobs_stat_data)<-c("min","max","mean","sd")
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# X11(width=12,height=12) |
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# #Plot statiscs (mean,min,max) for monthly LST images |
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png(paste("Stations_data_month_modeled_for_range_",range_years_clim[1],"_",range_years_clim[2],out_prefix,".png", sep=""))
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plot(1:12,LST_stat_data$mean,type="b",ylim=c(-15,70),col="black",xlab="month",ylab="tmax (degree C)") |
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lines(1:12,LST_stat_data$min,type="b",col="blue") |
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lines(1:12,LST_stat_data$max,type="b",col="red") |
| ... | ... | |
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lty=1,lwd=1.4,bty="n") |
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title(paste("LST statistics for Study area",sep=" "))
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# savePlot("lst_statistics_OR.png",type="png")
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#### Fig8...##### |
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dev.off() |
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#### Fig9...##### |
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# #Plot number of valid observations for LST |
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png(paste("Stations_data_month_modeled_for_range_",range_years_clim[1],"_",range_years_clim[2],out_prefix,".png", sep=""))
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plot(1:12,LSTnobs_stat_data$mean,type="b",ylim=c(0,280),col="black",xlab="month",ylab="tmax (degree C)") |
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lines(1:12,LSTnobs_stat_data$min,type="b",col="blue") |
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lines(1:12,LSTnobs_stat_data$max,type="b",col="red") |
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text(1:12,LSTnobs_stat_data$mean,rownames(LSTnobs_stat_data),cex=1,pos=2) |
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# |
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legend("topleft",legend=c("min","mean","max"), cex=1.5, col=c("blue","black","red"),lty=1)
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title(paste("LST number of valid observations for Oregon", "2010",sep=" "))
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| 155 | 249 |
# savePlot("lst_nobs_OR.png",type="png")
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# |
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#### Fig 9...##### |
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dev.off() |
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#### Fig 10...##### |
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#Use data_month!!! |
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d_month<-aggregate(TMax~month, data=dst, mean) #Calculate monthly mean for every station in OR |
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d_month<-aggregate(TMax~month, data=dst, length) #Calculate monthly mean for every station in OR |
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| ... | ... | |
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# |
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### MAP3: Majority land cover for every pixels in the study region |
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#Add barplot of majority map... |
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###Map 4: Elevation and LST in January |
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# tmp_s<-stack(LST,elev_1) |
Also available in: Unified diff
results stations and covar outputs modifications