Revision b4a28e3d
Added by Benoit Parmentier over 10 years ago
| climate/research/oregon/interpolation/global_run_scalingup_assessment_part1.R | ||
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#Part 1 create summary tables and inputs for figure in part 2 and part 3. |
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#AUTHOR: Benoit Parmentier |
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#CREATED ON: 03/23/2014 |
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#MODIFIED ON: 06/27/2014
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#MODIFIED ON: 08/14/2014
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#Version: 3 |
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#PROJECT: Environmental Layers project |
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#TO DO: |
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# - generate data_s and data_v inputs as giant table |
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# - generate accuracy for mosaic (part 2 and part3) |
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# - clean up |
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#First source file: |
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#source /nobackupp4/aguzman4/climateLayers/sharedModules/etc/environ.sh |
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################################################################################################# |
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### Loading R library and packages |
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#### FUNCTION USED IN SCRIPT |
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function_analyses_paper1 <-"contribution_of_covariates_paper_interpolation_functions_05212014.R" #first interp paper
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function_analyses_paper2 <-"multi_timescales_paper_interpolation_functions_05052014.R"
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function_analyses_paper1 <-"contribution_of_covariates_paper_interpolation_functions_07182014.R" #first interp paper
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function_analyses_paper2 <-"multi_timescales_paper_interpolation_functions_08132014.R"
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load_obj <- function(f) |
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{
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#### Parameters and constants |
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#in_dir1 <- "/data/project/layers/commons/NEX_data/test_run1_03232014/output" #On Atlas |
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in_dir1 <- "/nobackupp4/aguzman4/climateLayers/output10Deg/reg1/" #On NEX |
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#in_dir1 <- "/nobackupp4/aguzman4/climateLayers/output10Deg/reg1/" #On NEX |
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in_dir1 <- "/nobackupp4/aguzman4/climateLayers/output20Deg/" |
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#/nobackupp4/aguzman4/climateLayers/output20Deg/reg5/20.0_0.0/ |
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#/nobackupp4/aguzman4/climateLayers/output20Deg/reg3/-20.0_-70.0/ |
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#/nobackupp4/aguzman4/climateLayers/output20Deg/reg5/20.0_30.0/ |
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#/nobackupp4/aguzman4/climateLayers/output20Deg/reg4/40.0_0.0/ |
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#/nobackupp4/aguzman4/climateLayers/output20Deg/reg5/20.0_-10.0/ |
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#/nobackupp4/aguzman4/climateLayers/output20Deg/reg4/50.0_0.0/ |
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#/nobackupp4/aguzman4/climateLayers/output20Deg/reg6/60.0_40.0/ |
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#/nobackupp4/aguzman4/climateLayers/output20Deg/reg6/30.0_40.0/ |
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#/nobackupp4/aguzman4/climateLayers/output10Deg/reg1/finished.txt |
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in_dir_list <- list.dirs(path=in_dir1,recursive=FALSE) #get the list of directories with resutls by 10x10 degree tiles |
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#in_dir_list <- list.dirs(path=in_dir1,recursive=FALSE) #get the list of directories with resutls by 10x10 degree tiles |
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in_dir_list <- c("/nobackupp4/aguzman4/climateLayers/output20Deg/reg5/20.0_0.0/",
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg3/-20.0_-70.0/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg5/20.0_30.0/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg4/40.0_0.0/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg5/20.0_-10.0/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg4/50.0_0.0/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg6/60.0_40.0/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg6/30.0_40.0/") |
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#use subset for now: |
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#in_dir_list <- c( |
| ... | ... | |
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#in_dir_list <- file.path(in_dir1,read.table(file.path(in_dir1,"processed.txt"))$V1) |
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#in_dir_list <- as.list(in_dir_list[-1]) |
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#in_dir_list <- in_dir_list[grep("bak",basename(basename(in_dir_list)),invert=TRUE)] #the first one is the in_dir1
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#in_dir_shp <- in_dir_list[grep("shapefiles",basename(in_dir_list),invert=FALSE)] #select directory with shapefiles...
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in_dir_shp <- "/nobackupp4/aguzman4/climateLayers/output10Deg/reg1/subset/shapefiles/" |
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in_dir_shp_list <- list.files(in_dir_shp,".shp") |
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in_dir_shp <- in_dir_list[grep("shapefiles",basename(in_dir_list),invert=FALSE)] #select directory with shapefiles...
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in_dir_shp <- c( |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg3/subset/shapefiles/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg5/subset/shapefiles/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg4/subset/shapefiles/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg5/subset/shapefiles/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg4/subset/shapefiles/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg6/subset/shapefiles/", |
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"/nobackupp4/aguzman4/climateLayers/output20Deg/reg6/subset/shapefiles/") |
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#in_dir_shp <- "/nobackupp4/aguzman4/climateLayers/output10Deg/reg1/subset/shapefiles/" |
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#in_dir_shp <- "/nobackupp4/aguzman4/climateLayers/output20Deg/reg2/subset/shapefiles" |
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in_dir_shp_list <- list.files(in_dir_shp,".shp",full.names=T) |
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#in_dir_list <- in_dir_list[grep("shapefiles",basename(in_dir_list),invert=TRUE)]
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#the first one is the in_dir1 |
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# the last directory contains shapefiles |
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y_var_name <- "dailyTmax" |
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interpolation_method <- c("gam_CAI")
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out_prefix<-"run3_global_analyses_06192014"
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out_prefix<-"run4_global_analyses_08142014"
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#out_dir<-"/data/project/layers/commons/NEX_data/" #On NCEAS Atlas |
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out_dir <- "/nobackup/bparmen1/" #on NEX |
| ... | ... | |
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lf_covar_obj <- lapply(in_dir_list,FUN=function(x){list.files(path=x,pattern="covar_obj.*.RData",full.names=T)})
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lf_covar_tif <- lapply(in_dir_list,FUN=function(x){list.files(path=x,pattern="covar.*.tif",full.names=T)})
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lf_diagnostic_obj <- lapply(in_dir_list,FUN=function(x){list.files(path=x,pattern="diagnostic.*.RData",full.names=T)})
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########################## START SCRIPT ############################## |
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|
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###################################################### |
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####### PART 4: Get shapefile tiling with centroids ### |
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#in_dir_shp <- "/nobackupp4/aguzman4/climateLayers/output4/subset/shapefiles/" |
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#get shape files for the region being assessed: |
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list_shp_global_tiles_files <- list.files(path=in_dir_shp,pattern="*.shp") |
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l_shp<-lapply(1:length(in_dir_shp_list),FUN=function(i){paste(strsplit(in_dir_shp_list[i],"_")[[1]][2:3],collapse="_")})
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list_shp_global_tiles_files <- l_shp |
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pattern_str <- basename(in_dir_list) |
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list_shp_global_tiles_files |
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list_shp_reg_files <- lapply(pattern_str,function(x){list_shp_global_tiles_files[grep(x,invert=FALSE,list_shp_global_tiles_files)]}) #select directory with shapefiles...
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df_tile_processed$shp_files <- unlist(list_shp_reg_files) |
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list_shp_world <- list.files(path=in_dir_shp,pattern=".*.shp",full.names=T) |
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l_shp <- unlist(lapply(1:length(list_shp_world),FUN=function(i){paste(strsplit(list_shp_world[i],"_")[[1]][2:3],collapse="_")}))
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matching_index <- match(basename(in_dir_list),l_shp) |
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list_shp_reg_files <- list_shp_world[matching_index] |
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df_tile_processed$shp_files <-list_shp_world[matching_index] |
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tx<-strsplit(as.character(df_tile_processed$tile_coord),"_") |
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lat<- as.numeric(lapply(1:length(tx),function(i,x){x[[i]][1]},x=tx))
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| ... | ... | |
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df_tile_processed$lat <- lat |
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df_tile_processed$lon <- long |
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list_shp_world <- list.files(in_dir_shp,".shp") |
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l_shp <- unlist(lapply(1:length(list_shp_world),FUN=function(i){paste(strsplit(list_shp_world[i],"_")[[1]][2:3],collapse="_")}))
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list_shp_reg_files <- as.character(df_tile_processed$tile_coord) |
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#matching_index <- match(l_shp,list_shp_reg_files) |
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matching_index <- match(list_shp_reg_files,l_shp) |
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df_tile_processed$shp_files <-list_shp_world[matching_index] |
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df_tile_processed <- na.omit(df_tile_processed) #remove other list of folders irrelevant |
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list_shp_reg_files <- df_tile_processed$shp_files |
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list_shp_reg_files<- file.path(in_dir_shp,list_shp_reg_files) |
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#put that list in the df_processed and also the centroids!! |
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write.table(df_tile_processed, |
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file=file.path(out_dir,paste("df_tile_processed_",out_prefix,".txt",sep="")),sep=",")
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### This assumes the tree structure has been replicated on Atlas: |
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#for i in 1:length(df_tiled_processed$tile_coord) |
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output_atlas_dir <- "/data/project/layers/commons/NEX_data/output_run3_global_analyses_06192014/output10Deg/reg1" |
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#output_atlas_dir <- "/data/project/layers/commons/NEX_data/output_run3_global_analyses_06192014/output10Deg/reg1" |
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output_atlas_dir <- "/data/project/layers/commons/NEX_data/output_run4_global_analyses_08142014/output20Deg" |
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#Make directories on ATLAS |
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#for (i in 1:length(df_tiled_processed$tile_coord)){
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# create_dir_fun(file.path(output_atlas_dir,as.character(df_tiled_processed$tile_coord[i])),out_suffix=NULL) |
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#} |
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#Make directories on ATLAS for shapefiles |
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#for (i in 1:length(df_tiled_processed$tile_coord)){
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# create_dir_fun(file.path(output_atlas_dir,as.character(df_tiled_processed$tile_coord[i]),"/shapefiles"),out_suffix=NULL) |
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#} |
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#Copy summary textfiles and mosaic back to atlas |
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Atlas_dir <- file.path("/data/project/layers/commons/NEX_data/",basename(out_dir))#,"output/subset/shapefiles")
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Atlas_hostname <- "parmentier@atlas.nceas.ucsb.edu" |
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lf_cp_f <- list.files(out_dir,full.names=T)#copy all files can filter later |
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filenames_NEX <- paste(lf_cp_f,collapse=" ") #copy raster prediction object |
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cmd_str <- paste("scp -p",filenames_NEX,paste(Atlas_hostname,Atlas_dir,sep=":"), sep=" ")
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system(cmd_str) |
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#system("scp -p ./*.txt parmentier@atlas.nceas.ucsb.edu:/data/project/layers/commons/NEX_data/output_run2_global_analyses_05122014")
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#system("scp -p ./*.txt ./*.tif parmentier@atlas.nceas.ucsb.edu:/data/project/layers/commons/NEX_data/output_run2_global_analyses_05122014")
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#### COPY SHAPEFILES, TIF MOSAIC, COMBINED TEXT FILES etc... |
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#copy shapefiles defining regions |
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Atlas_dir <- file.path("/data/project/layers/commons/NEX_data/",basename(out_dir),"output/subset/shapefiles")
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Atlas_hostname <- "parmentier@atlas.nceas.ucsb.edu" |
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lf_cp_shp <- df_tile_processed$shp_files #get all the files... |
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#lf_cp_shp <- list.files(in_dir_shp, ".shp",full.names=T) |
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list_tile_scp <- 1:8 |
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for (j in 1:length(list_tile_scp)){
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tile_nb <- list_tile_scp[j] |
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in_dir_tile <-dirname(df_tile_processed$shp_files[tile_nb]) |
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#/data/project/layers/commons/NEX_data/output_run2_05122014/output |
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#output_atlas_dir |
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#Atlas_dir <- file.path(file.path("/data/project/layers/commons/NEX_data/",basename(out_dir),"output"),in_dir_tile)
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Atlas_dir <- file.path(output_atlas_dir,as.character(df_tile_processed$tile_coord[j]),"/shapefiles") |
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Atlas_hostname <- "parmentier@atlas.nceas.ucsb.edu" |
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filenames_NEX <- paste(lf_cp_shp,collapse=" ") #copy raster prediction object |
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cmd_str <- paste("scp -p",filenames_NEX,paste(Atlas_hostname,Atlas_dir,sep=":"), sep=" ")
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system(cmd_str) |
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} |
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#### FIRST COPY DATA FOR SPECIFIC TILES ##### |
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#Copy specific tiles info back...This assumes that the tree structre |
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#has been created on ATLAS: |
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#../$out_dir/ouput/tile_coord |
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list_tile_scp <- c(1,2) |
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#list_tile_scp <- c(1,2) |
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list_tile_scp <- 1:8 |
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for (j in 1:length(list_tile_scp)){
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tile_nb <- list_tile_scp[j] |
| ... | ... | |
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lf_cp_month[[i]] <- unlist(lapply(1:nb_mod,FUN=function(x){lf_clim_tif[[x]][[index]][[tile_nb]]}))
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} |
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##Add RData object for specified tile... |
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lf_cp_RData_tif <- c(lf_covar_obj[tile_nb],lf_covar_tif[tile_nb],list_raster_obj_files[[tile_nb]]) |
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lf_cp_RData_tif <- c(lf_covar_obj[tile_nb],lf_covar_tif[tile_nb],list_raster_obj_files[[tile_nb]],lf_diagnostic_obj[[tile_nb]])
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#unlist(lf_cp_RData_tif) |
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lf_cp <- unlist(c(lf_cp_day,lf_cp_month,lf_cp_RData_tif)) |
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#lf_cp <- c(unlist(c(lf_cp_day,lf_cp_month)),list_raster_obj_files[tile_nb]) |
| ... | ... | |
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system(cmd_str) |
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} |
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#### COPY SHAPEFILES, TIF MOSAIC, COMBINED TEXT FILES etc... |
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#copy shapefiles defining regions |
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Atlas_dir <- file.path("/data/project/layers/commons/NEX_data/",basename(out_dir),"output/subset/shapefiles")
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Atlas_hostname <- "parmentier@atlas.nceas.ucsb.edu" |
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lf_cp_shp <- list.files(in_dir_shp,full.names=T) #get all the files... |
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#lf_cp_shp <- list.files(in_dir_shp, ".shp",full.names=T) |
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filenames_NEX <- paste(lf_cp_shp,collapse=" ") #copy raster prediction object |
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cmd_str <- paste("scp -p",filenames_NEX,paste(Atlas_hostname,Atlas_dir,sep=":"), sep=" ")
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system(cmd_str) |
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#Copy summary textfiles and mosaic back to atlas |
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Atlas_dir <- file.path("/data/project/layers/commons/NEX_data/",basename(out_dir))#,"output/subset/shapefiles")
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Atlas_hostname <- "parmentier@atlas.nceas.ucsb.edu" |
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lf_cp_f <- list.files(out_dir,full.names=T)#copy all files can filter later |
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filenames_NEX <- paste(lf_cp_f,collapse=" ") #copy raster prediction object |
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cmd_str <- paste("scp -p",filenames_NEX,paste(Atlas_hostname,Atlas_dir,sep=":"), sep=" ")
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system(cmd_str) |
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#system("scp -p ./*.txt parmentier@atlas.nceas.ucsb.edu:/data/project/layers/commons/NEX_data/output_run2_global_analyses_05122014")
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#system("scp -p ./*.txt ./*.tif parmentier@atlas.nceas.ucsb.edu:/data/project/layers/commons/NEX_data/output_run2_global_analyses_05122014")
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system("scp -p /nobackupp4/aguzman4/climateLayers/output4/subset/shapefiles/* parmentier@atlas.nceas.ucsb.edu:/data/project/layers/commons/NEX_data/shapefiles")
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##################### END OF SCRIPT ###################### |
Also available in: Unified diff
run 4 assessment part1, gam fitting comparison k for 6 specific tiles