Revision 3fd24f79
Added by Benoit Parmentier over 11 years ago
climate/research/oregon/interpolation/master_script_temp.R | ||
---|---|---|
10 | 10 |
#STAGE 5: Output analyses-visualization of results for specific dates... |
11 | 11 |
# |
12 | 12 |
#AUTHOR: Benoit Parmentier |
13 |
#DATE: 03/18/2013
|
|
13 |
#DATE: 03/21/2013
|
|
14 | 14 |
|
15 | 15 |
#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363, TASK$568-- |
16 | 16 |
|
... | ... | |
47 | 47 |
|
48 | 48 |
#####SCRIPT USED FOR THE PREDICTIONS |
49 | 49 |
|
50 |
#master_script_temp_03052013.R
|
|
50 |
#master_script_temp_03192013.R
|
|
51 | 51 |
|
52 |
#IN MASTER SCRIPT:
|
|
52 |
#CALLED FROM MASTER SCRIPT:
|
|
53 | 53 |
|
54 |
#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_01252013b.py |
|
55 |
#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/covariates_production_temperatures_02062013.R |
|
56 |
|
|
57 |
#source(file.path(script_path,"Database_stations_covariates_processing_function_03052013.R")) |
|
58 |
#source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_03052013.R")) |
|
59 |
#source(file.path(script_path,"results_interpolation_date_output_analyses_03052013.R")) |
|
54 |
#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_03192013.py |
|
55 |
source(file.path(script_path,"covariates_production_temperatures_03212013.R")) |
|
56 |
source(file.path(script_path,"Database_stations_covariates_processing_function_03132013.R")) |
|
57 |
source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_03182013.R")) |
|
58 |
source(file.path(script_path,"results_interpolation_date_output_analyses_03182013.R")) |
|
60 | 59 |
|
61 | 60 |
#CALLED FROM GAM FUSION ANALYSIS RASTER PREDICTION |
62 | 61 |
|
63 |
#source(file.path(script_path,"sampling_script_functions_03052013.R"))
|
|
64 |
#source(file.path(script_path,"GAM_fusion_function_multisampling_03052013.R")) #Include GAM_CAI
|
|
65 |
#source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_02262013.R"))
|
|
62 |
source(file.path(script_path,"sampling_script_functions_03122013.R"))
|
|
63 |
source(file.path(script_path,"GAM_fusion_function_multisampling_03142013.R")) #Include GAM_CAI
|
|
64 |
source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_03182013.R"))
|
|
66 | 65 |
|
67 | 66 |
|
68 | 67 |
############ STAGE 1: LST Climatology ############### |
69 | 68 |
|
70 | 69 |
if (stages_to_run[1]==1){ |
71 | 70 |
#Call run through python |
72 |
#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_01252013b.py
|
|
71 |
#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_03182013.py
|
|
73 | 72 |
} |
74 | 73 |
|
75 | 74 |
############ STAGE 2: Covariate production ################ |
76 | 75 |
|
76 |
##Paths to inputs and output |
|
77 |
var<-"TMIN" |
|
78 |
in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/" |
|
79 |
out_path<- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/output_data/" |
|
80 |
|
|
81 |
lc_path<-"/home/layers/data/land-cover/lc-consensus-global" |
|
82 |
infile_modis_grid<-"modis_sinusoidal_grid_world.shp" |
|
83 |
infile_elev<-"/home/layers/data/terrain/dem-cgiar-srtm-1km-tif/srtm_1km.tif" #this is the global file: replace later with the input produced by the DEM team |
|
84 |
infile_canheight<-"Simard_Pinto_3DGlobalVeg_JGR.tif" #Canopy height |
|
85 |
list_tiles_modis = c('h11v08','h11v07','h12v07','h12v08','h10v07','h10v08') #tile for Venezuel and surrounding area |
|
86 |
infile_reg_outline="" #input region outline defined by polygon |
|
87 |
CRS_interp<-"+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs"; |
|
88 |
CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84 |
|
89 |
out_region_name<-"_venezuela_region" #generated on the fly |
|
90 |
out_suffix<-"_VE_03192013" |
|
91 |
ref_rast_name<-"" #local raster name defining resolution, exent, local projection--. set on the fly?? |
|
92 |
#The names of covariates can be changed...these names should be output/input from covar script!!! |
|
93 |
rnames<-c("x","y","lon","lat","N","E","N_w","E_w","elev","slope","aspect","CANHEIGHT","DISTOC") |
|
94 |
lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10","LC11","LC12") |
|
95 |
lst_names<-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", |
|
96 |
"nobs_01","nobs_02","nobs_03","nobs_04","nobs_05","nobs_06","nobs_07","nobs_08", |
|
97 |
"nobs_09","nobs_10","nobs_11","nobs_12") |
|
98 |
covar_names<-c(rnames,lc_names,lst_names) |
|
99 |
|
|
100 |
list_param_covar_production<-list(var,in_path,out_path,lc_path,infile_modis_grid,infile_elev,infile_canheight, |
|
101 |
list_tiles_modis,infile_reg_outline,CRS_interp,CRS_locs_WGS84,out_region_name, |
|
102 |
out_suffix,ref_rast_name,covar_names) |
|
103 |
|
|
104 |
names(list_param_covar_production)<-c("var","in_path","out_path","lc_path","infile_modis_grid","infile_elev","infile_canheight", |
|
105 |
"list_tiles_modis","infile_reg_outline","CRS_interp","CRS_locs_WGS84","out_region_name", |
|
106 |
"out_suffix","ref_rast_name","covar_names") |
|
107 |
|
|
77 | 108 |
if (stages_to_run[2]==2){ |
78 | 109 |
#Transform into function... |
79 |
#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/covariates_production_temperatures_02062013.R |
|
110 |
#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/covariates_production_temperatures_03212013.R |
|
111 |
infile_covar_brick<-covariates_production_temperature(list_param_covar_production) |
|
80 | 112 |
} |
81 | 113 |
|
82 | 114 |
############# STAGE 3: Data preparation ############### |
83 | 115 |
|
84 |
source(file.path(script_path,"Database_stations_covariates_processing_function_03132013.R")) |
|
85 | 116 |
|
86 | 117 |
#Setting up input argurments for script function... |
118 |
#set up earlier |
|
119 |
infile_covariates<-"covariates__venezuela_region__VE_01292013.tif" #this is an output from covariate script and used in stage 3 and stage 4 |
|
120 |
CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84: same as earlier |
|
121 |
infile1<- "outline_venezuela_region__VE_01292013.shp" #This is the shape file of outline of the study area #It is an input/output of the covariate script |
|
122 |
#covar_names see stage 2 |
|
123 |
var <- "TMAX" # name of the variables to keep: TMIN, TMAX or PRCP |
|
87 | 124 |
|
125 |
#specific to this stage |
|
88 | 126 |
db.name <- "ghcn" # name of the Postgres database |
89 |
var <- "TMAX" # name of the variables to keep: TMIN, TMAX or PRCP |
|
90 | 127 |
range_years<-c("2000","2001") #right bound not included in the range!! |
91 | 128 |
range_years_clim<-c("1980","2011") #right bound not included in the range!! |
92 |
infile1<- "outline_venezuela_region__VE_01292013.shp" #This is the shape file of outline of the study area #It is an input/output of the covariate script |
|
93 | 129 |
infile2<-"/home/layers/data/climate/ghcn/v2.92-upd-2012052822/ghcnd-stations.txt" #This is the textfile of station locations from GHCND |
94 |
infile_covariates<-"covariates__venezuela_region__VE_01292013.tif" #this is an output from covariate script and used in stage 3 and stage 4 |
|
95 |
CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84: same as earlier |
|
96 | 130 |
in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/" |
97 | 131 |
out_prefix<-"_365d_GAM_fus5_all_lstd_03182013" #User defined output prefix |
98 | 132 |
#qc_flags<- flags allowe for the query from the GHCND?? |
99 | 133 |
|
100 |
#The names of covariates can be changed...these names should be output/input from covar script!!! |
|
101 |
rnames<-c("x","y","lon","lat","N","E","N_w","E_w","elev","slope","aspect","CANHEIGHT","DISTOC") |
|
102 |
lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10","LC11","LC12") |
|
103 |
lst_names<-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", |
|
104 |
"nobs_01","nobs_02","nobs_03","nobs_04","nobs_05","nobs_06","nobs_07","nobs_08", |
|
105 |
"nobs_09","nobs_10","nobs_11","nobs_12") |
|
106 |
covar_names<-c(rnames,lc_names,lst_names) |
|
107 | 134 |
|
108 | 135 |
#list of 11 parameters for input in the function... |
109 | 136 |
|
... | ... | |
174 | 201 |
"interpolation_method") |
175 | 202 |
|
176 | 203 |
#Source file |
177 |
source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_03182013.R")) |
|
178 | 204 |
|
179 | 205 |
#Make the function call |
180 | 206 |
raster_prediction_gam_fus_obj <-raster_prediction_gam_fusion(list_param_raster_prediction) |
... | ... | |
182 | 208 |
|
183 | 209 |
############## STAGE 5: OUTPUT ANALYSES ################## |
184 | 210 |
|
185 |
source(file.path(script_path,"results_interpolation_date_output_analyses_03052013.R")) |
|
186 |
|
|
211 |
#source(file.path(script_path,"results_interpolation_date_output_analyses_03052013.R"))
|
|
212 |
#Call as function... |
|
187 | 213 |
|
188 | 214 |
############### END OF SCRIPT ################### |
189 | 215 |
##################################################### |
Also available in: Unified diff
master script set up call to covariate production function