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063_Data_process_df_Lon_strips.R
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#===========
# 9 May 2024
#===========
# Aim:
# process the data further for parallelisation
# Method:
# 1. divide the whole data into 8 strips by Lon_1, ..., Lon_8
# 2. within each Lon strip, Lat decrease
# 3. and Lat for Lon_3, Lon_5 will be further cut by Lat > 0, Lat < 0
# Lon3_pos, Lon3_neg, Lon5_pos, Lon5_neg, Lon7_pos, Lon7_neg, Lon8_pos, Lon8_neg
# Reason：
# 1. the HPC job longest running time is 10 days
# 2. 200 locations with 5 CAMS variates, parallelize over 51 CPU cores require
# 10 minutes 29 seconds
# so need to limit the data chunk for HPC to be able to finish within 10 days
#=============
# Pre-settings
#=============
install.packages("dplyr")
library(dplyr)
load("~/Library/CloudStorage/OneDrive-UniversityofExeter/XC_PhD/Data/Processed/XC_WORK/RData/df_Cmpt_Res_log_16.rda")
head(df_Cmpt_Res_log_16)
# Lon Lat Year BC_Residuals_log DU_Residuals_log OM_Residuals_log
# SS_Residuals_log SU_Residuals_log PM25_Residuals_log
# save to a new copy
df_Res_log_16 <- df_Cmpt_Res_log_16
range(df_Res_log_16$Lon)
# [1] -179.25 180.00
range(df_Res_log_16$Lat)
# [1] -55.50 83.25
# Define the latitude range and step
start_lon <- -179.25
end_lon <- 180
# The number of division
num_div <- 8
# division size
div_size_lon = (end_lon - start_lon) / num_div
# [1] 44.90625
breaks_lon = seq(start_lon, end_lon, length.out = num_div + 1)
length(breaks_lon) # [1] 9
breaks_lon
# [1] -179.25000 -134.34375 -89.43750 -44.53125
# [5] 0.37500 45.28125 90.18750 135.09375 180.00000
#
diff(breaks_lon)
# [1] 44.90625 44.90625 44.90625
# [4] 44.90625 44.90625 44.90625
# [7] 44.90625 44.90625
df_Res_log_16 <- df_Res_log_16 %>%
mutate(Lon_div_indx = cut(Lon, breaks = breaks_lon, labels = F))
#--------------------------------
# check NA for the boundary cut
#--------------------------------
which(is.na(df_Res_log_16$Lon_div_indx))
# [1] 1772 2782 3114 3474
df_Res_log_16[1770:1779,]
df_Res_log_16[2780:2784, ]
df_Res_log_16[3112:3116, ]
df_Res_log_16[3472:3475,]
# Lon Lat Year
# 1772 -179.25 71.25 2016
# 2782 -179.25 68.25 2016
# 3114 -179.25 67.50 2016
# 3474 -179.25 66.75 2016
## all corresponds to Lon: -179.25
# so shall categorize to Lon_div_indx = 1
df_Res_log_16$Lon_div_indx[1772] <- 1
df_Res_log_16$Lon_div_indx[2782] <- 1
df_Res_log_16$Lon_div_indx[3114] <- 1
df_Res_log_16$Lon_div_indx[3474] <- 1
nrow(df_Res_log_16) # [1] 27384
df_div_Lon_lst <- split(df_Res_log_16, df_Res_log_16$Lon_div_indx)
str(df_div_Lon_lst)
#List of 8
# $ 1:'data.frame': 630 obs. of 10 variables:
# $ 2:'data.frame': 3163 obs. of 10 variables:
# $ 3:'data.frame': 4648 obs. of 10 variables:
# $ 4:'data.frame': 1933 obs. of 10 variables:
# $ 5:'data.frame': 5910 obs. of 10 variables:
# $ 6:'data.frame': 4245 obs. of 10 variables:
# $ 7:'data.frame': 4978 obs. of 10 variables:
# $ 8:'data.frame': 1877 obs. of 10 variables:
#=====================
# GPU running strategy
#=====================
# 1, 2 list corresponds to Lon_strip 1: 3793 locations;
# 3, 4 list corresponds to Lon_strip 2: 6581 locations;
# 5, corresponds to half of Lon_strip 3: 5910 locations;
# 6 corresponds to the other half of Lon_strip 3: 4245 locations;
# 7, 8 list corresponds to Lon_strip 4: 6855 locations.
#------------------------------------
# bind into Lon_strip_1, 2, 31, 32, 4
#------------------------------------
df_Lon_strip_1 <- do.call(rbind, list(df_div_Lon_lst[[1]], df_div_Lon_lst[[2]]))
str(df_Lon_strip_1)
#'data.frame': 3793 obs. of 10 variables:
unique(df_Lon_strip_1$Lon_div_indx)
# [1] 1 2
df_Lon_strip_2 <- do.call(rbind, list(df_div_Lon_lst[[3]], df_div_Lon_lst[[4]]))
str(df_Lon_strip_2)
# 'data.frame': 6581 obs. of 10 variables:
unique(df_Lon_strip_2$Lon_div_indx)
# [1] 3 4
df_Lon_strip_31 <- df_div_Lon_lst[[5]]
str(df_Lon_strip_31)
unique(df_Lon_strip_31$Lon_div_indx)
# [1] 5
df_Lon_strip_32 <- df_div_Lon_lst[[6]]
str(df_Lon_strip_32)
# 'data.frame': 4245 obs. of 10 variables
unique(df_Lon_strip_32$Lon_div_indx)
# [1] 6
df_Lon_strip_4 <- do.call(rbind, list(df_div_Lon_lst[[7]], df_div_Lon_lst[[8]]))
str(df_Lon_strip_4)
# 'data.frame': 6855 obs. of 10 variables:
unique(df_Lon_strip_4$Lon_div_indx)
# [1] 7 8
#---------------------------
# sort within each Lon strip
#---------------------------
# Lon: ascending (small-large)
# if Lat: descending (large-smal) not good for DSP, lat will have all neg values, not good for further B calculation
# Lat: ascending (small-large)
df_Lon_strip_1_sort <- arrange(df_Lon_strip_1, Lon, Lat)
str(df_Lon_strip_1_sort)
# 'data.frame': 3793 obs. of 10 variables:
#$ Lon : num -179 -179 -179 -179 -178 ...
#$ Lat : num 66.8 67.5 68.2 71.2 66 ...
head(df_Lon_strip_1_sort, 30)
df_Lon_strip_2_sort <- arrange(df_Lon_strip_2, Lon, Lat)
str(df_Lon_strip_2_sort)
# 'data.frame': 6581 obs. of 10 variables:
#$ Lon : num -89.2 -89.2 -89.2 -89.2 -89.2 ...
#$ Lat : num 13.5 14.2 15 15.8 16.5 ...
df_Lon_strip_31_sort <- arrange(df_Lon_strip_31, Lon, Lat)
str(df_Lon_strip_31_sort)
# 'data.frame': 5910 obs. of 10 variables:
#$ Lon : num 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 ...
#$ Lat : num 6 6.75 7.5 8.25 9 ...
df_Lon_strip_32_sort <- arrange(df_Lon_strip_32, Lon, Lat)
str(df_Lon_strip_32_sort)
# 'data.frame': 4245 obs. of 10 variables:
#$ Lon : num 45.8 45.8 45.8 45.8 45.8 ...
#Lat : num -24.8 -24 -23.2 -22.5 -21.8 ...
df_Lon_strip_4_sort <- arrange(df_Lon_strip_4, Lon, Lat)
str(df_Lon_strip_4_sort)
# 'data.frame': 6855 obs. of 10 variables:
#$ Lon : num 90.8 90.8 90.8 90.8 90.8 ...
#$ Lat : num 22.5 23.2 24 24.8 25.5 ...
#=======================================================
# Re-organize the BC,DU,etc.order to align with the DAG
#=======================================================
# 1: DU; 2: SU; 3: BC; 4: OM; 5:SS
#------------
# Lon_Strip_1
#------------
df_Lon_Strip_1_Sort <- data.frame(Lon = df_Lon_strip_1_sort$Lon,
Lat = df_Lon_strip_1_sort$Lat,
Year = df_Lon_strip_1_sort$Year,
Z1 = df_Lon_strip_1_sort$DU_Residuals_log,
Z2 = df_Lon_strip_1_sort$SU_Residuals_log,
Z3 = df_Lon_strip_1_sort$BC_Residuals_log,
Z4 = df_Lon_strip_1_sort$OM_Residuals_log,
Z5 = df_Lon_strip_1_sort$SS_Residuals_log,
PM25_res = df_Lon_strip_1_sort$PM25_Residuals_log,
Lon_div_indx = df_Lon_strip_1_sort$Lon_div_indx)
str(df_Lon_Strip_1_Sort)
# 'data.frame': 3793 obs. of 10 variables:
df_Lon_Strip_1_Sort_new <- df_Lon_Strip_1_Sort
saveRDS(df_Lon_Strip_1_Sort_new, file = "df_Lon_Strip_1_Sort_new.rds")
range(df_Lon_Strip_1_Sort_new$Z1)
# [1] -3.308540 4.668558
quantile(df_Lon_Strip_1_Sort_new$Z1)
# 0% 25% 50% 75% 100%
# -3.3085399 -0.7825191 -0.2199278 0.5530506 4.6685585
var(df_Lon_Strip_1_Sort_new$Z1)
# [1] 1.151125
range(df_Lon_Strip_1_Sort_new$Z2)
# [1] -1.227585 4.270820
quantile(df_Lon_Strip_1_Sort_new$Z2)
# 0% 25% 50% 75% 100%
# -1.22758542 -0.24994444 -0.05963849 0.24968515 4.27082005
var(df_Lon_Strip_1_Sort_new$Z2)
# [1] 0.2406004
range(df_Lon_Strip_1_Sort_new$Z3)
# [1] -2.302818 3.978425
quantile(df_Lon_Strip_1_Sort_new$Z3)
# 0% 25% 50% 75% 100%
#-2.3028181 -0.5080320 -0.1693029 0.2157480 3.9784250
var(df_Lon_Strip_1_Sort_new$Z3)
# [1] 0.5071742
range(df_Lon_Strip_1_Sort_new$Z4)
# [1] -2.318861 2.494690
quantile(df_Lon_Strip_1_Sort_new$Z4)
# 0% 25% 50% 75% 100%
#-2.31886054 -0.38052471 -0.06471533 0.30779855 2.49468983
var(df_Lon_Strip_1_Sort_new$Z4)
# [1] 0.3915508
range(df_Lon_Strip_1_Sort_new$Z5)
# [1] -2.192750 2.578429
quantile(df_Lon_Strip_1_Sort_new$Z5)
# 0% 25% 50% 75% 100%
# -2.19275010 -0.42407572 -0.06511489 0.39396397 2.57842950
var(df_Lon_Strip_1_Sort_new$Z5)
# [1] 0.3902767
#------------
# Lon_Strip_2
#------------
df_Lon_Strip_2_Sort <- data.frame(Lon = df_Lon_strip_2_sort$Lon,
Lat = df_Lon_strip_2_sort$Lat,
Year = df_Lon_strip_2_sort$Year,
Z1 = df_Lon_strip_2_sort$DU_Residuals_log,
Z2 = df_Lon_strip_2_sort$SU_Residuals_log,
Z3 = df_Lon_strip_2_sort$BC_Residuals_log,
Z4 = df_Lon_strip_2_sort$OM_Residuals_log,
Z5 = df_Lon_strip_2_sort$SS_Residuals_log,
PM25_res = df_Lon_strip_2_sort$PM25_Residuals_log,
Lon_div_indx = df_Lon_strip_2_sort$Lon_div_indx)
str(df_Lon_Strip_2_Sort)
# 'data.frame': 6581 obs. of 10 variables:
df_Lon_Strip_2_Sort_new <- df_Lon_Strip_2_Sort
saveRDS(df_Lon_Strip_2_Sort_new, file = "df_Lon_Strip_2_Sort_new.rds")
#------------
# Lon_Strip_31
#------------
df_Lon_Strip_31_Sort <- data.frame(Lon = df_Lon_strip_31_sort$Lon,
Lat = df_Lon_strip_31_sort$Lat,
Year = df_Lon_strip_31_sort$Year,
Z1 = df_Lon_strip_31_sort$DU_Residuals_log,
Z2 = df_Lon_strip_31_sort$SU_Residuals_log,
Z3 = df_Lon_strip_31_sort$BC_Residuals_log,
Z4 = df_Lon_strip_31_sort$OM_Residuals_log,
Z5 = df_Lon_strip_31_sort$SS_Residuals_log,
PM25_res = df_Lon_strip_31_sort$PM25_Residuals_log,
Lon_div_indx = df_Lon_strip_31_sort$Lon_div_indx)
str(df_Lon_Strip_31_Sort)
# 'data.frame': 5910 obs. of 10 variables:
df_Lon_Strip_31_Sort_new <- df_Lon_Strip_31_Sort
saveRDS(df_Lon_Strip_31_Sort_new, file = "df_Lon_Strip_31_Sort_new.rds")
#------------
# Lon_Strip_32
#------------
df_Lon_Strip_32_Sort <- data.frame(Lon = df_Lon_strip_32_sort$Lon,
Lat = df_Lon_strip_32_sort$Lat,
Year = df_Lon_strip_32_sort$Year,
Z1 = df_Lon_strip_32_sort$DU_Residuals_log,
Z2 = df_Lon_strip_32_sort$SU_Residuals_log,
Z3 = df_Lon_strip_32_sort$BC_Residuals_log,
Z4 = df_Lon_strip_32_sort$OM_Residuals_log,
Z5 = df_Lon_strip_32_sort$SS_Residuals_log,
PM25_res = df_Lon_strip_32_sort$PM25_Residuals_log,
Lon_div_indx = df_Lon_strip_32_sort$Lon_div_indx)
str(df_Lon_Strip_32_Sort)
# 'data.frame': 4245 obs. of 10 variables:
df_Lon_Strip_32_Sort_new <- df_Lon_Strip_32_Sort
saveRDS(df_Lon_Strip_32_Sort_new, file = "df_Lon_Strip_32_Sort_new.rds")
#------------
# Lon_Strip_4
#------------
df_Lon_Strip_4_Sort <- data.frame(Lon = df_Lon_strip_4_sort$Lon,
Lat = df_Lon_strip_4_sort$Lat,
Year = df_Lon_strip_4_sort$Year,
Z1 = df_Lon_strip_4_sort$DU_Residuals_log,
Z2 = df_Lon_strip_4_sort$SU_Residuals_log,
Z3 = df_Lon_strip_4_sort$BC_Residuals_log,
Z4 = df_Lon_strip_4_sort$OM_Residuals_log,
Z5 = df_Lon_strip_4_sort$SS_Residuals_log,
PM25_res = df_Lon_strip_4_sort$PM25_Residuals_log,
Lon_div_indx = df_Lon_strip_4_sort$Lon_div_indx)
df_Lon_Strip_4_Sort_new <- df_Lon_Strip_4_Sort
str(df_Lon_Strip_4_Sort_new)
# 'data.frame': 6855 obs. of 10 variables:
saveRDS(df_Lon_Strip_4_Sort_new, file = "df_Lon_Strip_4_Sort_new.rds")
head(df_Lon_Strip_4_Sort_new, 30)