Standardized Precipitation-Evapotranspiration Index (SPEI)
Last updated: 2021-03-24
Checks: 5 1
Knit directory:
thesis/analysis/
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1 Loading the data
files = list.files("../data/vector/extraction/", pattern = "_SPEI", full.names = T)
data = lapply(files, function(x){
filename = str_split(basename(x), "_")[[1]]
if(length(filename) == 3){
unit = filename[1]
buffer = as.numeric(filename[2])
var = str_remove(filename[3], ".gpkg")
} else {
unit = filename[1]
buffer = 0
var = str_remove(filename[2], ".gpkg")
}
layers = ogrListLayers(x)
layers = layers[grep("attr_", layers)]
data = do.call(cbind, lapply(layers, function(l){
tmp = st_read(x, layer = l, quiet = TRUE)
lnames = c("SPI1", "SPI3", "SPI6", "SPI12")
names(tmp) = paste(l, lnames, sep = "-")
tmp
}))
data$id = 1:nrow(data)
data %>%
as_tibble () %>%
gather("tmp", "value", -id) %>%
separate(tmp, into = c("time","SPI"), sep = "-SPI") %>%
mutate(SPI = as.factor(SPI),
time = str_remove(time, "attr_"),
unit = unit, buffer = buffer, var = var)
})
data = do.call(rbind, data)
str(data)tibble [7,142,400 × 7] (S3: tbl_df/tbl/data.frame)
$ id : int [1:7142400] 1 2 3 4 5 6 7 8 9 10 ...
$ time : chr [1:7142400] "2000-02" "2000-02" "2000-02" "2000-02" ...
$ SPI : Factor w/ 4 levels "1","12","3","6": 1 1 1 1 1 1 1 1 1 1 ...
$ value : num [1:7142400] 0.32 0.584 0.771 0.343 0.285 ...
$ unit : chr [1:7142400] "basins" "basins" "basins" "basins" ...
$ buffer: num [1:7142400] 100 100 100 100 100 100 100 100 100 100 ...
$ var : chr [1:7142400] "SPEI" "SPEI" "SPEI" "SPEI" ...2 Missing values
data %>%
group_by(unit, buffer) %>%
summarise(N = n(), isna = sum(is.na(value)), isnotna = sum(!is.na(value)), perc = sum(is.na(value)) / n() * 100)# A tibble: 8 x 6
# Groups: unit [2]
unit buffer N isna isnotna perc
<chr> <dbl> <int> <int> <int> <dbl>
1 basins 0 972480 23604 948876 2.43
2 basins 50 972480 18280 954200 1.88
3 basins 100 972480 18234 954246 1.88
4 basins 200 972480 18234 954246 1.88
5 states 0 813120 19053 794067 2.34
6 states 50 813120 15246 797874 1.88
7 states 100 813120 15246 797874 1.88
8 states 200 813120 15246 797874 1.883 Time Series
data %>%
filter(buffer==0, unit == "states") %>%
mutate(time = as.Date(paste0(time, "-01"))) %>%
group_by(time, unit, SPI) %>%
summarise(value = median(value, na.rm = T)) %>%
mutate(sign = if_else(value>0, "pos", "neg"),
cap = paste0("Scale of ", SPI, " months"),
scale = as.numeric(as.character(SPI))) %>%
mutate(cap = fct_reorder(cap, scale, min)) %>%
ggplot(aes(x=time, y=value, fill = sign)) +
geom_bar(stat = "identity", show.legend = FALSE) +
#scale_x_date(date_breaks = "year", date_labels = "%Y") +
#scale_y_continuous(breaks = seq(-2, 2, 1)) +
scale_fill_manual(values = c("#99000d", "#034e7b")) +
labs(y = "SPI", x = "") +
theme_classic() +
facet_wrap(~cap, nrow = 4)
data %>%
filter(buffer==0, unit == "basins") %>%
mutate(time = as.Date(paste0(time, "-01"))) %>%
group_by(time, unit, SPI) %>%
summarise(value = median(value, na.rm = T)) %>%
mutate(sign = if_else(value>0, "pos", "neg"),
cap = paste0("Scale of ", SPI, " months"),
scale = as.numeric(as.character(SPI))) %>%
mutate(cap = fct_reorder(cap, scale, min)) %>%
ggplot(aes(x=time, y=value, fill = sign)) +
geom_bar(stat = "identity", show.legend = FALSE) +
#scale_x_date(date_breaks = "year", date_labels = "%Y") +
#scale_y_continuous(breaks = seq(-2, 2, 1)) +
scale_fill_manual(values = c("#99000d", "#034e7b")) +
labs(y = "SPI", x = "") +
theme_classic() +
facet_wrap(~cap, nrow = 4)
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.7.9.2 rgdal_1.5-18 countrycode_1.2.0 welchADF_0.3.2
[5] rstatix_0.6.0 ggpubr_0.4.0 scales_1.1.1 RColorBrewer_1.1-2
[9] latex2exp_0.4.0 cubelyr_1.0.0 gridExtra_2.3 ggtext_0.1.1
[13] magrittr_2.0.1 tmap_3.2 sf_0.9-7 raster_3.4-5
[17] sp_1.4-4 forcats_0.5.0 stringr_1.4.0 purrr_0.3.4
[21] readr_1.4.0 tidyr_1.1.2 tibble_3.0.6 tidyverse_1.3.0
[25] huwiwidown_0.0.1 kableExtra_1.3.1 knitr_1.31 rmarkdown_2.7.3
[29] bookdown_0.21 ggplot2_3.3.3 dplyr_1.0.2 devtools_2.3.2
[33] usethis_2.0.0
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.2.0 workflowr_1.6.2
[4] lwgeom_0.2-5 splines_3.6.3 crosstalk_1.1.0.1
[7] leaflet_2.0.3 digest_0.6.27 htmltools_0.5.1.1
[10] fansi_0.4.2 memoise_1.1.0 openxlsx_4.2.3
[13] remotes_2.2.0 modelr_0.1.8 prettyunits_1.1.1
[16] colorspace_2.0-0 rvest_0.3.6 haven_2.3.1
[19] xfun_0.21 leafem_0.1.3 callr_3.5.1
[22] crayon_1.4.0 jsonlite_1.7.2 lme4_1.1-26
[25] glue_1.4.2 stars_0.4-3 gtable_0.3.0
[28] webshot_0.5.2 car_3.0-10 pkgbuild_1.2.0
[31] abind_1.4-5 DBI_1.1.0 Rcpp_1.0.5
[34] viridisLite_0.3.0 gridtext_0.1.4 units_0.6-7
[37] foreign_0.8-71 htmlwidgets_1.5.3 httr_1.4.2
[40] ellipsis_0.3.1 farver_2.0.3 pkgconfig_2.0.3
[43] XML_3.99-0.3 dbplyr_2.0.0 utf8_1.1.4
[46] labeling_0.4.2 tidyselect_1.1.0 rlang_0.4.10
[49] later_1.1.0.1 tmaptools_3.1 munsell_0.5.0
[52] cellranger_1.1.0 tools_3.6.3 cli_2.3.0
[55] generics_0.1.0 broom_0.7.2 evaluate_0.14
[58] yaml_2.2.1 processx_3.4.5 leafsync_0.1.0
[61] fs_1.5.0 zip_2.1.1 nlme_3.1-150
[64] xml2_1.3.2 compiler_3.6.3 rstudioapi_0.13
[67] curl_4.3 png_0.1-7 e1071_1.7-4
[70] testthat_3.0.1 ggsignif_0.6.0 reprex_0.3.0
[73] statmod_1.4.35 stringi_1.5.3 highr_0.8
[76] ps_1.5.0 desc_1.2.0 lattice_0.20-41
[79] Matrix_1.2-18 nloptr_1.2.2.2 classInt_0.4-3
[82] vctrs_0.3.6 pillar_1.4.7 lifecycle_0.2.0
[85] data.table_1.13.2 httpuv_1.5.5 R6_2.5.0
[88] promises_1.1.1 KernSmooth_2.23-18 rio_0.5.16
[91] sessioninfo_1.1.1 codetools_0.2-16 dichromat_2.0-0
[94] boot_1.3-25 MASS_7.3-53 assertthat_0.2.1
[97] pkgload_1.1.0 rprojroot_2.0.2 withr_2.4.1
[100] parallel_3.6.3 hms_1.0.0 grid_3.6.3
[103] minqa_1.2.4 class_7.3-17 carData_3.0-4
[106] git2r_0.27.1 base64enc_0.1-3