Last updated: 2023-12-14

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Rmd 64fd104 ds2n19 2023-12-14 revised coverage analysis and SO focused cluster analysis.

Task

This script loads the nitrate climatology as described in Garcia et al. (2018). The climatology netCDF has previously been downloaded. The lat and lon fields are harmonised to our requirements, i.e -89.5 ≥ lat ≤ 89.5 and 20.5 ≥ lon ≤ 379.5.

Garcia, H. E., K. Weathers, C. R. Paver, I. Smolyar, T. P. Boyer, R. A. Locarnini, M. M. Zweng, A. V. Mishonov, O. K. Baranova, D. Seidov, and J. R. Reagan, 2018. World Ocean Atlas 2018, Volume 4: Dissolved Inorganic Nutrients (phosphate, nitrate and nitrate+nitrite, silicate). A. Mishonov Technical Ed.; NOAA Atlas NESDIS 84, 35pp.

Dependencies

WOA nitrate climatology - /nfs/kryo/work/datasets/gridded/ocean/interior/observation/woa/2018/nitrate/all/1.00/woa18_all_n01_01.nc

Outputs (in BGC preprocessed folder)

woa_nitrate_clim.rds

library(tidyverse)
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.4     ✔ purrr   1.0.2
✔ tibble  3.2.1     ✔ dplyr   1.1.3
✔ tidyr   1.3.0     ✔ stringr 1.5.0
✔ readr   2.1.3     ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
#library(ggOceanMaps)
library(oce)
Loading required package: gsw
#library(ncdf4)
library(stars)
Loading required package: abind
Loading required package: sf
Linking to GEOS 3.11.1, GDAL 3.4.1, PROJ 7.2.1; sf_use_s2() is TRUE
WARNING: different compile-time and runtime versions for GEOS found:
Linked against: 3.11.1-CAPI-1.17.1 compiled against: 3.9.1-CAPI-1.14.2
It is probably a good idea to reinstall sf, and maybe rgeos and rgdal too
path_argo <- '/nfs/kryo/work/datasets/ungridded/3d/ocean/floats/bgc_argo'
path_argo_preprocessed <- paste0(path_argo, "/preprocessed_bgc_data")

path_WOA_nitrate <-"/nfs/kryo/work/datasets/gridded/ocean/interior/observation/woa/2018/nitrate/all/1.00"
# monthly files of the form woa18_all_nMM_01.nc where MM = 01,....12

theme_set(theme_bw())

Read data

for (i_month in 1:12) {

  fn_WOA_nitrate <- paste0(path_WOA_nitrate, "/woa18_all_n", formatC(i_month, width=2, flag="0"), "_01.nc")
  
  nc_nitrate_mean <- read_ncdf(fn_WOA_nitrate, var = c("n_an")) %>% 
    as_tibble() %>%
    select(-time)
  
  # harmonise data 
  if (!exists("clim_argo_nitrate")) {
    clim_argo_nitrate <- nc_nitrate_mean %>%
      rename(clim_nitrate = "n_an") %>%
      mutate(month = i_month,
             lon = if_else(lon < 20, lon + 360, lon))
  } else {
    clim_argo_nitrate <- rbind(
      clim_argo_nitrate,
      nc_nitrate_mean %>%
        rename(clim_nitrate = "n_an") %>%
        mutate(month = i_month,
               lon = if_else(lon < 20, lon + 360, lon))
    )
  }

}
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees
Will return stars object with 2786400 cells.
Warning: ignoring unrecognized unit: micromoles_per_kilogram
Warning in .get_nc_dimensions(dimensions, coord_var = all_coord_var, coords =
coords, : bounds not enveloping depth coordinates. Ignoring.
Warning in CPL_crs_from_input(x): GDAL Error 1: PROJ: proj_create: Error -7
(unknown unit conversion id)
Warning in value[[3L]](cond): failed to create crs based on grid mapping
and coordinate variable units. Will return NULL crs.
Original error: 
Error in st_crs.character(base_gm): invalid crs: +proj=longlat +a=6378137 +f=0.0033528105624174 +pm=0 +no_defs +units=degrees

Maps

clim_argo_nitrate %>%
   filter(depth < 30) %>%
   ggplot() +
   geom_tile(aes(lon, lat, fill = clim_nitrate)) +
   facet_wrap(~depth) +
   scale_fill_viridis_c() +
   coord_quickmap()

clim_argo_nitrate %>%
   ggplot(aes(clim_nitrate)) +
   geom_histogram(binwidth = 2) +
   facet_wrap(~depth) +
   scale_y_log10()
Warning: Removed 13272396 rows containing non-finite values (`stat_bin()`).
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 309 rows containing missing values (`geom_bar()`).

Write data to file

clim_argo_nitrate %>% 
  drop_na() %>% 
  write_rds(file = paste0(path_argo_preprocessed, "/woa_nitrate_clim.rds"))

sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.5

Matrix products: default
BLAS:   /usr/local/R-4.2.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.2.2/lib64/R/lib/libRlapack.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=en_US.UTF-8   
 [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] stars_0.6-0     sf_1.0-9        abind_1.4-5     oce_1.7-10     
 [5] gsw_1.1-1       forcats_0.5.2   stringr_1.5.0   dplyr_1.1.3    
 [9] purrr_1.0.2     readr_2.1.3     tidyr_1.3.0     tibble_3.2.1   
[13] ggplot2_3.4.4   tidyverse_1.3.2

loaded via a namespace (and not attached):
 [1] fs_1.5.2            lubridate_1.9.0     httr_1.4.4         
 [4] rprojroot_2.0.3     tools_4.2.2         backports_1.4.1    
 [7] bslib_0.4.1         utf8_1.2.2          R6_2.5.1           
[10] KernSmooth_2.23-20  DBI_1.1.3           colorspace_2.0-3   
[13] withr_2.5.0         tidyselect_1.2.0    compiler_4.2.2     
[16] git2r_0.30.1        cli_3.6.1           rvest_1.0.3        
[19] RNetCDF_2.6-1       xml2_1.3.3          labeling_0.4.2     
[22] sass_0.4.4          scales_1.2.1        classInt_0.4-8     
[25] proxy_0.4-27        digest_0.6.30       rmarkdown_2.18     
[28] pkgconfig_2.0.3     htmltools_0.5.3     highr_0.9          
[31] dbplyr_2.2.1        fastmap_1.1.0       rlang_1.1.1        
[34] readxl_1.4.1        rstudioapi_0.15.0   jquerylib_0.1.4    
[37] generics_0.1.3      farver_2.1.1        jsonlite_1.8.3     
[40] googlesheets4_1.0.1 magrittr_2.0.3      ncmeta_0.3.5       
[43] Rcpp_1.0.10         munsell_0.5.0       fansi_1.0.3        
[46] lifecycle_1.0.3     stringi_1.7.8       whisker_0.4        
[49] yaml_2.3.6          grid_4.2.2          parallel_4.2.2     
[52] promises_1.2.0.1    crayon_1.5.2        haven_2.5.1        
[55] hms_1.1.2           knitr_1.41          pillar_1.9.0       
[58] reprex_2.0.2        glue_1.6.2          evaluate_0.18      
[61] modelr_0.1.10       vctrs_0.6.4         tzdb_0.3.0         
[64] httpuv_1.6.6        cellranger_1.1.0    gtable_0.3.1       
[67] assertthat_0.2.1    cachem_1.0.6        xfun_0.35          
[70] lwgeom_0.2-10       broom_1.0.5         e1071_1.7-12       
[73] later_1.3.0         class_7.3-20        googledrive_2.0.0  
[76] viridisLite_0.4.1   gargle_1.2.1        workflowr_1.7.0    
[79] units_0.8-0         timechange_0.1.1    ellipsis_0.3.2