Last updated: 2023-12-19

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Knit directory: bgc_argo_r_argodata/analysis/

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

Task

This script loads the O2 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 3: Dissolved Oxygen, Apparent Oxygen Utilization, and Oxygen Saturation. A. Mishonov Technical Ed.; NOAA Atlas NESDIS 83, 38pp. https://www.ncei.noaa.gov/access/world-ocean-atlas-2018/

Dependencies

WOA O2 climatology - /nfs/kryo/work/datasets/gridded/ocean/interior/observation/woa/2018/oxygen/all/1.00/woa18_all_o01_01.nc

Outputs (in BGC preprocessed folder)

woa_doxy_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_WOAO2 <-"/nfs/kryo/work/datasets/gridded/ocean/interior/observation/woa/2018/oxygen/all/1.00"
# monthly files of the form woa18_all_oMM_01.nc where MM = 01,....12

theme_set(theme_bw())

Read data

for (i_month in 1:12) {

  fn_WOAO2 <- paste0(path_WOAO2, "/woa18_all_o", formatC(i_month, width=2, flag="0"), "_01.nc")
  
  nc_doxy_mean <- read_ncdf(fn_WOAO2, var = c("o_an")) %>% 
    as_tibble() %>%
    select(-time)
  
  # harmonise data 
  if (!exists("clim_argo_doxy")) {
    clim_argo_doxy <- nc_doxy_mean %>%
      rename(clim_doxy = "o_an") %>%
      mutate(month = i_month,
             lon = if_else(lon < 20, lon + 360, lon))
  } else {
    clim_argo_doxy <- rbind(
      clim_argo_doxy,
      nc_doxy_mean %>%
        rename(clim_doxy = "o_an") %>%
        mutate(month = i_month,
               lon = if_else(lon < 20, lon + 360, lon))
    )
  }

}
Will return stars object with 3693600 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 3693600 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 3693600 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 3693600 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 3693600 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 3693600 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 3693600 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 3693600 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 3693600 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 3693600 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 3693600 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 3693600 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_doxy %>%
   filter(depth < 30) %>%
   ggplot() +
   geom_tile(aes(lon, lat, fill = clim_doxy)) +
   facet_wrap(~depth) +
   scale_fill_viridis_c() +
   coord_quickmap()

Version Author Date
fa6cf38 ds2n19 2023-12-14 
clim_argo_doxy %>%
   ggplot(aes(clim_doxy)) +
   geom_histogram(binwidth = 25) +
   facet_wrap(~depth) +
   scale_y_log10()
Warning: Removed 18119100 rows containing non-finite values (`stat_bin()`).
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 547 rows containing missing values (`geom_bar()`).

Version Author Date
fa6cf38 ds2n19 2023-12-14

Write data to file

clim_argo_doxy %>% 
  drop_na() %>% 
  write_rds(file = paste0(path_argo_preprocessed, "/woa_doxy_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