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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

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

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()

Version Author Date
fa6cf38 ds2n19 2023-12-14 
clim_argo_nitrate %>%
   ggplot(aes(clim_nitrate)) +
   geom_histogram(binwidth = 2) +
   facet_wrap(~depth) +
   scale_y_log10()

Version Author Date
fa6cf38 ds2n19 2023-12-14

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_1.2.2           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_0.5.8.1   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