WOA O2 Climatology
David Stappard & Jens Daniel Müller
13 May, 2024
Last updated: 2024-05-13
Checks: 7 0
Knit directory:
bgc_argo_r_argodata/analysis/
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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
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
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()
clim_argo_doxy %>%
ggplot(aes(clim_doxy)) +
geom_histogram(binwidth = 25) +
facet_wrap(~depth) +
scale_y_log10()
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 workflowr_1.7.0
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 processx_3.8.0
[16] compiler_4.2.2 git2r_0.30.1 cli_3.6.1
[19] rvest_1.0.3 RNetCDF_2.6-1 xml2_1.3.3
[22] labeling_0.4.2 sass_0.4.4 scales_1.2.1
[25] classInt_0.4-8 callr_3.7.3 proxy_0.4-27
[28] digest_0.6.30 rmarkdown_2.18 pkgconfig_2.0.3
[31] htmltools_0.5.8.1 highr_0.9 dbplyr_2.2.1
[34] fastmap_1.1.0 rlang_1.1.1 readxl_1.4.1
[37] rstudioapi_0.15.0 farver_2.1.1 jquerylib_0.1.4
[40] generics_0.1.3 jsonlite_1.8.3 googlesheets4_1.0.1
[43] magrittr_2.0.3 ncmeta_0.3.5 Rcpp_1.0.10
[46] munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.3
[49] stringi_1.7.8 whisker_0.4 yaml_2.3.6
[52] grid_4.2.2 parallel_4.2.2 promises_1.2.0.1
[55] crayon_1.5.2 haven_2.5.1 hms_1.1.2
[58] knitr_1.41 ps_1.7.2 pillar_1.9.0
[61] reprex_2.0.2 glue_1.6.2 evaluate_0.18
[64] getPass_0.2-2 modelr_0.1.10 vctrs_0.6.4
[67] tzdb_0.3.0 httpuv_1.6.6 cellranger_1.1.0
[70] gtable_0.3.1 assertthat_0.2.1 cachem_1.0.6
[73] xfun_0.35 lwgeom_0.2-10 broom_1.0.5
[76] e1071_1.7-12 later_1.3.0 viridisLite_0.4.1
[79] class_7.3-20 googledrive_2.0.0 gargle_1.2.1
[82] units_0.8-0 timechange_0.1.1 ellipsis_0.3.2