GLODAPv2_2016: Mapped Climatologies

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Last updated: 2022-04-07

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Rmd	1b9b1af	jens-daniel-mueller	2021-06-03	included revelle factor calculation
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Rmd	2f37595	jens-daniel-mueller	2020-11-27	first rebuild after splitting the preprocessing part
Rmd	92e10aa	Jens Müller	2020-11-27	Initial commit
html	92e10aa	Jens Müller	2020-11-27	Initial commit

---

1 Read source files

Data source: Globally mapped climatologies from Lauvset et al. (2016) downloaded in June 2020 from glodap.info.

file_list <- c(
  "GLODAPv2.2016b.Cant.nc",
  "GLODAPv2.2016b.NO3.nc",
  "GLODAPv2.2016b.oxygen.nc",
  "GLODAPv2.2016b.PO4.nc",
  "GLODAPv2.2016b.salinity.nc",
  "GLODAPv2.2016b.silicate.nc",
  "GLODAPv2.2016b.TAlk.nc",
  "GLODAPv2.2016b.TCO2.nc",
  "GLODAPv2.2016b.temperature.nc"
)

# use only three basin to assign general basin mask
# ie this is not specific to the MLR fitting
basinmask <- basinmask %>% 
  filter(MLR_basins == "2") %>% 
  select(lat, lon, basin_AIP)

2 Plot data and write csv

Below, subsets of the climatologies are plotted. For all relevant parameters, the plots show:

• maps at depth levels
• concentration along global section

The global section path is indicated as white line in maps.

Please note that NA values in the climatologies were filled with neighbouring values on the longitudinal axis.

for (file in file_list) {
  # file <- file_list[2]
  
  print(file)
  # open file
  
  clim <-
    read_stars(paste(path_glodapv2_2016b, file, sep = ""),
               quiet = TRUE)
  
  # extract parameter name
  
  parameter <-
    str_split(file, pattern = "GLODAPv2.2016b.", simplify = TRUE)[2]
  parameter <-
    str_split(parameter, pattern = ".nc", simplify = TRUE)[1]
  
  # extract parameter
  
  clim <- clim %>% select(all_of(parameter))
  
  #convert to table
  
  clim_tibble <- clim %>%
    as_tibble()
  
  # harmonize column names
  
  clim_tibble <- clim_tibble %>%
    rename(lat = y,
           lon = x,
           depth = depth_surface)
  
  # join with basin mask and remove data outside basin mask
  
  clim_tibble <- inner_join(clim_tibble, basinmask)
  
  # determine bottom depth
  
  bottom_depth <- clim_tibble %>%
    filter(!is.na(!!sym(parameter))) %>%
    group_by(lon, lat) %>%
    summarise(bottom_depth = max(depth)) %>%
    ungroup()
  
  # remove data below bottom depth
  clim_tibble <- left_join(clim_tibble, bottom_depth)
  rm(bottom_depth)
  
  clim_tibble <- clim_tibble %>%
    filter(depth <= bottom_depth) %>%
    select(-bottom_depth)
  
  # fill NAs with closest value along longitude
  
  clim_tibble <- clim_tibble %>%
    group_by(lat, depth, basin_AIP) %>%
    arrange(lon) %>%
    fill(!!sym(parameter), .direction = "downup") %>%
    ungroup()
  
  # remove NAs
  
  clim_tibble <- clim_tibble %>%
    drop_na()
  
  # plot maps
  
  print(p_map_climatology(df = clim_tibble,
                          var = parameter))
  
  # plot sections
  
  print(
    p_section_global(
      df = clim_tibble,
      var = parameter,
      title_text = "GLODAPv2_2016_Mapped_Climatology"
    )
  )
  
  
  # write csv file
  
  clim_tibble %>%
    write_csv(paste(
      path_preprocessing,
      paste("GLODAPv2_2016_MappedClimatology_",
            parameter,
            ".csv",
            sep = ""),
      sep = ""
    ))
  
}

[1] "GLODAPv2.2016b.Cant.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-1.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-2.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

[1] "GLODAPv2.2016b.NO3.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-3.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-4.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

[1] "GLODAPv2.2016b.oxygen.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-5.png

Version	Author	Date
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-6.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

[1] "GLODAPv2.2016b.PO4.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-7.png

Version	Author	Date
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-8.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

[1] "GLODAPv2.2016b.salinity.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-9.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-10.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

[1] "GLODAPv2.2016b.silicate.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-11.png

Version	Author	Date
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-12.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

[1] "GLODAPv2.2016b.TAlk.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-13.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-14.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

[1] "GLODAPv2.2016b.TCO2.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-15.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-16.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

[1] "GLODAPv2.2016b.temperature.nc"

Past versions of GLODAPv2_2016_Mappedclimatologies-17.png

Version	Author	Date
dde77eb	jens-daniel-mueller	2022-04-01
0908ee5	jens-daniel-mueller	2021-11-15
ace484d	jens-daniel-mueller	2021-05-12
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

Past versions of GLODAPv2_2016_Mappedclimatologies-18.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6ff516e	jens-daniel-mueller	2021-03-30
88967c0	jens-daniel-mueller	2020-12-16
fd1a2c9	jens-daniel-mueller	2020-12-15
5c773fa	jens-daniel-mueller	2020-12-11
58359ac	jens-daniel-mueller	2020-11-27
92e10aa	Jens Müller	2020-11-27

3 Revelle factor

variables <-
  c("salinity", "temperature", "PO4", "silicate", "TAlk", "TCO2")

# i_variable <- variables[1]

for (i_variable in variables) {
  temp <- read_csv(paste(
    path_preprocessing,
    paste("GLODAPv2_2016_MappedClimatology_", i_variable, ".csv", sep = ""),
    sep = ""
  ))
  
  if (exists("GLODAP_predictors")) {
    GLODAP_predictors <- full_join(GLODAP_predictors, temp)
  }
  
  if (!exists("GLODAP_predictors")) {
    GLODAP_predictors <- temp
  }
}

rm(temp, i_variable, variables)

# removed na's attributable to slightly different coverage of predictor fields
GLODAP_predictors <- GLODAP_predictors %>%
  drop_na()

GLODAP_predictors <- GLODAP_predictors %>%
  mutate(
    rev_fac = buffer(
      flag = 15,
      var1 = TAlk * 1e-6,
      var2 = TCO2 * 1e-6,
      S = salinity,
      T = temperature,
      P = depth / 10,
      Pt = PO4 * 1e-6,
      Sit = silicate * 1e-6,
      k1k2 = "l"
    )$BetaD
  )

p_map_climatology(df = GLODAP_predictors,
                  var = "rev_fac")

Past versions of calculate_revelle_factor-1.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6e65117	jens-daniel-mueller	2022-02-16
0908ee5	jens-daniel-mueller	2021-11-15
028b5f9	jens-daniel-mueller	2021-06-03

p_section_global(df = GLODAP_predictors,
                 var = "rev_fac",
                 title_text = "GLODAPv2_2016_Mapped_Climatology")

Past versions of calculate_revelle_factor-2.png

Version	Author	Date
f088f55	jens-daniel-mueller	2022-04-01
dde77eb	jens-daniel-mueller	2022-04-01
6e65117	jens-daniel-mueller	2022-02-16
028b5f9	jens-daniel-mueller	2021-06-03

GLODAP_predictors %>%
  select(lon, lat, depth, basin_AIP, rev_fac) %>%
  write_csv(paste(
    path_preprocessing,
    paste("GLODAPv2_2016_MappedClimatology_",
          "rev_fac",
          ".csv",
          sep = ""),
    sep = ""
  ))

Session information

sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.3

Matrix products: default
BLAS:   /usr/local/R-4.1.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.1.2/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] seacarb_3.3.0    SolveSAPHE_2.1.0 oce_1.5-0        gsw_1.0-6       
 [5] stars_0.5-5      sf_1.0-5         abind_1.4-5      colorspace_2.0-2
 [9] marelac_2.1.10   shape_1.4.6      ggforce_0.3.3    metR_0.11.0     
[13] scico_1.3.0      patchwork_1.1.1  collapse_1.7.0   forcats_0.5.1   
[17] stringr_1.4.0    dplyr_1.0.7      purrr_0.3.4      readr_2.1.1     
[21] tidyr_1.1.4      tibble_3.1.6     ggplot2_3.3.5    tidyverse_1.3.1 
[25] workflowr_1.7.0 

loaded via a namespace (and not attached):
 [1] fs_1.5.2           bit64_4.0.5        lubridate_1.8.0    httr_1.4.2        
 [5] rprojroot_2.0.2    tools_4.1.2        backports_1.4.1    bslib_0.3.1       
 [9] utf8_1.2.2         R6_2.5.1           KernSmooth_2.23-20 DBI_1.1.2         
[13] withr_2.4.3        tidyselect_1.1.1   processx_3.5.2     bit_4.0.4         
[17] compiler_4.1.2     git2r_0.29.0       cli_3.1.1          rvest_1.0.2       
[21] xml2_1.3.3         isoband_0.2.5      labeling_0.4.2     sass_0.4.0        
[25] scales_1.1.1       checkmate_2.0.0    classInt_0.4-3     proxy_0.4-26      
[29] callr_3.7.0        digest_0.6.29      rmarkdown_2.11     pkgconfig_2.0.3   
[33] htmltools_0.5.2    highr_0.9          dbplyr_2.1.1       fastmap_1.1.0     
[37] rlang_0.4.12       readxl_1.3.1       rstudioapi_0.13    jquerylib_0.1.4   
[41] generics_0.1.1     farver_2.1.0       jsonlite_1.7.3     vroom_1.5.7       
[45] magrittr_2.0.1     Rcpp_1.0.8         munsell_0.5.0      fansi_1.0.2       
[49] lifecycle_1.0.1    stringi_1.7.6      whisker_0.4        yaml_2.2.1        
[53] MASS_7.3-55        grid_4.1.2         parallel_4.1.2     promises_1.2.0.1  
[57] crayon_1.4.2       haven_2.4.3        hms_1.1.1          knitr_1.37        
[61] ps_1.6.0           pillar_1.6.4       reprex_2.0.1       glue_1.6.0        
[65] evaluate_0.14      getPass_0.2-2      data.table_1.14.2  modelr_0.1.8      
[69] vctrs_0.3.8        tzdb_0.2.0         tweenr_1.0.2       httpuv_1.6.5      
[73] cellranger_1.1.0   gtable_0.3.0       polyclip_1.10-0    assertthat_0.2.1  
[77] xfun_0.29          lwgeom_0.2-8       broom_0.7.11       e1071_1.7-9       
[81] later_1.3.0        viridisLite_0.4.0  class_7.3-20       units_0.7-2       
[85] ellipsis_0.3.2