eMLR - data preparation

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Last updated: 2020-11-26

Checks: 7 0

Knit directory: Cant_eMLR/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20200707)

The command set.seed(20200707) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: bbffe70

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version bbffe70. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .Rproj.user/
    Ignored:    data/
    Ignored:    dump/

Untracked files:
    Untracked:  code/biogeochemical_functions.R
    Untracked:  code/test_scripts/analysis_previous_studies.Rmd
    Untracked:  code/test_scripts/read_World_Ocean_Atlas_2013_Clement.Rmd

Unstaged changes:
    Modified:   analysis/eMLR_assumption_testing.Rmd
    Modified:   analysis/eMLR_model_fitting.Rmd
    Modified:   analysis/mapping_cant_calculation.Rmd
    Modified:   code/mapping_functions.R
    Modified:   code/plotting_functions.R
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---

1 Libraries

Loading libraries specific to the the analysis performed in this section.

library(marelac)
library(lubridate)

2 Required data

Required are:

• GLODAPv2.2020
  • cleaned data file
  • horizontal grid of sampling coordinates
• Cant from GLODAPv2_2016b_MappedClimatologies
• annual mean atmospheric pCO₂

GLODAP <-
  read_csv(
    here::here(
      "data/interim",
      "GLODAPv2.2020_clean.csv"
    )
  )

GLODAP_obs_grid <-
  read_csv(
    here::here(
      "data/interim",
      "GLODAPv2.2020_clean_obs_grid.csv"
    )
  )

S04_cant_3d <-
  read_csv(
    here::here(
      "data/interim",
      "S04_cant_3d.csv"
    )
  )

# G19_cant_3d <-
#   read_csv(
#     here::here(
#       "data/interim",
#       "G19_cant_3d.csv"
#     )
#   )

co2_atm <-
  read_csv(here::here(
    "data/interim",
    "co2_atm.csv"
  ))

3 C*

C* serves as a conservative tracer of anthropogenic CO₂ uptake. It is derived from measured DIC by removing the impact of

• organic matter formation and respiration
• calcification and calcium carbonate dissolution

Contributions of those processes are estimated from phosphate and alkalinity concentrations.

3.1 Stoichiometric ratios

The stoichiometric nutrient ratios for the production and mineralization of organic matter were set to:

• C/P: 117
• N/P: 16

3.2 Calculation

C* is calculated as:

print(b_cstar)

function (tco2, phosphate, talk) 
{
    cstar = tco2 - (parameters$rCP * phosphate) - 0.5 * (talk - 
        (parameters$rNP * phosphate))
    return(cstar)
}

GLODAP <- GLODAP %>% 
  mutate(rCP_phosphate = -parameters$rCP * phosphate,
         talk_05 = -0.5 * talk,
         rNP_phosphate_05 = -0.5 * parameters$rNP * phosphate,
         cstar = b_cstar(tco2, phosphate, talk))

4 PO₄* calculation

The predictor PO₄* was be calculated according to Clement and Gruber (2018), ie based on oxygen. Please note that an errornous equations for PO4* calculation is given in the supplement of Gruber et al (2019), based on nitrate.

GLODAP <- GLODAP %>% 
  mutate(phosphate_star = b_phosphate_star(phosphate, oxygen))

5 Reference year adjustment

The reference year adjustment relies on an apriori estimate of Cant at a given location and depth, which is used as a scaling factor for the concurrent change in atmospheric CO₂. The underlying assumption is a transient steady state for the oceanic Cant uptake. Here, Cant from the GLODAP mapped Climatology was used.

Note that eq. 6 in Clement and Gruber (2018) misses pCO₂ pre-industrial in the denominator. Here we use the equation published in Gruber et al. (2019).

5.1 Merge data sets

5.1.1 GLODAP + Cant

S04_cant_3d_obs <- left_join(
  GLODAP_obs_grid,
  S04_cant_3d %>% select(-c(cant, eras))
  )

# calculate number of cant data points per grid cell
S04_cant_3d_obs <- S04_cant_3d_obs %>%
  group_by(lon, lat) %>% 
  mutate(n = n()) %>% 
  ungroup()

# S04_cant_3d_obs %>%
#   filter(n <= 1) %>%
#   ggplot(aes(lon,lat)) +
#   geom_point(data = GLODAP_obs_grid, aes(lon, lat)) +
#   geom_point(col = "red")

rm(S04_cant_3d, GLODAP_obs_grid)

GLODAP_cant_obs <- full_join(GLODAP, S04_cant_3d_obs)

rm(GLODAP, S04_cant_3d_obs)

# fill number of cant data points per grid cell to all observations
GLODAP_cant_obs <- GLODAP_cant_obs %>%
  group_by(lon, lat) %>% 
  fill(n, .direction = "updown") %>% 
  ungroup()

The mapped Cant product was merged with GLODAP observation by:

• using an identical 1x1° horizontal grid
• linear interpolation of C_ant from standard to sampling depth

# interpolate cant to observation depth
GLODAP_cant_obs_int <- GLODAP_cant_obs %>%
  filter(n > 1) %>% 
  group_by(lat, lon) %>%
  arrange(depth) %>%
  mutate(cant_pos_int = approxfun(depth, cant_pos, rule = 2)(depth)) %>%
  ungroup()

# set cant for observation depth if only one cant available
GLODAP_cant_obs_set <- GLODAP_cant_obs %>%
  filter(n == 1) %>%
  group_by(lat, lon) %>%
  mutate(cant_pos_int = mean(cant_pos, na.rm = TRUE)) %>%
  ungroup()

# bin data sets with interpolated and set cant
GLODAP_cant_obs <- bind_rows(GLODAP_cant_obs_int, GLODAP_cant_obs_set)
rm(GLODAP_cant_obs_int, GLODAP_cant_obs_set)


ggplot() +
  geom_path(
    data = GLODAP_cant_obs %>%
      filter(lat == 48.5, lon == 165.5,!is.na(cant_pos)) %>%
      arrange(depth),
    aes(cant_pos, depth, col = "mapped")
  ) +
  geom_point(
    data = GLODAP_cant_obs %>%
      filter(lat == 48.5, lon == 165.5,!is.na(cant_pos)) %>%
      arrange(depth),
    aes(cant_pos, depth, col = "mapped")
  ) +
  geom_point(
    data = GLODAP_cant_obs %>%
      filter(lat == 48.5, lon == 165.5, date == ymd("2018-06-27")),
    aes(cant_pos_int, depth, col = "interpolated")
  ) +
  scale_y_reverse() +
  scale_color_brewer(palette = "Dark2", name = "") +
  labs(title = "Cant interpolation to sampling depth - example profile")

# remove cant data at grid cells without observations
GLODAP <- GLODAP_cant_obs %>%
  filter(!is.na(cstar)) %>%
  mutate(cant_pos = cant_pos_int) %>%
  select(-cant_pos_int, n)

rm(GLODAP_cant_obs)

5.1.2 GLODAP + atm. pCO₂

GLODAP observations were merged with mean annual atmospheric pCO₂ levels by year.

GLODAP <- left_join(GLODAP, co2_atm)

5.2 Calculate adjustment

C_ant for tref = 2007 was calculated by applying alpha = 0.28 to the estimate of Sabine et al. (2004).

For tref = 2015 we scaled alpha as 0.28/13 * dt.

# assign reference year
GLODAP <- GLODAP %>% 
  group_by(era) %>% 
  mutate(tref = median(year)) %>% 
  ungroup()

# calculate reference year
tref <- GLODAP %>% 
  group_by(era) %>% 
  summarise(year = median(year)) %>% 
  ungroup()

# extract atm pCO2 at reference year
co2_atm_tref <- right_join(co2_atm, tref) %>% 
  select(-year) %>% 
  rename(pCO2_tref = pCO2)

# merge atm pCO2 at tref with GLODAP
GLODAP <- full_join(GLODAP, co2_atm_tref)
rm(co2_atm, tref)

# scale cant to reference year
GLODAP <- GLODAP %>%
  mutate(alpha = (tref - min(tref)) * (0.28 / 13),
         cant_pos = cant_pos * (1 + alpha))

# calculate cstar for reference year
GLODAP <- GLODAP %>%
  mutate(
    cstar_tref_delta =
      ((pCO2 - pCO2_tref) / (pCO2_tref - parameters$preind_atm_pCO2)) * cant_pos,
    cstar_tref = cstar - cstar_tref_delta)

5.3 Control plots

5.3.1 Histogram

GLODAP %>% 
  ggplot(aes(cstar_tref_delta)) +
  geom_histogram()

5.3.2 Time series

GLODAP %>% 
  sample_n(1e4) %>% 
  ggplot(aes(year, cstar_tref_delta, col = cant_pos)) +
  geom_point() +
  scale_color_viridis_c() +
  labs(title = "random subsample 1e4")

GLODAP %>% 
  ggplot(aes(year, cstar_tref_delta)) +
  geom_bin2d() +
  scale_fill_viridis_c()

6 Selected section plots

A selected section is plotted to demonstrate the magnitude of various parameters and corrections relevant to C*.

GLODAP_cruise <- GLODAP %>% 
  filter(cruise %in% parameters$cruises_meridional)

map +
  geom_path(data = GLODAP_cruise %>%
              arrange(date),
            aes(lon, lat)) +
  geom_point(data = GLODAP_cruise %>%
              arrange(date),
             aes(lon, lat, col = date)) +
  scale_color_viridis_c(trans = "date") +
  labs(title = paste("Cruise year:", mean(GLODAP_cruise$year)))

lat_section <- 
GLODAP_cruise %>%
  ggplot(aes(lat, depth)) +
  scale_y_reverse() +
  scale_color_viridis_c() +
  theme(axis.title.x = element_blank())

lat_section +
  geom_point(aes(col = tco2))

lat_section +
  geom_point(aes(col = rCP_phosphate))

lat_section +
  geom_point(aes(col = talk_05))

lat_section +
  geom_point(aes(col = rNP_phosphate_05))

lat_section +
  geom_point(aes(col = cstar))

lat_section +
  geom_point(aes(col = cstar_tref))

rm(lat_section, GLODAP_cruise)

# remove columns not required for further analysis
GLODAP <- GLODAP %>% 
  select(-c(rCP_phosphate:cstar, cant_pos:cstar_tref_delta))

7 Isoneutral slabs

The following boundaries for isoneutral slabs were defined:

• Atlantic: -, 26, 26.5, 26.75, 27, 27.25, 27.5, 27.75, 27.85, 27.95, 28.05, 28.1, 28.15, 28.2,
• Indo-Pacific: -, 26, 26.5, 26.75, 27, 27.25, 27.5, 27.75, 27.85, 27.95, 28.05, 28.1,

Continuous neutral densities (gamma) values from GLODAP are grouped into isoneutral slabs.

GLODAP <- m_cut_gamma(GLODAP, "gamma")

GLODAP_cruise <- GLODAP %>% 
  filter(cruise %in% parameters$cruises_meridional)

lat_section <- 
GLODAP_cruise %>%
  ggplot(aes(lat, depth)) +
  scale_y_reverse() +
  theme(legend.position = "bottom")

lat_section +
  geom_point(aes(col = gamma_slab)) +
  scale_color_viridis_d()

rm(lat_section, GLODAP_cruise)

GLODAP_cruise <- GLODAP %>% 
  filter(cruise %in% parameters$cruises_meridional)

library(oce)
library(gsw)
# calculate pressure from depth

GLODAP_cruise <- GLODAP_cruise %>% 
  mutate(CTDPRS = gsw_p_from_z(-depth,
                               lat))

GLODAP_cruise <- GLODAP_cruise %>% 
  mutate(THETA = swTheta(salinity = sal,
                         temperature = tem,
                         pressure = CTDPRS,
                         referencePressure = 0,
                         longitude = lon-180,
                         latitude = lat))

GLODAP_cruise <- GLODAP_cruise %>% 
  rename(LATITUDE = lat,
         LONGITUDE = lon,
         SALNTY = sal,
         gamma_provided = gamma)

library(reticulate)
source_python(here::here("code/python_scripts",
                         "Gamma_GLODAP_python.py"))

GLODAP_cruise <- calculate_gamma(GLODAP_cruise)

GLODAP_cruise <- GLODAP_cruise %>% 
  mutate(gamma_delta = gamma_provided - GAMMA)

lat_section <- 
GLODAP_cruise %>%
  ggplot(aes(LATITUDE, CTDPRS)) +
  scale_y_reverse() +
  theme(legend.position = "bottom")

lat_section +
  geom_point(aes(col = gamma_delta)) +
  scale_color_viridis_c()

GLODAP_cruise %>% 
  ggplot(aes(gamma_delta))+
  geom_histogram()

rm(lat_section, GLODAP_cruise, cruises_meridional)

8 Observations coverage

GLODAP <- GLODAP %>% 
  mutate(era = factor(era, c("JGOFS_WOCE", "GO_SHIP", "new_era"))) %>%
  mutate(gamma_slab = factor(gamma_slab), 
         gamma_slab = factor(gamma_slab, levels = rev(levels(gamma_slab))))

GLODAP %>% 
  filter(basin == "Atlantic") %>% 
  ggplot(aes(lat, gamma_slab)) +
  geom_bin2d(binwidth = 5) +
  scale_fill_viridis_c(option = "magma", direction = -1, trans = "log10") +
  scale_x_continuous(breaks = seq(-100,100,20)) +
  facet_grid(era~basin)

GLODAP %>% 
  filter(basin == "Indo-Pacific") %>% 
  ggplot(aes(lat, gamma_slab)) +
  geom_bin2d(binwidth = 5) +
  scale_fill_viridis_c(option = "magma", direction = -1, trans = "log10") +
  scale_x_continuous(breaks = seq(-100,100,20)) +
  facet_grid(era~basin)

9 Individual cruise sections

Zonal and meridional section plots are produce for each cruise individually and can be downloaded here.

cruises <- GLODAP %>% 
  group_by(cruise) %>% 
  summarise(date_mean = mean(date, na.rm = TRUE),
            n = n()) %>% 
  ungroup() %>% 
  arrange(date_mean)

GLODAP <- full_join(GLODAP, cruises)

n <- 0
for (i_cruise in unique(cruises$cruise)) {

# i_cruise <- unique(cruises$cruise)[1]
n <- n + 1
print(n)  
  
GLODAP_cruise <- GLODAP %>%
  filter(cruise == i_cruise) %>% 
  arrange(date)

cruises_cruise <- cruises %>%
  filter(cruise == i_cruise)
  
map_plot <- 
  map +
  geom_point(data = GLODAP_cruise,
             aes(lon, lat, col = date)) +
  scale_color_viridis_c(trans = "date") +
  labs(title = paste("Mean date:", cruises_cruise$date_mean,
                     "| cruise:", cruises_cruise$cruise,
                     "| n(samples):", cruises_cruise$n))


lon_section <- GLODAP_cruise %>%
  ggplot(aes(lon, depth)) +
  scale_y_reverse() +
  scale_color_viridis_c()

lon_tco2 <- lon_section+
  geom_point(aes(col=tco2))

lon_talk <- lon_section+
  geom_point(aes(col=talk))

lon_phosphate <- lon_section+
  geom_point(aes(col=phosphate))

lon_oxygen <- lon_section+
  geom_point(aes(col=oxygen))

lon_aou <- lon_section+
  geom_point(aes(col=aou))

lon_phosphate_star <- lon_section+
  geom_point(aes(col=phosphate_star))

lon_nitrate <- lon_section+
  geom_point(aes(col=nitrate))

lon_cstar <- lon_section+
  geom_point(aes(col=cstar_tref))


lat_section <- GLODAP_cruise %>%
  ggplot(aes(lat, depth)) +
  scale_y_reverse() +
  scale_color_viridis_c()

lat_tco2 <- lat_section+
  geom_point(aes(col=tco2))

lat_talk <- lat_section+
  geom_point(aes(col=talk))

lat_phosphate <- lat_section+
  geom_point(aes(col=phosphate))

lat_oxygen <- lat_section+
  geom_point(aes(col=oxygen))

lat_aou <- lat_section+
  geom_point(aes(col=aou))

lat_phosphate_star <- lat_section+
  geom_point(aes(col=phosphate_star))

lat_nitrate <- lat_section+
  geom_point(aes(col=nitrate))

lat_cstar <- lat_section+
  geom_point(aes(col=cstar_tref))

hist_tco2 <- GLODAP_cruise %>%
  ggplot(aes(tco2)) +
  geom_histogram()

hist_talk <- GLODAP_cruise %>%
  ggplot(aes(talk)) +
  geom_histogram()

hist_phosphate <- GLODAP_cruise %>%
  ggplot(aes(phosphate)) +
  geom_histogram()

hist_oxygen <- GLODAP_cruise %>%
  ggplot(aes(oxygen)) +
  geom_histogram()

hist_aou <- GLODAP_cruise %>%
  ggplot(aes(aou)) +
  geom_histogram()

hist_phosphate_star <- GLODAP_cruise %>%
  ggplot(aes(phosphate_star)) +
  geom_histogram()

hist_nitrate <- GLODAP_cruise %>%
  ggplot(aes(nitrate)) +
  geom_histogram()

hist_cstar <- GLODAP_cruise %>%
  ggplot(aes(cstar_tref)) +
  geom_histogram()

(map_plot /
    ((hist_tco2 / hist_talk / hist_phosphate / hist_cstar) |
       (hist_oxygen / hist_phosphate_star / hist_nitrate / hist_aou)
    )) |
  ((lat_tco2 / lat_talk / lat_phosphate / lat_oxygen / lat_aou / lat_phosphate_star / lat_nitrate / lat_cstar) |
     (lon_tco2 / lon_talk / lon_phosphate / lon_oxygen /  lon_aou /lon_phosphate_star / lon_nitrate / lon_cstar))    

ggsave(here::here("output/figure/eMLR/data_preparation/all_cruises_clean",
                  paste("GLODAP_cruise_date",
                        cruises_cruise$date_mean,
                        "n",
                        cruises_cruise$n,
                        "cruise",
                        cruises_cruise$cruise,
                        ".png",
                        sep = "_")),
                  width = 20, height = 12)

rm(map_plot,
   lon_section, lat_section,
   lat_tco2, lat_talk, lat_phosphate, lon_tco2, lon_talk, lon_phosphate,
   GLODAP_cruise, cruises_cruise)

}

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10 Write files

GLODAP <- GLODAP %>% 
  rename(cstar = cstar_tref)

GLODAP %>% write_csv(here::here("data/interim",
                                "GLODAPv2.2020_MLR_fitting_ready.csv"))

co2_atm_tref  %>%
  write_csv(here::here(
    "data/interim",
    "co2_atm_tref.csv"
  ))

Session information

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_Germany.1252  LC_CTYPE=English_Germany.1252   
[3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C                    
[5] LC_TIME=English_Germany.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] lubridate_1.7.9 marelac_2.1.10  shape_1.4.4     metR_0.7.0     
 [5] scico_1.2.0     patchwork_1.0.1 collapse_1.3.2  forcats_0.5.0  
 [9] stringr_1.4.0   dplyr_1.0.0     purrr_0.3.4     readr_1.3.1    
[13] tidyr_1.1.0     tibble_3.0.3    ggplot2_3.3.2   tidyverse_1.3.0
[17] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] httr_1.4.2         viridisLite_0.3.0  jsonlite_1.7.0     here_0.1          
 [5] modelr_0.1.8       Formula_1.2-3      assertthat_0.2.1   blob_1.2.1        
 [9] cellranger_1.1.0   yaml_2.2.1         pillar_1.4.6       backports_1.1.8   
[13] lattice_0.20-41    glue_1.4.1         digest_0.6.25      RColorBrewer_1.1-2
[17] promises_1.1.1     checkmate_2.0.0    rvest_0.3.6        colorspace_1.4-1  
[21] sandwich_2.5-1     htmltools_0.5.0    httpuv_1.5.4       Matrix_1.2-18     
[25] pkgconfig_2.0.3    broom_0.7.0        seacarb_3.2.13     haven_2.3.1       
[29] xtable_1.8-4       scales_1.1.1       whisker_0.4        later_1.1.0.1     
[33] git2r_0.27.1       farver_2.0.3       generics_0.0.2     ellipsis_0.3.1    
[37] withr_2.2.0        cli_2.0.2          magrittr_1.5       crayon_1.3.4      
[41] readxl_1.3.1       evaluate_0.14      fs_1.4.2           fansi_0.4.1       
[45] xml2_1.3.2         oce_1.2-0          tools_4.0.2        data.table_1.13.0 
[49] hms_0.5.3          lifecycle_0.2.0    munsell_0.5.0      reprex_0.3.0      
[53] gsw_1.0-5          compiler_4.0.2     lfe_2.8-5.1        rlang_0.4.7       
[57] grid_4.0.2         rstudioapi_0.11    labeling_0.3       rmarkdown_2.3     
[61] testthat_2.3.2     gtable_0.3.0       DBI_1.1.0          R6_2.4.1          
[65] zoo_1.8-8          knitr_1.30         rprojroot_1.3-2    stringi_1.4.6     
[69] parallel_4.0.2     Rcpp_1.0.5         vctrs_0.3.2        dbplyr_1.4.4      
[73] tidyselect_1.1.0   xfun_0.16