GLODAPv2_2020

workflowr

• Summary
• Checks
• Past versions

Last updated: 2021-07-02

Checks: 7 0

Knit directory: emlr_obs_preprocessing/

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.

---

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: ba6b773

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 ba6b773. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/

Unstaged changes:
    Modified:   code/Workflowr_project_managment.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/read_GLODAPv2_2021.Rmd) and HTML (docs/read_GLODAPv2_2021.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	98599d8	jens-daniel-mueller	2021-06-27	Build site.
Rmd	4f9c370	jens-daniel-mueller	2021-06-27	update to latest GLODAP pre-release
html	265c4ef	jens-daniel-mueller	2021-06-04	Build site.
html	c79346a	jens-daniel-mueller	2021-06-03	Build site.
html	9d8353f	jens-daniel-mueller	2021-05-31	Build site.
Rmd	b948168	jens-daniel-mueller	2021-05-31	ingest GLODAPv2_2021 beta data

---

path_glodapv2_2021  <- "/nfs/kryo/work/updata/glodapv2_2021/"
path_preprocessing  <- paste(path_root, "/observations/preprocessing/", sep = "")

1 Read files

Main data source for this project is GLODAPv2.2020_Merged_Master_File.csv downloaded from glodap.info in June 2020.

GLODAP <-
  read_csv(
    paste(
      path_glodapv2_2021,
      "GLODAPv2.2021_Merged_Master_File_beta_20210624.csv",
      sep = ""
    ),
    na = "-9999",
    col_types = cols(.default = col_double())
  )

# select relevant columns
GLODAP <- GLODAP %>%
  rename_with(~str_remove(., 'G2'))

# select relevant columns
GLODAP <- GLODAP %>%
  select(cruise:talkqc)

# create date column
GLODAP <- GLODAP %>%
  mutate(date = ymd(paste(year, month, day))) %>%
  relocate(date)

# harmonize column names
GLODAP <- GLODAP  %>%
  rename(sal = salinity,
         temp = temperature)

# harmonize coordinates
GLODAP <- GLODAP  %>%
  rename(lon = longitude,
         lat = latitude) %>%
  mutate(lon = if_else(lon < 20, lon + 360, lon))

# remove irrelevant columns
GLODAP <- GLODAP %>%
  select(-c(month:minute,
            maxsampdepth, bottle, sigma0:sigma4,
            nitrite:nitritef))

2 Data preparation

2.1 Subset tco2 data

The vast majority of rows is removed due to missing tco2 observations.

GLODAP <- GLODAP %>% 
  filter(!is.na(tco2))

2.2 Horizontal gridding

For merging with other data sets, all observations were grouped into latitude intervals of:

• 1° x 1°

GLODAP <- m_grid_horizontal(GLODAP)

2.3 Apply basin mask

# 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)

GLODAP <- inner_join(GLODAP, basinmask)

2.4 Create clean observations grid

GLODAP_obs_grid <- GLODAP %>% 
  count(lat, lon)

2.5 Add row number

GLODAP <- GLODAP  %>%  
  mutate(row_number = row_number()) %>% 
  relocate(row_number)

2.6 Write GLODAP file

GLODAP  %>%  
  write_csv(paste(path_preprocessing,
                             "GLODAPv2.2021_preprocessed.csv",
                             sep = ""))

3 Overview plots

3.1 Assign coarse spatial grid

For the following plots, the cleaned data set was re-opened and observations were gridded spatially to intervals of:

• 5° x 5°

GLODAP <- m_grid_horizontal_coarse(GLODAP)

3.2 Histogram Zonal coverage

GLODAP_histogram_lat <- GLODAP %>%
  group_by(lat_grid) %>%
  tally() %>%
  ungroup()

GLODAP_histogram_lat %>%
  ggplot(aes(lat_grid, n)) +
  geom_col() +
  coord_flip() +
  theme(legend.title = element_blank())

Past versions of coverage_histogram_zonal-1.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

rm(GLODAP_histogram_lat)

3.3 Histogram temporal coverage

GLODAP_histogram_year <- GLODAP %>%
  group_by(year) %>%
  tally() %>%
  ungroup()

GLODAP_histogram_year %>%
  ggplot() +
  geom_col(aes(year, n)) +
  theme(
    axis.title.x = element_blank()
  )

Past versions of coverage_histogram_temporal-1.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

rm(GLODAP_histogram_year)

3.4 Zonal temporal coverage (Hovmoeller)

GLODAP_hovmoeller_year <- GLODAP %>%
  group_by(year, lat_grid) %>%
  tally() %>%
  ungroup()

GLODAP_hovmoeller_year %>%
  ggplot(aes(year, lat_grid, fill = log10(n))) +
  geom_tile() +
  geom_vline(xintercept = c(1999.5, 2012.5)) +
  scale_fill_viridis_c(option = "magma", direction = -1) +
  theme(legend.position = "top",
        axis.title.x = element_blank())

Past versions of coverage_hovmoeller-1.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

rm(GLODAP_hovmoeller_year)

3.5 Coverage map

map +
  geom_raster(data = GLODAP_obs_grid,
              aes(lon, lat, fill = log10(n))) +
  scale_fill_viridis_c(option = "magma",
                       direction = -1)

Past versions of coverage_map-1.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

4 CANYON-B

4.1 Comparison to GLODAP

source("/net/kryo/work/uptools/co2_calculation/CANYON-B/CANYONB.R")

GLODAP_Can_B <- GLODAP %>%
  mutate(lon = if_else(lon > 180, lon - 360, lon)) %>%
  arrange(year) %>% 
  select(row_number, year, date, lat, lon, depth, basin_AIP,
         temp, sal, oxygen,
         talk, tco2, nitrate, phosphate, silicate)

# filter rows with essential variables for Canyon-B
GLODAP_Can_B <- GLODAP_Can_B %>%
  filter(across(c(lat, lon, depth,
                  temp, sal, oxygen), ~ !is.na(.x)))

GLODAP_Can_B <- GLODAP_Can_B %>%
  mutate(as_tibble(
    CANYONB(
      date = paste0(as.character(date), " 12:00"),
      lat = lat,
      lon = lon,
      pres = depth,
      temp = temp,
      psal = sal,
      doxy = oxygen,
      param = c("AT", "CT", "NO3", "PO4", "SiOH4")
    )
  ))

GLODAP_Can_B <- GLODAP_Can_B %>%
  select(-ends_with(c("_ci", "_cim", "_cin", "_cii")))


GLODAP_Can_B <- GLODAP_Can_B %>%
  rename(
    "talk_CANYONB" = "AT",
    "tco2_CANYONB" = "CT",
    "nitrate_CANYONB" = "NO3",
    "phosphate_CANYONB" = "PO4",
    "silicate_CANYONB" = "SiOH4"
  )


variables <- c("talk", "tco2", "nitrate", "phosphate", "silicate")

for (i_variable in variables) {
  # i_variable <- variables[1]
  
  # calculate equal axis limits and binwidth
  axis_lims <- GLODAP_Can_B %>%
    drop_na() %>% 
    summarise(max_value = max(c(max(
      !!sym(i_variable)
    ),
    max(!!sym(
      paste0(i_variable, "_CANYONB")
    )))),
    min_value = min(c(min(
      !!sym(i_variable)
    ),
    min(!!sym(
      paste0(i_variable, "_CANYONB")
    )))))
  
  binwidth_value <- (axis_lims$max_value - axis_lims$min_value) / 60
  axis_lims <- c(axis_lims$min_value, axis_lims$max_value)
  
  print(
    ggplot(GLODAP_Can_B, aes(
      x = !!sym(i_variable),
      y = !!sym(paste0(i_variable, "_CANYONB"))
    )) +
      geom_bin2d(binwidth = binwidth_value) +
      scale_fill_viridis_c(trans = "log10") +
      geom_abline(slope = 1, col = 'red') +
      coord_equal(xlim = axis_lims,
                  ylim = axis_lims) +
      facet_wrap( ~ basin_AIP) +
      labs(title = "All years")
  ) 
  
  
  for (i_year in unique(GLODAP_Can_B$year)) {
    # i_year <- 2017
    
    print(
      ggplot(
        GLODAP_Can_B %>% filter(year == i_year),
        aes(x = !!sym(i_variable),
            y = !!sym(paste0(
              i_variable, "_CANYONB"
            )))
      ) +
        geom_bin2d(binwidth = binwidth_value) +
        scale_fill_viridis_c(trans = "log10") +
        geom_abline(slope = 1, col = 'red') +
        coord_equal(xlim = axis_lims,
                    ylim = axis_lims) +
        facet_wrap( ~ basin_AIP) +
        labs(title = paste("Year:", i_year))
    )
  }
  
}

Past versions of CANYON-B-1.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-2.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-3.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-4.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-5.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-6.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-7.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-8.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-9.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-10.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-11.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-12.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-13.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-14.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-15.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-16.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-17.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-18.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-19.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-20.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-21.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-22.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-23.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-24.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-25.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-26.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-27.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-28.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-29.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-30.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-31.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-32.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-33.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-34.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-35.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-36.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-37.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-38.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-39.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-40.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-41.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-42.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-43.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-44.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-45.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-46.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-47.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-48.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-49.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-50.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-51.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-52.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-53.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-54.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-55.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-56.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-57.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-58.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-59.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-60.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-61.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-62.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-63.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-64.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-65.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-66.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-67.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-68.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-69.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-70.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-71.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-72.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-73.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-74.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-75.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-76.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-77.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-78.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-79.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-80.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-81.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-82.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-83.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-84.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-85.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-86.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-87.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-88.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-89.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-90.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-91.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-92.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-93.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-94.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-95.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-96.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-97.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-98.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-99.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-100.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-101.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-102.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-103.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-104.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-105.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-106.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-107.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-108.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-109.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-110.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-111.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-112.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-113.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-114.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-115.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-116.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-117.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-118.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-119.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-120.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-121.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-122.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-123.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-124.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-125.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-126.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-127.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-128.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-129.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-130.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-131.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-132.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-133.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-134.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-135.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-136.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-137.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-138.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-139.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-140.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-141.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-142.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-143.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-144.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-145.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-146.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-147.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-148.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-149.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-150.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-151.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-152.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-153.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-154.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-155.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-156.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-157.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-158.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-159.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-160.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-161.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-162.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-163.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-164.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-165.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-166.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-167.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-168.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-169.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-170.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-171.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-172.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-173.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-174.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-175.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-176.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-177.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-178.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-179.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-180.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-181.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-182.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-183.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-184.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-185.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-186.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-187.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-188.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-189.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-190.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-191.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-192.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-193.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-194.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-195.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-196.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-197.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-198.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-199.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-200.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-201.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-202.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-203.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-204.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-205.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-206.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-207.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-208.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-209.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-210.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-211.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-212.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-213.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-214.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-215.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-216.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-217.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-218.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-219.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-220.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-221.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-222.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-223.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-224.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-225.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-226.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-227.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-228.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-229.png

Version	Author	Date
98599d8	jens-daniel-mueller	2021-06-27
9d8353f	jens-daniel-mueller	2021-05-31

Past versions of CANYON-B-230.png

Version	Author	Date
9d8353f	jens-daniel-mueller	2021-05-31

4.2 Write Canyon-B file

GLODAP_Can_B %>% 
  select(row_number,
         talk_CANYONB, tco2_CANYONB,
         nitrate_CANYONB, phosphate_CANYONB, silicate_CANYONB) %>% 
  write_csv(paste(path_preprocessing,
                             "GLODAPv2.2021_Canyon-B.csv",
                             sep = ""))

5 CONTENT

5.1 Comparison to GLODAP

source("/net/kryo/work/uptools/co2_calculation/CONTENT/CO2CONTENT.R")

GLODAP_Cont <- GLODAP %>%
  mutate(lon = if_else(lon > 180, lon - 360, lon)) %>%
  arrange(year) %>% 
  select(row_number, year, date, lat, lon, depth, basin_AIP,
         temp, sal, oxygen,
         talk, tco2) %>% 
  filter(year == 2015)

# filter rows with essential variables for Canyon-B
GLODAP_Cont <- GLODAP_Cont %>%
  filter(across(c(lat, lon, depth,
                  temp, sal, oxygen), ~ !is.na(.x)))

GLODAP_Cont <- GLODAP_Cont %>%
  mutate(as_tibble(
    CO2CONTENT(
      date = paste0(as.character(date), " 12:00"),
      lat = lat,
      lon = lon,
      pres = depth,
      temp = temp,
      psal = sal,
      doxy = oxygen,
      param = c("AT", "CT")
    )
  ))

GLODAP_Cont <- GLODAP_Cont %>%
  select(-ends_with(c("_ci", "_cim", "_cin", "_cii")))


GLODAP_Cont <- GLODAP_Cont %>%
  rename(
    "talk_CANYONB" = "AT",
    "tco2_CANYONB" = "CT"
  )


variables <- c("talk", "tco2")

for (i_variable in variables) {
  # i_variable <- variables[1]
  
  # calculate equal axis limits and binwidth
  axis_lims <- GLODAP_Cont %>%
    drop_na() %>% 
    summarise(max_value = max(c(max(
      !!sym(i_variable)
    ),
    max(!!sym(
      paste0(i_variable, "_CANYONB")
    )))),
    min_value = min(c(min(
      !!sym(i_variable)
    ),
    min(!!sym(
      paste0(i_variable, "_CANYONB")
    )))))
  
  binwidth_value <- (axis_lims$max_value - axis_lims$min_value) / 60
  axis_lims <- c(axis_lims$min_value, axis_lims$max_value)
  
  print(
    ggplot(GLODAP_Cont, aes(
      x = !!sym(i_variable),
      y = !!sym(paste0(i_variable, "_CANYONB"))
    )) +
      geom_bin2d(binwidth = binwidth_value) +
      scale_fill_viridis_c(trans = "log10") +
      geom_abline(slope = 1, col = 'red') +
      coord_equal(xlim = axis_lims,
                  ylim = axis_lims) +
      facet_wrap( ~ basin_AIP) +
      labs(title = "All years")
  ) 
  
  
  for (i_year in unique(GLODAP_Cont$year)) {
    # i_year <- 2017
    
    print(
      ggplot(
        GLODAP_Cont %>% filter(year == i_year),
        aes(x = !!sym(i_variable),
            y = !!sym(paste0(
              i_variable, "_CANYONB"
            )))
      ) +
        geom_bin2d(binwidth = binwidth_value) +
        scale_fill_viridis_c(trans = "log10") +
        geom_abline(slope = 1, col = 'red') +
        coord_equal(xlim = axis_lims,
                    ylim = axis_lims) +
        facet_wrap( ~ basin_AIP) +
        labs(title = paste("Year:", i_year))
    )
  }
  
}

5.2 Write CONTENT file

GLODAP_Cont %>% 
  select(row_number,
         talk_CANYONB, tco2_CANYONB) %>% 
  write_csv(paste(path_preprocessing,
                             "GLODAPv2.2021_Canyon-B.csv",
                             sep = ""))

Session information

sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2

Matrix products: default
BLAS:   /usr/local/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.0.3/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] mgcv_1.8-33     nlme_3.1-149    lubridate_1.7.9 metR_0.9.0     
 [5] scico_1.2.0     patchwork_1.1.1 collapse_1.5.0  forcats_0.5.0  
 [9] stringr_1.4.0   dplyr_1.0.5     purrr_0.3.4     readr_1.4.0    
[13] tidyr_1.1.2     tibble_3.0.4    ggplot2_3.3.3   tidyverse_1.3.0
[17] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] httr_1.4.2               splines_4.0.3            jsonlite_1.7.1          
 [4] viridisLite_0.3.0        modelr_0.1.8             assertthat_0.2.1        
 [7] blob_1.2.1               cellranger_1.1.0         yaml_2.2.1              
[10] pillar_1.4.7             backports_1.1.10         lattice_0.20-41         
[13] glue_1.4.2               RcppEigen_0.3.3.7.0      digest_0.6.27           
[16] promises_1.1.1           checkmate_2.0.0          rvest_0.3.6             
[19] colorspace_1.4-1         htmltools_0.5.0          httpuv_1.5.4            
[22] Matrix_1.2-18            pkgconfig_2.0.3          broom_0.7.5             
[25] haven_2.3.1              scales_1.1.1             whisker_0.4             
[28] later_1.1.0.1            git2r_0.27.1             generics_0.0.2          
[31] farver_2.0.3             ellipsis_0.3.1           withr_2.3.0             
[34] cli_2.1.0                magrittr_1.5             crayon_1.3.4            
[37] readxl_1.3.1             evaluate_0.14            fs_1.5.0                
[40] fansi_0.4.1              xml2_1.3.2               RcppArmadillo_0.10.1.2.0
[43] tools_4.0.3              data.table_1.13.2        hms_0.5.3               
[46] lifecycle_1.0.0          munsell_0.5.0            reprex_0.3.0            
[49] compiler_4.0.3           rlang_0.4.10             grid_4.0.3              
[52] rstudioapi_0.11          labeling_0.4.2           rmarkdown_2.5           
[55] gtable_0.3.0             DBI_1.1.0                R6_2.5.0                
[58] knitr_1.30               rprojroot_2.0.2          stringi_1.5.3           
[61] parallel_4.0.3           Rcpp_1.0.5               vctrs_0.3.5             
[64] dbplyr_1.4.4             tidyselect_1.1.0         xfun_0.18