GLODAPv2_2020 subsetting

workflowr

• Summary
• Checks
• Past versions

Last updated: 2021-08-18

Checks: 7 0

Knit directory: emlr_obs_v_XXX/

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: 3fdf621

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 3fdf621. 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/

Unstaged changes:
    Modified:   code/Workflowr_project_managment.R
    Modified:   data/auxillary/params_local.rds

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.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/eMLR_GLODAPv2_2020_subsetting.Rmd) and HTML (docs/eMLR_GLODAPv2_2020_subsetting.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	9335b31	jens-daniel-mueller	2021-08-10	Build site.
Rmd	26d595c	jens-daniel-mueller	2021-08-10	with P, AIP basins
html	9943b45	jens-daniel-mueller	2021-08-10	Build site.
html	0b00a2b	jens-daniel-mueller	2021-08-09	Build site.
html	755c6b1	jens-daniel-mueller	2021-08-09	Build site.
Rmd	dd6419c	jens-daniel-mueller	2021-08-09	revised global MLR cleaning
html	ed62e96	jens-daniel-mueller	2021-08-09	Build site.
Rmd	8f004f2	jens-daniel-mueller	2021-08-09	revised flag filtering only for predictors used
html	c65f2e3	jens-daniel-mueller	2021-08-09	Build site.
Rmd	f0efda5	jens-daniel-mueller	2021-08-09	revised canyon-b cleaning and created stats files
html	70b290d	jens-daniel-mueller	2021-08-09	Build site.
Rmd	dee6b31	jens-daniel-mueller	2021-08-09	revised canyon-b cleaning
html	cd8e0d5	jens-daniel-mueller	2021-08-06	Build site.
html	15773a0	jens-daniel-mueller	2021-08-06	included calculation of revelle factor
html	da61d1a	jens-daniel-mueller	2021-08-06	Build site.
html	340d731	jens-daniel-mueller	2021-08-06	Build site.
html	71546e4	jens-daniel-mueller	2021-08-06	test with stricter CANYON-B filtering
Rmd	b3c194b	jens-daniel-mueller	2021-08-05	test with cruise and sample bases CANYON-B filtering
html	29444a1	jens-daniel-mueller	2021-08-05	Build site.
Rmd	019702d	jens-daniel-mueller	2021-08-05	test with cruise and sample bases CANYON-B filtering
html	c4b789f	jens-daniel-mueller	2021-08-05	Build site.
Rmd	8f73f84	jens-daniel-mueller	2021-08-05	depth threshold for CANYON-B filtering
html	42e80c0	jens-daniel-mueller	2021-08-04	Build site.
html	48f6eed	jens-daniel-mueller	2021-08-04	Build site.
html	1c597ab	jens-daniel-mueller	2021-08-04	Build site.
html	81a46a4	jens-daniel-mueller	2021-08-03	Build site.
html	b88c61b	jens-daniel-mueller	2021-08-03	Build site.
html	0f0d5e5	jens-daniel-mueller	2021-08-03	Build site.
html	a53656d	jens-daniel-mueller	2021-08-03	Build site.
html	88f7356	jens-daniel-mueller	2021-08-02	Build site.
html	d759279	jens-daniel-mueller	2021-08-02	Build site.
html	127b801	jens-daniel-mueller	2021-07-24	Build site.
html	1f65ef1	jens-daniel-mueller	2021-07-23	Build site.
html	912d90e	jens-daniel-mueller	2021-07-23	Build site.
html	2477316	jens-daniel-mueller	2021-07-23	rebuild: surface dcant mapping seperate
html	c9ccc00	jens-daniel-mueller	2021-07-22	Build site.
html	426b2df	jens-daniel-mueller	2021-07-21	Build site.
html	971ce87	jens-daniel-mueller	2021-07-13	Build site.
html	c18a8b1	jens-daniel-mueller	2021-07-09	Build site.
Rmd	795a3b0	jens-daniel-mueller	2021-07-09	complete revision
html	910d64a	jens-daniel-mueller	2021-07-02	Build site.
Rmd	3d5f350	jens-daniel-mueller	2021-07-02	testrun with CANYON-B NA filling
html	1cbf907	jens-daniel-mueller	2021-07-02	Build site.
Rmd	a2c1536	jens-daniel-mueller	2021-07-02	testrun with CANYON-B NA filling
html	955f5dc	jens-daniel-mueller	2021-06-29	Build site.
html	9480f94	jens-daniel-mueller	2021-06-29	Build site.
html	d054c39	jens-daniel-mueller	2021-06-24	Build site.
html	4fcd066	jens-daniel-mueller	2021-06-24	Build site.
Rmd	ee48dee	jens-daniel-mueller	2021-06-24	test coarse grid rarefication
html	3b6387f	jens-daniel-mueller	2021-06-18	Build site.
html	3052a6c	jens-daniel-mueller	2021-06-15	Build site.
html	3cb64bd	jens-daniel-mueller	2021-06-15	Build site.
html	c6b3da6	jens-daniel-mueller	2021-06-14	Build site.
html	48c73fc	jens-daniel-mueller	2021-06-14	Build site.
html	439ee80	jens-daniel-mueller	2021-06-11	Build site.
html	33ffcab	jens-daniel-mueller	2021-06-10	Build site.
html	7e1f407	jens-daniel-mueller	2021-06-10	Build site.
html	2cbe18c	jens-daniel-mueller	2021-06-10	added zonal mean section control plots
html	69c79d0	jens-daniel-mueller	2021-06-08	Build site.
html	1772903	jens-daniel-mueller	2021-06-07	Build site.
html	594ed9a	jens-daniel-mueller	2021-06-04	Build site.
html	db7df0e	jens-daniel-mueller	2021-06-04	rebuild without overlapping eras
Rmd	71f97a3	jens-daniel-mueller	2021-06-04	rebuild without overlapping eras
html	2edc791	jens-daniel-mueller	2021-06-04	Build site.
html	207339d	jens-daniel-mueller	2021-06-03	Build site.
html	315710b	jens-daniel-mueller	2021-06-03	include anomalous changes
html	47708ab	jens-daniel-mueller	2021-06-02	Build site.
Rmd	8164b5e	jens-daniel-mueller	2021-06-02	offset histogram canyon-B for GLODAP prerelease
html	be90356	jens-daniel-mueller	2021-06-02	Build site.
html	d37a85d	jens-daniel-mueller	2021-05-31	Build site.
Rmd	1c2aff8	jens-daniel-mueller	2021-05-31	test run with beta version of GLODAPv2.2021
html	4b7a5ee	jens-daniel-mueller	2021-05-28	Build site.
html	12b455a	jens-daniel-mueller	2021-05-27	Build site.
Rmd	ee13efb	jens-daniel-mueller	2021-05-27	optional source of local params fully implemented
html	8c736a6	jens-daniel-mueller	2021-05-27	Build site.
Rmd	dc8e4e1	jens-daniel-mueller	2021-05-27	optional source of local params implemented
html	25bd183	jens-daniel-mueller	2021-05-26	Build site.
Rmd	e2b3434	jens-daniel-mueller	2021-05-26	generate seperate output
html	5fe3035	jens-daniel-mueller	2021-05-26	Build site.
Rmd	3f36c74	jens-daniel-mueller	2021-05-26	generate seperate output
html	4c5302d	jens-daniel-mueller	2021-05-26	Build site.
Rmd	e705cec	jens-daniel-mueller	2021-05-26	generate seperate output
html	189f362	jens-daniel-mueller	2021-05-26	Build site.
Rmd	1dd10ef	jens-daniel-mueller	2021-05-26	generate seperate output
html	f314fc7	jens-daniel-mueller	2021-05-26	Build site.
html	cf773c5	jens-daniel-mueller	2021-05-26	Build site.
Rmd	5b0e29c	jens-daniel-mueller	2021-05-26	generate seperate output
html	b79cb2d	jens-daniel-mueller	2021-05-20	Build site.
html	62bd574	jens-daniel-mueller	2021-05-20	Build site.
Rmd	14a7aac	jens-daniel-mueller	2021-05-20	rerun overlapping eras
html	7c56c39	jens-daniel-mueller	2021-05-19	Build site.
Rmd	4a1fd72	jens-daniel-mueller	2021-05-19	test completely overlapping eras
html	0de759e	jens-daniel-mueller	2021-05-13	Build site.
html	0a84f2a	jens-daniel-mueller	2021-05-12	Build site.
Rmd	1f6771f	jens-daniel-mueller	2021-05-12	rerun without sea of japan
html	969e631	jens-daniel-mueller	2021-05-12	Build site.
Rmd	5f542d0	jens-daniel-mueller	2021-05-12	rerun without sea of japan
html	aa676ca	jens-daniel-mueller	2021-05-12	Build site.
Rmd	a093821	jens-daniel-mueller	2021-05-12	offset map canyon-B
html	53c31b8	jens-daniel-mueller	2021-05-11	Build site.
Rmd	e6edd0e	jens-daniel-mueller	2021-05-11	offset map canyon-B
html	87c1aee	jens-daniel-mueller	2021-05-11	Build site.
Rmd	01c7a3a	jens-daniel-mueller	2021-05-11	property-property plots for GLODAP added
html	7abd5c9	jens-daniel-mueller	2021-04-19	Build site.
Rmd	e51e059	jens-daniel-mueller	2021-04-19	write grid with duplicated data
html	d2a83bc	jens-daniel-mueller	2021-04-16	Build site.
Rmd	f7f10e1	jens-daniel-mueller	2021-04-16	overlapping eras manually defined
html	84b1fe3	jens-daniel-mueller	2021-04-16	Build site.
html	c0a47df	jens-daniel-mueller	2021-04-16	Build site.
html	50290e8	jens-daniel-mueller	2021-04-16	overlapping eras
Rmd	934e795	jens-daniel-mueller	2021-04-16	overlapping eras
html	a00ec94	jens-daniel-mueller	2021-04-16	Build site.
Rmd	10ffab3	jens-daniel-mueller	2021-04-16	use consistent tref
html	7e4f671	jens-daniel-mueller	2021-04-16	Build site.
Rmd	bdd1c8a	jens-daniel-mueller	2021-04-16	use consistent tref
html	b6fe355	jens-daniel-mueller	2021-04-16	Build site.
Rmd	6e80fb5	jens-daniel-mueller	2021-04-16	manual cruise shifting, Indian only
html	858c4e6	jens-daniel-mueller	2021-04-16	Build site.
Rmd	f82b9f2	jens-daniel-mueller	2021-04-16	manual cruise shifting
html	81b7c6d	jens-daniel-mueller	2021-04-16	Build site.
html	ddec5b7	jens-daniel-mueller	2021-04-15	Build site.
html	29edae5	jens-daniel-mueller	2021-04-14	Build site.
html	099d566	jens-daniel-mueller	2021-04-14	Build site.
Rmd	e76af46	jens-daniel-mueller	2021-04-14	2 basins, high VIF
html	bb44686	jens-daniel-mueller	2021-04-14	Build site.
html	bf40480	jens-daniel-mueller	2021-04-13	Build site.
html	9f31fe3	jens-daniel-mueller	2021-04-13	Build site.
Rmd	80e1ee3	jens-daniel-mueller	2021-04-13	rerun post-2000 with model data
html	c98be84	jens-daniel-mueller	2021-04-13	Build site.
html	338dd3c	jens-daniel-mueller	2021-04-09	Build site.
html	a79ca2c	jens-daniel-mueller	2021-04-09	included model data
html	7831fd3	jens-daniel-mueller	2021-04-09	Build site.
html	20b26d4	jens-daniel-mueller	2021-04-08	Build site.
html	c0895f8	jens-daniel-mueller	2021-04-07	Build site.
html	156d5b7	jens-daniel-mueller	2021-04-07	Build site.
html	eb827c9	jens-daniel-mueller	2021-04-07	Build site.
html	857bad3	jens-daniel-mueller	2021-03-24	Build site.
Rmd	02e91d4	jens-daniel-mueller	2021-03-24	included model data
html	05cc66b	jens-daniel-mueller	2021-03-24	Build site.
Rmd	b897e71	jens-daniel-mueller	2021-03-24	included model data
html	03b6009	jens-daniel-mueller	2021-03-23	removed before copying template
html	555750f	jens-daniel-mueller	2021-03-23	Build site.
Rmd	2021931	jens-daniel-mueller	2021-03-23	restriction to two eras and new definition procedure
html	685338e	jens-daniel-mueller	2021-03-23	Build site.
Rmd	64b4756	jens-daniel-mueller	2021-03-23	restriction to two eras and new definition procedure
html	886f523	jens-daniel-mueller	2021-03-23	Build site.
Rmd	8a3a9dd	jens-daniel-mueller	2021-03-23	restriction to two eras and new definition procedure
html	d7831b0	jens-daniel-mueller	2021-03-23	Build site.
Rmd	d9dec77	jens-daniel-mueller	2021-03-23	restriction to two eras and new definition procedure
html	10c1346	jens-daniel-mueller	2021-03-23	Build site.
Rmd	b697e7a	jens-daniel-mueller	2021-03-23	restriction to two eras and new definition procedure
html	f155edd	jens-daniel-mueller	2021-03-23	Build site.
html	380d215	jens-daniel-mueller	2021-03-21	Build site.
html	33b385b	jens-daniel-mueller	2021-03-20	Build site.
html	330dcd0	jens-daniel-mueller	2021-03-20	Build site.
html	83a13de	jens-daniel-mueller	2021-03-20	Build site.
html	cf98c6d	jens-daniel-mueller	2021-03-16	Build site.
html	a1d52ff	jens-daniel-mueller	2021-03-15	Build site.
html	0bade3b	jens-daniel-mueller	2021-03-15	Build site.
html	27c1f4b	jens-daniel-mueller	2021-03-14	Build site.
html	af75ebf	jens-daniel-mueller	2021-03-14	Build site.
Rmd	e3dde84	jens-daniel-mueller	2021-03-14	test without filtering
html	5017709	jens-daniel-mueller	2021-03-11	Build site.
html	585b07f	jens-daniel-mueller	2021-03-11	Build site.
html	6482ed7	jens-daniel-mueller	2021-03-11	Build site.
Rmd	0ad56e3	jens-daniel-mueller	2021-03-11	cleaned filtering based on comparison to CANYON-B
html	85a5ed2	jens-daniel-mueller	2021-03-10	Build site.
Rmd	749b5db	jens-daniel-mueller	2021-03-10	filter based on comparison to CANYON-B
html	52a5ea4	jens-daniel-mueller	2021-03-10	Build site.
Rmd	0e57f29	jens-daniel-mueller	2021-03-10	rerun with GLODAP row numbers
html	6b260df	jens-daniel-mueller	2021-03-10	Build site.
html	00688a1	jens-daniel-mueller	2021-03-05	Build site.
html	6c0bec6	jens-daniel-mueller	2021-03-05	Build site.
html	3c2ec33	jens-daniel-mueller	2021-03-05	Build site.
html	af70b94	jens-daniel-mueller	2021-03-04	Build site.
html	86406d5	jens-daniel-mueller	2021-02-24	Build site.
html	3d3b4cc	jens-daniel-mueller	2021-02-23	Build site.
html	7b672f7	jens-daniel-mueller	2021-01-11	Build site.
Rmd	ba7cb46	jens-daniel-mueller	2021-01-11	run sensitivity test
html	33ba23c	jens-daniel-mueller	2021-01-07	Build site.
Rmd	0ad30ba	jens-daniel-mueller	2021-01-07	removed GLODAP gamma filter, target variable mapped by eras+era
Rmd	a8c4dce	jens-daniel-mueller	2020-12-23	manual activation of A16 switch
Rmd	cfef575	jens-daniel-mueller	2020-12-23	Option to select era shift of A16 cruise
html	318609d	jens-daniel-mueller	2020-12-23	adapted more variable predictor selection
html	6949b06	jens-daniel-mueller	2020-12-23	Build site.
Rmd	d3ad704	jens-daniel-mueller	2020-12-23	test 106
html	0aa2b50	jens-daniel-mueller	2020-12-23	remove html before duplication
html	39113c3	jens-daniel-mueller	2020-12-23	Build site.
html	2886da0	jens-daniel-mueller	2020-12-19	Build site.
html	02f0ee9	jens-daniel-mueller	2020-12-18	cleaned up for copying template
html	965dba3	jens-daniel-mueller	2020-12-18	Build site.
html	5d452fe	jens-daniel-mueller	2020-12-18	Build site.
Rmd	ca65bf5	jens-daniel-mueller	2020-12-18	rebuild after final cleaning
html	7bcb4eb	jens-daniel-mueller	2020-12-18	Build site.
html	d397028	jens-daniel-mueller	2020-12-18	Build site.
html	7131186	jens-daniel-mueller	2020-12-17	Build site.
html	22b07fb	jens-daniel-mueller	2020-12-17	Build site.
html	f3a708f	jens-daniel-mueller	2020-12-17	Build site.
html	e4ca289	jens-daniel-mueller	2020-12-16	Build site.
html	158fe26	jens-daniel-mueller	2020-12-15	Build site.
Rmd	449195a	jens-daniel-mueller	2020-12-15	rebuild without subsetting nitrate
html	7a9a4cb	jens-daniel-mueller	2020-12-15	Build site.
html	61b263c	jens-daniel-mueller	2020-12-15	Build site.
html	4d612dd	jens-daniel-mueller	2020-12-15	Build site.
html	953caf3	jens-daniel-mueller	2020-12-15	Build site.
html	42daf5c	jens-daniel-mueller	2020-12-14	Build site.
html	5cc68e2	jens-daniel-mueller	2020-12-14	Build site.
Rmd	00de567	jens-daniel-mueller	2020-12-14	rebuild with new path
html	984697e	jens-daniel-mueller	2020-12-12	Build site.
html	3ebff89	jens-daniel-mueller	2020-12-12	Build site.
Rmd	a1aaa71	jens-daniel-mueller	2020-12-12	selectable basinmask, rebuild
html	7d82772	jens-daniel-mueller	2020-12-11	Build site.
Rmd	6069c23	jens-daniel-mueller	2020-12-11	selectable basinmask, try 5
html	c8acfcb	jens-daniel-mueller	2020-12-11	Build site.
html	2fd0a2a	jens-daniel-mueller	2020-12-11	Build site.
Rmd	cd436c1	jens-daniel-mueller	2020-12-11	selectable basinmask
html	b01a367	jens-daniel-mueller	2020-12-09	Build site.
Rmd	71c63b0	jens-daniel-mueller	2020-12-09	rerun with variable predictor assignment
html	24a632f	jens-daniel-mueller	2020-12-07	Build site.
html	92dca91	jens-daniel-mueller	2020-12-07	Build site.
html	6a8004b	jens-daniel-mueller	2020-12-07	Build site.
Rmd	a4ec6a0	jens-daniel-mueller	2020-12-07	Keppler comparison run
html	70bf1a5	jens-daniel-mueller	2020-12-07	Build site.
html	7555355	jens-daniel-mueller	2020-12-07	Build site.
html	143d6fa	jens-daniel-mueller	2020-12-07	Build site.
html	abc6818	jens-daniel-mueller	2020-12-03	Build site.
html	090e4d5	jens-daniel-mueller	2020-12-02	Build site.
html	37e9dac	jens-daniel-mueller	2020-12-02	Build site.
Rmd	9ff071b	jens-daniel-mueller	2020-12-02	minor improvement of tref adejustment, formatting
html	7c25f7a	jens-daniel-mueller	2020-12-02	Build site.
Rmd	5ffd065	jens-daniel-mueller	2020-12-02	rebuild with nice era labels
html	ec8dc38	jens-daniel-mueller	2020-12-02	Build site.
html	c987de1	jens-daniel-mueller	2020-12-02	Build site.
html	d5c5378	jens-daniel-mueller	2020-12-02	Build site.
Rmd	3cc6d3c	jens-daniel-mueller	2020-12-02	code cleaning and commenting
html	083b3b0	jens-daniel-mueller	2020-12-02	Build site.
Rmd	f4520b2	jens-daniel-mueller	2020-12-02	code cleaning and commenting
html	632c84f	jens-daniel-mueller	2020-12-02	Build site.
Rmd	8f3d29d	jens-daniel-mueller	2020-12-02	code cleaning and commenting
html	22d0127	jens-daniel-mueller	2020-12-01	Build site.
html	0ff728b	jens-daniel-mueller	2020-12-01	Build site.
Rmd	6287a18	jens-daniel-mueller	2020-12-01	auto eras naming
html	b02b7a4	jens-daniel-mueller	2020-12-01	Build site.
Rmd	60bea48	jens-daniel-mueller	2020-12-01	auto eras naming
html	cf19652	jens-daniel-mueller	2020-11-30	Build site.
html	196be51	jens-daniel-mueller	2020-11-30	Build site.
Rmd	7a4b015	jens-daniel-mueller	2020-11-30	first rebuild on ETH server

---

1 Version ID

The results displayed on this site correspond to the Version_ID:

params$Version_ID

[1] "v_XXX"

2 Read files

Main data source for this project is the preprocessed version of GLODAPv2:

params_local$GLODAPv2_version

[1] "2021"

CAVEAT: This file still contains neutral densities gamma calculated with a preliminary method. However, this is consistent with the way gamma is currently calculated in this script and should therefore be maintained until changed on all levels.

GLODAP <-
  read_csv(
    paste0(
      path_preprocessing_model,
      "GLODAPv2.",
      params_local$GLODAPv2_version,
      "_preprocessed_model_runA_both_NA_filled.csv")
  )

GLODAP_CB <-
  read_csv(
    paste0(
      path_preprocessing,
      "GLODAPv2.",
      params_local$GLODAPv2_version,
      "_Canyon-B.csv"
    )
  )

3 Data preparation

3.1 Filter eras

Samples were assigned to following eras:

# create labels for era
era_labels <- bind_cols(
  start = params_local$era_start,
  end = params_local$era_end)

era_labels <- era_labels %>% 
  mutate(start = if_else(start == -Inf, max(GLODAP$year), start),
         end = if_else(end == Inf, max(GLODAP$year), end),
         era = as.factor(paste(start, end, sep = "-")))

era_labels

# A tibble: 2 × 3
  start   end era      
  <dbl> <dbl> <fct>    
1  2000  2009 2000-2009
2  2010  2019 2010-2019

# filter GLODAP data within eras
GLODAP <- expand_grid(
  GLODAP,
  era_labels
)

# select data within each era
GLODAP <- GLODAP %>% 
  filter(year >= start & year <= end)

GLODAP <- GLODAP %>% 
  select(-c(start, end))

3.2 Spatial boundaries

3.2.1 Basin mask

The basin mask from the World Ocean Atlas was used. For details consult the data base subsection for WOA18 data.

Please note that some GLODAP observations were made outside the WOA18 basin mask (i.e. in marginal seas) and will be removed for further analysis.

# use only data inside basinmask
GLODAP <- inner_join(GLODAP, basinmask)

3.2.2 Depth

Observations collected shallower than:

• minimum sampling depth: 150m

were excluded from the analysis to avoid seasonal bias.

GLODAP <- GLODAP %>% 
  filter(depth >= params_local$depth_min)

3.2.3 Bottomdepth

Observations collected in an area with a:

• minimum bottom depth: 0m

were excluded from the analysis to avoid coastal impacts. Please note that minimum bottom depth criterion of 0m means that no filtering was applied here.

GLODAP <- GLODAP %>% 
  filter(bottomdepth >= params_local$bottomdepth_min)

GLODAP <- GLODAP %>% 
  group_by(cruise) %>% 
  mutate(max_depth = max(depth)) %>% 
  ungroup()

GLODAP_grid <- GLODAP %>% 
  distinct(lat, lon, cruise, max_depth)

map +
  geom_raster(data = GLODAP_grid,
              aes(lon, lat, fill = "all depth")) +
  geom_raster(data = GLODAP_grid %>% filter(max_depth < 1000),
              aes(lon, lat, fill = "shallow filter")) +
  scale_fill_manual(values = c("grey60", "red"))

3.3 CANYON-B cleaning

Data cleaning based on comparison to CANYOB-B predictions is done individually for each variable required in the eMLR approach and constrained to samples collected deeper than 1000 m.

# join data frames
GLODAP_combined_raw <- left_join(GLODAP,
                                 GLODAP_CB)

# calculate offset by parameter
GLODAP_combined <- GLODAP_combined_raw %>%
  mutate(
    offset_talk = talk - talk_CANYONB,
    offset_tco2 = tco2 - tco2_CANYONB,
    offset_nitrate = nitrate - nitrate_CANYONB,
    offset_phosphate = phosphate - phosphate_CANYONB,
    offset_silicate = silicate - silicate_CANYONB
  ) %>%
  select(row_number,
         year,
         cruise,
         basin_AIP,
         lat,
         lon,
         depth,
         starts_with("offset_"))


# GLODAP_combined %>% 
#   filter(cruise == 695) %>% 
#   arrange(depth) %>% 
#   ggplot(aes(offset_talk, depth)) +
#   geom_point() +
#   scale_y_reverse() +
#   labs(title = "GLODAPv2.2021 vs CANYON-B | cruise 695")
# 
# GLODAP %>% 
#   filter(cruise == 695) %>% 
#   arrange(depth) %>% 
#   ggplot(aes(talk, depth,
#              fill = as.factor(talkf),
#              col = as.factor(talkqc))) +
#   geom_point(shape = 21) +
#   scale_y_reverse() +
#   scale_color_manual(values = "black", name = "talkqc") +
#   scale_fill_manual(values = c("black", "white", "grey"), name = "talkf") +
#   labs(title = "GLODAPv2.2021 | cruise 695")


# pivot to long format
GLODAP_combined <- GLODAP_combined %>%
  pivot_longer(
    starts_with("offset"),
    names_to = "parameter",
    names_prefix = "offset_",
    values_to = "offset"
  )

GLODAP_combined <- GLODAP_combined %>%
  filter(parameter %in% c("tco2", "talk", params_local$MLR_predictors))

GLODAP_combined <- left_join(GLODAP_combined,
                             GLODAP %>% distinct(row_number, era))

3.3.1 Residual histograms

# flag data according to sampling depth
GLODAP_combined <- GLODAP_combined %>%
  mutate(sampling_depth =
           if_else(depth >= params_local$CANYON_B_depth,
                   "deep", "shallow"))

GLODAP_combined %>%
  # filter(cruise == 695) %>%
  ggplot(aes(offset, fill=sampling_depth)) +
  geom_histogram() +
  scale_y_continuous(trans = "log10") +
  facet_grid(basin_AIP ~ parameter, scales = "free_x")

Past versions of CANYON_B_residual_histograms-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
47708ab	jens-daniel-mueller	2021-06-02
d37a85d	jens-daniel-mueller	2021-05-31
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
6482ed7	jens-daniel-mueller	2021-03-11

# filter only deep water samples
GLODAP_combined <- GLODAP_combined %>% 
  filter(sampling_depth == "deep")

GLODAP_combined %>%
  # filter(cruise == 695) %>% 
  ggplot(aes(offset, fill=sampling_depth)) +
  geom_histogram() +
  scale_y_continuous(trans = "log10") +
  facet_grid(basin_AIP ~ parameter, scales = "free_x")

Past versions of CANYON_B_residual_histograms-2.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05

GLODAP_combined <- GLODAP_combined %>% 
  select(-sampling_depth)

3.3.2 Property-property plots

variables <- unique(GLODAP_combined$parameter)

for (i_variable in variables) {
  # i_variable <- variables[1]
  print(p_prop_prop(
    df = GLODAP_combined_raw %>%
      filter(depth >= params_local$CANYON_B_depth),
    var1 = i_variable,
    var2 = paste0(i_variable, "_CANYONB")
  ))
}

Past versions of CANYON_B_property_property-1.png

Version	Author	Date
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
c18a8b1	jens-daniel-mueller	2021-07-09
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
87c1aee	jens-daniel-mueller	2021-05-11

Past versions of CANYON_B_property_property-2.png

Version	Author	Date
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
c18a8b1	jens-daniel-mueller	2021-07-09
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
87c1aee	jens-daniel-mueller	2021-05-11

Past versions of CANYON_B_property_property-3.png

Version	Author	Date
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
c18a8b1	jens-daniel-mueller	2021-07-09
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
87c1aee	jens-daniel-mueller	2021-05-11

Past versions of CANYON_B_property_property-4.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
c18a8b1	jens-daniel-mueller	2021-07-09
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
87c1aee	jens-daniel-mueller	2021-05-11

Past versions of CANYON_B_property_property-5.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
c18a8b1	jens-daniel-mueller	2021-07-09
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
87c1aee	jens-daniel-mueller	2021-05-11

rm(variables, GLODAP_combined_raw, i_variable)

3.3.3 Residual time series

GLODAP_combined %>%
  ggplot(aes(year, offset)) +
  geom_bin2d() +
  geom_hline(yintercept = 0, col = "red") +
  scale_fill_viridis_c(trans = "log10") +
  facet_grid(parameter ~ basin_AIP, scales = "free_y")

Past versions of CANYON_B_residual_time_series-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
aa676ca	jens-daniel-mueller	2021-05-12

3.3.4 Cruise offset metrics

# calculate mean cruise offset by parameter
cruise_stats <- GLODAP_combined %>%
  group_by(cruise, parameter) %>%
  summarise(
    mean_offset = mean(offset, na.rm = TRUE),
    sd_offset = sd(offset, na.rm = TRUE)
  ) %>%
  ungroup()

cruise_stats <- cruise_stats %>%
  group_by(parameter) %>%
  mutate(
    mean_offset_rank = rank(mean_offset)
  ) %>%
  ungroup() %>% 
  arrange(mean_offset_rank)

# calculate offset parameters across all observations
GLODAP_stats <- cruise_stats %>%
  group_by(parameter) %>%
  summarise(
    mean_offset_max = sd(mean_offset, na.rm = TRUE) *
      params_local$CANYON_B_cruise_mean,
    sd_offset_max = median(sd_offset, na.rm = TRUE) *
      params_local$CANYON_B_sample_SD
  ) %>%
  ungroup()


# rank offsets and calculate offset thresholds
cruise_stats <- full_join(cruise_stats,
                          GLODAP_stats) %>%
  mutate(cruise = as.factor(cruise))

3.3.5 Filter cruises

Cruises are removed, when the mean offset of the observation from the value predicted with CANYON-B is higher than times the standard deviation of all cruise mean offsets.

# identify cruises to be removed
cruise_stats <- cruise_stats %>%
  mutate(cruise_flag = if_else(abs(mean_offset) > mean_offset_max,
                               "removed",
                               "included"))

cruise_stats %>% 
  ggplot() +
  geom_vline(data = GLODAP_stats,
             aes(xintercept = mean_offset_max * c(1),
             col = "threshold")) +
  geom_vline(data = GLODAP_stats,
             aes(xintercept = mean_offset_max * c(-1),
             col = "threshold")) +
  geom_histogram(aes(mean_offset, fill = cruise_flag)) +
  facet_grid(. ~ parameter, scales = "free_x") +
  scale_color_manual(values = "red") +
  scale_fill_brewer(palette = "Set1", direction = -1) +
  theme(legend.title = element_blank())

Past versions of CANYON_B_filter_cruises-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

for (i_parameter in unique(cruise_stats$parameter)) {
  # i_parameter <- unique(cruise_stats$parameter)[4]
  
  i_cruise_stats <- cruise_stats %>%
    filter(parameter == i_parameter)
  
  i_cruise_out <- cruise_stats %>%
    filter(parameter == i_parameter,
           cruise_flag == "removed")
  
  print(
    ggplot() +
      geom_hline(
        data = i_cruise_stats,
        aes(yintercept = c(-1, 1) * mean_offset_max),
        lty = 2
      ) +
      geom_ribbon(
        data = i_cruise_stats,
        aes(
          x = mean_offset_rank,
          ymax = mean_offset + sd_offset,
          ymin = mean_offset - sd_offset
        ),
        alpha = 0.3
      ) +
      geom_path(data = i_cruise_stats,
                aes(mean_offset_rank, mean_offset)) +
      geom_point(data = i_cruise_out,
                 aes(mean_offset_rank, mean_offset, col = cruise)) +
      labs(title = i_parameter)
  )
  
  print(
    ggplot() +
      geom_point(data = i_cruise_stats,
                 aes(mean_offset, sd_offset)) +
      geom_point(data = i_cruise_out,
                 aes(mean_offset, sd_offset, col = cruise)) +
      labs(title = i_parameter)
  )
  
}

Past versions of CANYON_B_filter_cruises-2.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-3.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-4.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-5.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-6.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-7.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-8.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-9.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-10.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

Past versions of CANYON_B_filter_cruises-11.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10

rm(i_parameter, i_cruise_stats, i_cruise_out)

cruise_removal_grid <-
  left_join(
    GLODAP_combined %>%
      distinct(era, parameter, cruise, lon, lat) %>%
      mutate(cruise = as.factor(cruise)),
    cruise_stats %>% select(cruise, parameter, cruise_flag)
  )


map +
  geom_raster(data = GLODAP %>% distinct(lat, lon, era),
              aes(lon, lat), fill = "grey70") +
  geom_raster(data = cruise_removal_grid %>% filter(cruise_flag == "removed"),
              aes(lon, lat, fill = cruise_flag)) +
  scale_fill_brewer(palette = "Set1") +
  facet_grid(parameter ~ era) +
  labs(title = "Cruise filtering") +
  theme(legend.title = element_blank())

Past versions of CANYON_B_removed_cruises_map-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
81a46a4	jens-daniel-mueller	2021-08-03
b88c61b	jens-daniel-mueller	2021-08-03
d759279	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
cf773c5	jens-daniel-mueller	2021-05-26
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
555750f	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
0bade3b	jens-daniel-mueller	2021-03-15
27c1f4b	jens-daniel-mueller	2021-03-14
af75ebf	jens-daniel-mueller	2021-03-14
5017709	jens-daniel-mueller	2021-03-11
6482ed7	jens-daniel-mueller	2021-03-11

map +
  geom_raster(data = GLODAP %>% distinct(lat, lon, era),
              aes(lon, lat), fill = "grey70") +
  geom_raster(data = cruise_removal_grid %>% filter(cruise_flag == "included"),
              aes(lon, lat, fill = cruise_flag)) +
  scale_fill_brewer(palette = "Set1") +
  facet_grid(parameter ~ era) +
  labs(title = "Cruise filtering") +
  theme(legend.title = element_blank())

Past versions of CANYON_B_removed_cruises_map-2.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09

map +
  geom_raster(data = GLODAP %>% distinct(lat, lon, era),
              aes(lon, lat), fill = "grey70") +
  geom_raster(data = cruise_removal_grid %>% filter(is.na(cruise_flag)),
              aes(lon, lat, fill = "NA")) +
  scale_fill_brewer(palette = "Set1") +
  facet_grid(parameter ~ era) +
  labs(title = "Cruise filtering") +
  theme(legend.title = element_blank())

Past versions of CANYON_B_removed_cruises_map-3.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
70b290d	jens-daniel-mueller	2021-08-09

The ratio (%) of removed observations is:

cruise_out <- cruise_stats %>% 
  filter(cruise_flag == "removed") %>% 
  distinct(cruise) %>% 
  pull()

GLODAP <- GLODAP %>%
  mutate(cruise_flag = if_else(
    cruise %in% cruise_out,
    "removed",
    "included"))


cruise_removal_ratio <-
  nrow(GLODAP %>% filter(cruise_flag == "removed")) /
  nrow(GLODAP) * 100

stats_CANYON_B_cleaning_cruises <- tibble(
  cruise_removal_ratio = cruise_removal_ratio,
  cruise_removal_n = length(cruise_out)
)

stats_CANYON_B_cleaning_cruises

# A tibble: 1 × 2
  cruise_removal_ratio cruise_removal_n
                 <dbl>            <int>
1               0.0539                4

3.3.6 Filter samples

cruise_stats %>% 
  ggplot() +
  geom_vline(aes(xintercept = sd_offset_max,
             col = "threshold")) +
  geom_histogram(aes(sd_offset)) +
  facet_grid(. ~ parameter, scales = "free_x") +
  scale_color_manual(values = "red") +
  scale_fill_brewer(palette = "Set1", direction = -1) +
  theme(legend.title = element_blank())

Past versions of filter_samples-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05

GLODAP_combined <-
  full_join(GLODAP_combined %>% mutate(cruise = as.factor(cruise)),
            cruise_stats)

GLODAP_combined <- GLODAP_combined %>%
  mutate(sample_flag = if_else(abs(offset) <= sd_offset_max,
                               "included", 
                               "removed"))

GLODAP_combined %>%
  ggplot(aes(offset, fill=sample_flag)) +
  geom_histogram() +
  scale_y_continuous(trans = "log10") +
  facet_grid(basin_AIP ~ parameter, scales = "free_x")

Past versions of filter_samples-2.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05

GLODAP_combined %>%
  filter(sample_flag == "removed") %>% 
  ggplot(aes(offset, fill=sample_flag)) +
  geom_histogram() +
  scale_y_continuous() +
  facet_grid(basin_AIP ~ parameter, scales = "free_x")

Past versions of filter_samples-3.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09

samples_out <- GLODAP_combined %>% 
  filter(sample_flag == "removed") %>% 
  distinct(row_number) %>% 
  pull()

stats_CANYON_B_cleaning_samples <- GLODAP_combined %>% 
  group_by(parameter) %>% 
  count(sample_flag)

stats_CANYON_B_cleaning_samples

# A tibble: 15 × 3
# Groups:   parameter [5]
   parameter sample_flag      n
   <chr>     <chr>        <int>
 1 nitrate   included    107939
 2 nitrate   removed       3267
 3 nitrate   NA            7443
 4 phosphate included    100151
 5 phosphate removed       3321
 6 phosphate NA           15177
 7 silicate  included    107468
 8 silicate  removed       4365
 9 silicate  NA            6816
10 talk      included    103083
11 talk      removed       7263
12 talk      NA            8303
13 tco2      included    115915
14 tco2      removed       1472
15 tco2      NA            1262

grid_CANYON_B_cleaning_samples <- GLODAP_combined %>% 
  count(lat, lon, era, parameter, sample_flag) %>% 
  pivot_wider(names_from = sample_flag,
              values_from = n,
              values_fill = 0) %>% 
  mutate(removal_ratio = removed / (removed + included))
  
map +
    geom_raster(data = grid_CANYON_B_cleaning_samples,
                aes(lon, lat, fill = removal_ratio)) +
    scale_fill_viridis_c(direction = -1) +
    facet_grid(parameter ~ era) +
    labs(title = "Maps of removed samples") +
    theme(legend.title = element_blank())

Past versions of CANYON_B_removed_samples_map-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06

The ratio (%) of removed observations is:

GLODAP <- GLODAP %>% 
  mutate(sample_flag = if_else(row_number %in% samples_out,
                                "removed",
                                "included"))

nrow(GLODAP %>% filter(sample_flag == "removed")) /
  nrow(GLODAP) * 100

[1] 7.87843

GLODAP %>% 
  filter(sample_flag == "removed",
         cruise_flag == "removed") %>% 
  nrow()

[1] 47

GLODAP %>% 
  filter(sample_flag == "removed",
         cruise_flag == "included") %>% 
  nrow()

[1] 16914

GLODAP %>% 
  filter(sample_flag == "included",
         cruise_flag == "removed") %>% 
  nrow()

[1] 69

GLODAP <- GLODAP %>% 
  filter(sample_flag != "removed",
         cruise_flag != "removed")

3.4 Gap filling

if (params_local$gap_filling == "CANYON-B") {
  
GLODAP <- left_join(GLODAP,
                    GLODAP_CB)

# label rows with missing values that should be filled
GLODAP <- GLODAP %>%
  mutate(
    fill_nitrate = if_else(is.na(nitrate), "filled", "measured"),
    fill_phosphate = if_else(is.na(phosphate), "filled", "measured"),
    fill_silicate = if_else(is.na(silicate), "filled", "measured"),
    fill_talk = if_else(is.na(talk), "filled", "measured")
  )

# fill missing values with CANYON-B estimate, if available
GLODAP <- GLODAP %>% 
  mutate(nitrate = if_else(is.na(nitrate), nitrate_CANYONB, nitrate),
         phosphate = if_else(is.na(phosphate), phosphate_CANYONB, phosphate),
         silicate = if_else(is.na(silicate), silicate_CANYONB, silicate),
         talk = if_else(is.na(talk), talk_CANYONB, talk))

# label rows with remaining missing values that could not be filled
GLODAP <- GLODAP %>%
  mutate(
    fill_nitrate = if_else(is.na(nitrate), "missing", fill_nitrate),
    fill_phosphate = if_else(is.na(phosphate), "missing", fill_phosphate),
    fill_silicate = if_else(is.na(silicate), "missing", fill_silicate),
    fill_talk = if_else(is.na(talk), "missing", fill_talk)
  )

GLODAP_filling_long <- GLODAP %>% 
  select(lon, lat, era, fill_nitrate, fill_phosphate, fill_silicate, fill_talk) %>% 
  pivot_longer(fill_nitrate:fill_talk,
               names_to = "parameter",
               values_to = "filling",
               names_prefix = "fill_") %>% 
  count(lon, lat, era, parameter, filling)

GLODAP_filling_wide <- GLODAP_filling_long %>% 
  pivot_wider(names_from = filling,
              values_from = n,
              values_fill = 0) %>% 
  mutate(total = measured + filled + missing,
         filled_ratio = 100*filled/total,
         missing_ratio = 100*missing/total)

map + 
  geom_raster(data = GLODAP_filling_wide,
              aes(lon, lat, fill = filled_ratio)) +
  facet_grid(parameter ~ era) +
  scale_fill_viridis_c(direction = -1)

map + 
  geom_raster(data = GLODAP_filling_wide,
              aes(lon, lat, fill = missing_ratio)) +
  facet_grid(parameter ~ era) +
  scale_fill_viridis_c(direction = -1)

GLODAP_filling_long %>% 
  group_by(era, parameter, filling) %>% 
  summarise(n = sum(n)) %>% 
  ggplot(aes(parameter, n, fill = filling)) +
  coord_flip() +
  geom_col() +
  facet_grid(era~.) +
  scale_fill_viridis_d()

GLODAP <- GLODAP %>% 
  select(!ends_with("_CANYONB")) %>% 
  select(!starts_with("fill_"))

rm(GLODAP_filling_long, GLODAP_filling_wide)

}

3.5 Flags and missing data

Only rows (samples) for which all relevant parameters are available were selected, ie NA’s were removed.

According to Olsen et al (2020), flags within the merged master file identify:

• f:

  • 2: Acceptable
  • 0: Interpolated (nutrients/oxygen) or calculated (CO[2] variables)
  • 9: Data not used (so, only NA data should have this flag)

• qc:

  • 1: Adjusted or unadjusted data
  • 0: Data appear of good quality but have not been subjected to full secondary QC
  • data with poor or uncertain quality are excluded.

Following flagging criteria were taken into account:

• flag_f: 0, 2, 9
• flag_qc: 1, 0

The cleaning process was performed successively and the maps below represent the data coverage at various cleaning levels.

Summary statistics were calculated during cleaning process.

3.5.1 tco2

3.5.1.1 NA

Rows with missing tco2 observations were already removed in the preprocessing. The map below shows the coverage of preprocessed GLODAP data.

GLODAP_stats <- GLODAP %>% 
  summarise(tco2_values = n())

GLODAP_obs_grid <- GLODAP %>% 
  count(lat, lon, era) %>% 
  mutate(cleaning_level = "tco2_values")

GLODAP_obs <- GLODAP %>% 
  group_by(lat, lon) %>% 
  summarise(n = n()) %>% 
  ungroup()

map +
  geom_raster(data = basinmask, aes(lon, lat, fill = basin)) +
  geom_raster(data = GLODAP_obs, aes(lon, lat)) +
  scale_fill_brewer(palette = "Dark2") +
  theme(legend.position = "top",
        legend.title = element_blank())

Past versions of WOA18_basin_mask_GLODAP_observations_map-1.png

Version	Author	Date
9943b45	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
da61d1a	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
955f5dc	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
5fe3035	jens-daniel-mueller	2021-05-26
4c5302d	jens-daniel-mueller	2021-05-26
969e631	jens-daniel-mueller	2021-05-12
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
81b7c6d	jens-daniel-mueller	2021-04-16
099d566	jens-daniel-mueller	2021-04-14
bb44686	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
984697e	jens-daniel-mueller	2020-12-12
3ebff89	jens-daniel-mueller	2020-12-12
c8acfcb	jens-daniel-mueller	2020-12-11
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

rm(GLODAP_obs)

3.5.1.2 f flag

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era, tco2f)

map +
  geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
  scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  facet_grid(era ~ tco2f) +
  theme(legend.position = "top")

Past versions of tco2_f_subset-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
d7831b0	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

rm(GLODAP_obs_grid_temp)

GLODAP <- GLODAP %>%
  filter(tco2f %in% params_local$flag_f)

3.5.1.3 qc flag

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era, tco2qc)

map +
  geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
  scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  facet_grid(era ~ tco2qc) +
  theme(legend.position = "top")

Past versions of tco2_qc_subset-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
d7831b0	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

##

GLODAP <- GLODAP %>%
  filter(tco2qc %in% params_local$flag_qc)

GLODAP_stats_temp <- GLODAP %>%
  summarise(tco2_flag = n())

GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)

##

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era) %>%
  mutate(cleaning_level = "tco2_flag")

GLODAP_obs_grid <-
  bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)

rm(GLODAP_obs_grid_temp)

3.5.2 talk

3.5.2.1 NA

GLODAP <- GLODAP %>% 
  mutate(talkna = if_else(is.na(talk), "NA", "Value"))

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era, talkna)

map +
  geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
  scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  facet_grid(era ~ talkna) +
  theme(legend.position = "top")

Past versions of talk_na_subset-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
d7831b0	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

GLODAP <- GLODAP %>% 
  select(-talkna) %>% 
  filter(!is.na(talk))

##

GLODAP_stats_temp <- GLODAP %>% 
  summarise(talk_values = n())

GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)

##

GLODAP_obs_grid_temp <- GLODAP %>% 
  count(lat, lon, era) %>% 
  mutate(cleaning_level = "talk_values")

GLODAP_obs_grid <-
  bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)

rm(GLODAP_obs_grid_temp)

3.5.2.2 f flag

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era, talkf)

map +
  geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
  scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  facet_grid(era ~ talkf) +
  theme(legend.position = "top",
        legend.title = element_blank())

Past versions of talk_f_subset-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
d7831b0	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

# ###

GLODAP <- GLODAP %>%
  filter(talkf %in% params_local$flag_f)

3.5.2.3 qc flag

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era, talkqc)

map +
  geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
  scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  facet_grid(era ~ talkqc) +
  theme(legend.position = "top",
        legend.title = element_blank())

Past versions of talk_qc_subset-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
d7831b0	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

###

GLODAP <- GLODAP %>%
  filter(talkqc %in% params_local$flag_qc)

##

GLODAP_stats_temp <- GLODAP %>%
  summarise(talk_flag = n())

GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)

##

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era) %>%
  mutate(cleaning_level = "talk_flag")

GLODAP_obs_grid <-
  bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)

rm(GLODAP_obs_grid_temp)

3.5.3 Phosphate

Phosphate was used as predictor:

P_used <- "phosphate" %in% params_local$MLR_predictors
P_used

[1] TRUE

3.5.3.1 NA

GLODAP <- GLODAP %>% 
  mutate(phosphatena = if_else(is.na(phosphate), "NA", "Value"))

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era, phosphatena)

map +
  geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
  scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  facet_grid(era ~ phosphatena) +
  theme(legend.position = "top")

Past versions of phosphate_na_subset-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
ed62e96	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
d7831b0	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

GLODAP <- GLODAP %>% 
  select(-phosphatena) %>% 
  filter(!is.na(phosphate))

##

GLODAP_stats_temp <- GLODAP %>% 
  summarise(phosphate_values = n())

GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)

##

GLODAP_obs_grid_temp <- GLODAP %>% 
  count(lat, lon, era) %>% 
  mutate(cleaning_level = "phosphate_values")

GLODAP_obs_grid <-
  bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)

rm(GLODAP_obs_grid_temp)

3.5.3.2 f flag

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era, phosphatef)

map +
  geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
    scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  facet_grid(era~phosphatef) +
  theme(legend.position = "top",
        legend.title = element_blank())

Past versions of phosphate_f_subset-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
ed62e96	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
d7831b0	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

###

GLODAP <- GLODAP %>%
  filter(phosphatef %in% params_local$flag_f)

3.5.3.3 qc flag

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era, phosphateqc)

map +
  geom_raster(data = GLODAP_obs_grid_temp, aes(lon, lat, fill = n)) +
    scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  facet_grid(era~phosphateqc) +
  theme(legend.position = "top",
        legend.title = element_blank())

Past versions of phosphate_qc_subset-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
ed62e96	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
d7831b0	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

###

GLODAP <- GLODAP %>%
  filter(phosphateqc %in% params_local$flag_qc)

##

GLODAP_stats_temp <- GLODAP %>%
  summarise(phosphate_flag = n())

GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)
rm(GLODAP_stats_temp)

##

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era) %>%
  mutate(cleaning_level = "phosphate_flag")

GLODAP_obs_grid <-
  bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)

rm(GLODAP_obs_grid_temp)

3.5.4 eMLR variables

Variables required as predictors for the MLR fits, are subsetted for NAs and flags.

if ("temp" %in% params_local$MLR_predictors) {
  GLODAP <- GLODAP %>%
    filter(!is.na(temp))
}

##

if ("sal" %in% params_local$MLR_predictors) {
  GLODAP <- GLODAP %>%
    filter(!is.na(sal))
  
  GLODAP <- GLODAP %>%
    filter(salinityf %in% params_local$flag_f)
  
  GLODAP <- GLODAP %>%
    filter(salinityqc %in% params_local$flag_qc)
}

##

if ("silicate" %in% params_local$MLR_predictors) {
  GLODAP <- GLODAP %>%
    filter(!is.na(silicate))
  
  GLODAP <- GLODAP %>%
    filter(silicatef %in% params_local$flag_f)
  
  GLODAP <- GLODAP %>%
    filter(silicateqc %in% params_local$flag_qc)
}

##

if ("oxygen" %in% params_local$MLR_predictors) {
  GLODAP <- GLODAP %>%
    filter(!is.na(oxygen))
  
  GLODAP <- GLODAP %>%
    filter(oxygenf %in% params_local$flag_f)
  
  GLODAP <- GLODAP %>%
    filter(oxygenqc %in% params_local$flag_qc)
}

##

if ("aou" %in% params_local$MLR_predictors) {
  GLODAP <- GLODAP %>%
    filter(!is.na(aou))
  
  GLODAP <- GLODAP %>%
    filter(aouf %in% params_local$flag_f)
}

##

if ("nitrate" %in% params_local$MLR_predictors) {
  GLODAP <- GLODAP %>%
    filter(!is.na(nitrate))
  
  GLODAP <- GLODAP %>%
    filter(nitratef %in% params_local$flag_f)
  
  GLODAP <- GLODAP %>%
    filter(nitrateqc %in% params_local$flag_qc)
}

##

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

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

##

GLODAP_stats_temp <- GLODAP %>%
  summarise(eMLR_variables = n())

GLODAP_stats <- cbind(GLODAP_stats, GLODAP_stats_temp)

rm(GLODAP_stats_temp)

##

GLODAP_obs_grid_temp <- GLODAP %>%
  count(lat, lon, era) %>%
  mutate(cleaning_level = "eMLR_variables")

GLODAP_obs_grid <-
  bind_rows(GLODAP_obs_grid, GLODAP_obs_grid_temp)

rm(GLODAP_obs_grid_temp)

GLODAP <- GLODAP %>% 
  select(-ends_with(c("f", "qc")))

3.6 Reference years (tref)

3.6.1 Median years

Median years of each era (tref) were determined as:

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

tref

# A tibble: 2 × 2
  era       median_year
  <fct>           <dbl>
1 2000-2009        2005
2 2010-2019        2014

3.6.2 Fixed tref

tref were manually set to:

tref <- tref %>%
  arrange(median_year)

tref1 <- tref %>%
  head(1)

tref2 <- tref %>%
  tail(1)

if (!is.null(params_local$tref1)) {
  tref1 <- tref1 %>%
    mutate(median_year = params_local$tref1)
}

if (!is.null(params_local$tref2)) {
  tref2 <- tref2 %>%
    mutate(median_year = params_local$tref2)
}

tref <- bind_rows(tref1, tref2)

tref <- full_join(tref, era_labels)
tref

# A tibble: 2 × 4
  era       median_year start   end
  <fct>           <dbl> <dbl> <dbl>
1 2000-2009        2009  2000  2009
2 2010-2019        2010  2010  2019

3.7 Write files

# select relevant columns for further analysis
GLODAP <- GLODAP %>% 
  select(year, date, era, basin, basin_AIP, lat, lon, cruise,
         bottomdepth, depth,
         temp, sal, gamma,
         tco2, talk, phosphate,
         oxygen, aou, nitrate, silicate,
         temp_model, sal_model = so_model, gamma_model,
         tco2_model = dissic_model, talk_model, phosphate_model = po4_model,
         oxygen_model = o2_model, aou_model,
         nitrate_model = no3_model, silicate_model = si_model
         )


GLODAP  %>%  write_csv(paste(path_version_data,
                             "GLODAPv2.2020_clean.csv",
                             sep = ""))

tref  %>%  write_csv(paste(path_version_data,
                           "tref.csv",
                           sep = ""))

cruise_stats  %>%  write_csv(paste(
  path_version_data,
  "CANYON_B_cleaning_cruise_stats.csv",
  sep = ""
))

GLODAP_stats  %>%  write_csv(paste(
  path_version_data,
  "CANYON_B_cleaning_GLODAP_stats.csv",
  sep = ""
))

stats_CANYON_B_cleaning_cruises  %>%  write_csv(paste(
  path_version_data,
  "CANYON_B_cleaning_GLODAP_cruise_removal_stats.csv",
  sep = ""
))

stats_CANYON_B_cleaning_samples  %>%  write_csv(paste(
  path_version_data,
  "CANYON_B_cleaning_GLODAP_sample_removal_stats.csv",
  sep = ""
))

grid_CANYON_B_cleaning_samples  %>%  write_csv(paste(
  path_version_data,
  "CANYON_B_cleaning_GLODAP_sample_removal_grid.csv",
  sep = ""
))

4 Overview plots

4.1 Number of overservations

GLODAP %>% 
  group_by(era, basin_AIP) %>% 
  count() %>% 
  ggplot(aes(basin_AIP, n, fill = era)) +
  geom_col() +
  scale_fill_brewer(palette = "Dark2")

Past versions of counts-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
81a46a4	jens-daniel-mueller	2021-08-03
b88c61b	jens-daniel-mueller	2021-08-03
88f7356	jens-daniel-mueller	2021-08-02
d759279	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
cf773c5	jens-daniel-mueller	2021-05-26
62bd574	jens-daniel-mueller	2021-05-20
7c56c39	jens-daniel-mueller	2021-05-19
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
d2a83bc	jens-daniel-mueller	2021-04-16
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
b6fe355	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13

4.2 Cleaning stats

Number of observations at various steps of data cleaning.

GLODAP_stats_long <- GLODAP_stats %>%
  pivot_longer(1:length(GLODAP_stats),
               names_to = "parameter",
               values_to = "n")

GLODAP_stats_long <- GLODAP_stats_long %>%
  mutate(parameter = fct_reorder(parameter, n))

GLODAP_stats_long %>% 
  ggplot(aes(parameter, n/1000)) +
  geom_col() +
  coord_flip() +
  theme(axis.title.y = element_blank())

Past versions of GLODAP_cleaning_stats-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
ed62e96	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
5d452fe	jens-daniel-mueller	2020-12-18
158fe26	jens-daniel-mueller	2020-12-15
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

rm(GLODAP_stats_long)

4.3 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)

4.4 Histogram Zonal coverage

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

GLODAP_histogram_lat %>%
  ggplot(aes(lat_grid, n, fill = era)) +
  geom_col() +
  scale_fill_brewer(palette = "Dark2") +
  facet_wrap( ~ basin_AIP) +
  coord_flip(expand = 0) +
  theme(legend.position = "top",
        legend.title = element_blank())

Past versions of coverage_histogram_zonal-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
81a46a4	jens-daniel-mueller	2021-08-03
b88c61b	jens-daniel-mueller	2021-08-03
88f7356	jens-daniel-mueller	2021-08-02
d759279	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
cf773c5	jens-daniel-mueller	2021-05-26
62bd574	jens-daniel-mueller	2021-05-20
7c56c39	jens-daniel-mueller	2021-05-19
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
d2a83bc	jens-daniel-mueller	2021-04-16
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
b6fe355	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
bb44686	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
555750f	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
0bade3b	jens-daniel-mueller	2021-03-15
27c1f4b	jens-daniel-mueller	2021-03-14
af75ebf	jens-daniel-mueller	2021-03-14
5017709	jens-daniel-mueller	2021-03-11
85a5ed2	jens-daniel-mueller	2021-03-10
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
158fe26	jens-daniel-mueller	2020-12-15
984697e	jens-daniel-mueller	2020-12-12
3ebff89	jens-daniel-mueller	2020-12-12
c8acfcb	jens-daniel-mueller	2020-12-11
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
7c25f7a	jens-daniel-mueller	2020-12-02
0ff728b	jens-daniel-mueller	2020-12-01
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

rm(GLODAP_histogram_lat)

4.5 Histogram temporal coverage

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

GLODAP_histogram_year %>%
  ggplot() +
  geom_vline(xintercept = sort(params_local$era_end)[1] + 0.5) +
  geom_col(aes(year, n,
               fill = basin_AIP)) +
  geom_point(
    data = tref,
    aes(median_year, 100, shape = "tref"),
    size = 2,
    fill = "white"
  ) +
  scale_fill_brewer(palette = "Dark2") +
  scale_shape_manual(values = 24, name = "") +
  scale_y_continuous() +
  coord_cartesian(expand = 0) +
  theme(
    legend.position = "top",
    legend.direction = "vertical",
    legend.title = element_blank(),
    axis.title.x = element_blank()
  )

Past versions of coverage_histogram_temporal-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
81a46a4	jens-daniel-mueller	2021-08-03
b88c61b	jens-daniel-mueller	2021-08-03
88f7356	jens-daniel-mueller	2021-08-02
d759279	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
c18a8b1	jens-daniel-mueller	2021-07-09
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
cf773c5	jens-daniel-mueller	2021-05-26
62bd574	jens-daniel-mueller	2021-05-20
7c56c39	jens-daniel-mueller	2021-05-19
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
d2a83bc	jens-daniel-mueller	2021-04-16
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
7e4f671	jens-daniel-mueller	2021-04-16
b6fe355	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
099d566	jens-daniel-mueller	2021-04-14
bb44686	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
555750f	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
0bade3b	jens-daniel-mueller	2021-03-15
27c1f4b	jens-daniel-mueller	2021-03-14
af75ebf	jens-daniel-mueller	2021-03-14
5017709	jens-daniel-mueller	2021-03-11
85a5ed2	jens-daniel-mueller	2021-03-10
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
158fe26	jens-daniel-mueller	2020-12-15
984697e	jens-daniel-mueller	2020-12-12
3ebff89	jens-daniel-mueller	2020-12-12
c8acfcb	jens-daniel-mueller	2020-12-11
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
0ff728b	jens-daniel-mueller	2020-12-01
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

rm(GLODAP_histogram_year,
   era_median_year)

4.6 Zonal temporal coverage (Hovmoeller)

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

GLODAP_hovmoeller_year %>%
  ggplot(aes(year, lat_grid, fill = n)) +
  geom_tile() +
  geom_vline(xintercept = sort(params_local$era_end)[1] + 0.5) +
  scale_fill_viridis_c(option = "magma",
                       direction = -1,
                       trans = "log10") +
  coord_cartesian(expand = 0) +
  facet_wrap( ~ basin_AIP, ncol = 1) +
  theme(legend.position = "top",
        axis.title.x = element_blank())

Past versions of coverage_hovmoeller-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
81a46a4	jens-daniel-mueller	2021-08-03
b88c61b	jens-daniel-mueller	2021-08-03
88f7356	jens-daniel-mueller	2021-08-02
d759279	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
cf773c5	jens-daniel-mueller	2021-05-26
62bd574	jens-daniel-mueller	2021-05-20
7c56c39	jens-daniel-mueller	2021-05-19
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
d2a83bc	jens-daniel-mueller	2021-04-16
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
b6fe355	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
099d566	jens-daniel-mueller	2021-04-14
bb44686	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
555750f	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
0bade3b	jens-daniel-mueller	2021-03-15
27c1f4b	jens-daniel-mueller	2021-03-14
af75ebf	jens-daniel-mueller	2021-03-14
5017709	jens-daniel-mueller	2021-03-11
85a5ed2	jens-daniel-mueller	2021-03-10
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
158fe26	jens-daniel-mueller	2020-12-15
984697e	jens-daniel-mueller	2020-12-12
3ebff89	jens-daniel-mueller	2020-12-12
c8acfcb	jens-daniel-mueller	2020-12-11
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

rm(GLODAP_hovmoeller_year)

4.7 Coverage maps by era

4.7.1 Subsetting process

The following plots show the remaining data after individual cleaning steps, separately for each era.

GLODAP_obs_grid <- GLODAP_obs_grid %>%
  mutate(cleaning_level = factor(
           cleaning_level,
           unique(GLODAP_obs_grid$cleaning_level)
         ))

map +
  geom_raster(data = GLODAP_obs_grid %>%
                filter(cleaning_level == "tco2_values") %>%
                select(-cleaning_level),
              aes(lon, lat, fill = "tco2_values")) +
  geom_raster(data = GLODAP_obs_grid %>%
                filter(cleaning_level != "tco2_values"),
              aes(lon, lat, fill = "subset")) +
  scale_fill_brewer(palette = "Set1", name = "") +
  facet_grid(cleaning_level ~ era) +
  theme(legend.position = "top",
        axis.title = element_blank())

Past versions of coverage_maps_era_subsetting_era_cleaning_level-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
ed62e96	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
88f7356	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
969e631	jens-daniel-mueller	2021-05-12
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
158fe26	jens-daniel-mueller	2020-12-15
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
d5c5378	jens-daniel-mueller	2020-12-02
0ff728b	jens-daniel-mueller	2020-12-01
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

4.7.2 Final input data

The following plots show the remaining data density in each grid cell after all cleaning steps, separately for each era.

GLODAP_tco2_grid <- GLODAP %>%
  count(lat, lon)

map +
  geom_bin2d(data = GLODAP,
             aes(lon, lat),
             binwidth = c(1,1)) +
  scale_fill_viridis_c(option = "magma", direction = -1, trans = "log10") +
  facet_wrap(~era, ncol = 1) +
  labs(title = "Cleaned GLODAP observations",
       subtitle = paste("Version:", params_local$Version_ID)) +
  theme(axis.title = element_blank())

Past versions of coverage_maps_era_clean-1.png

Version	Author	Date
9335b31	jens-daniel-mueller	2021-08-10
755c6b1	jens-daniel-mueller	2021-08-09
c65f2e3	jens-daniel-mueller	2021-08-09
70b290d	jens-daniel-mueller	2021-08-09
cd8e0d5	jens-daniel-mueller	2021-08-06
15773a0	jens-daniel-mueller	2021-08-06
340d731	jens-daniel-mueller	2021-08-06
71546e4	jens-daniel-mueller	2021-08-06
29444a1	jens-daniel-mueller	2021-08-05
c4b789f	jens-daniel-mueller	2021-08-05
42e80c0	jens-daniel-mueller	2021-08-04
48f6eed	jens-daniel-mueller	2021-08-04
81a46a4	jens-daniel-mueller	2021-08-03
b88c61b	jens-daniel-mueller	2021-08-03
88f7356	jens-daniel-mueller	2021-08-02
d759279	jens-daniel-mueller	2021-08-02
127b801	jens-daniel-mueller	2021-07-24
912d90e	jens-daniel-mueller	2021-07-23
2477316	jens-daniel-mueller	2021-07-23
c9ccc00	jens-daniel-mueller	2021-07-22
910d64a	jens-daniel-mueller	2021-07-02
1cbf907	jens-daniel-mueller	2021-07-02
9480f94	jens-daniel-mueller	2021-06-29
7e1f407	jens-daniel-mueller	2021-06-10
2cbe18c	jens-daniel-mueller	2021-06-10
594ed9a	jens-daniel-mueller	2021-06-04
db7df0e	jens-daniel-mueller	2021-06-04
207339d	jens-daniel-mueller	2021-06-03
315710b	jens-daniel-mueller	2021-06-03
d37a85d	jens-daniel-mueller	2021-05-31
cf773c5	jens-daniel-mueller	2021-05-26
62bd574	jens-daniel-mueller	2021-05-20
7c56c39	jens-daniel-mueller	2021-05-19
0a84f2a	jens-daniel-mueller	2021-05-12
969e631	jens-daniel-mueller	2021-05-12
d2a83bc	jens-daniel-mueller	2021-04-16
84b1fe3	jens-daniel-mueller	2021-04-16
c0a47df	jens-daniel-mueller	2021-04-16
50290e8	jens-daniel-mueller	2021-04-16
b6fe355	jens-daniel-mueller	2021-04-16
858c4e6	jens-daniel-mueller	2021-04-16
ddec5b7	jens-daniel-mueller	2021-04-15
29edae5	jens-daniel-mueller	2021-04-14
9f31fe3	jens-daniel-mueller	2021-04-13
338dd3c	jens-daniel-mueller	2021-04-09
a79ca2c	jens-daniel-mueller	2021-04-09
eb827c9	jens-daniel-mueller	2021-04-07
05cc66b	jens-daniel-mueller	2021-03-24
03b6009	jens-daniel-mueller	2021-03-23
555750f	jens-daniel-mueller	2021-03-23
685338e	jens-daniel-mueller	2021-03-23
886f523	jens-daniel-mueller	2021-03-23
10c1346	jens-daniel-mueller	2021-03-23
f155edd	jens-daniel-mueller	2021-03-23
a1d52ff	jens-daniel-mueller	2021-03-15
0bade3b	jens-daniel-mueller	2021-03-15
27c1f4b	jens-daniel-mueller	2021-03-14
af75ebf	jens-daniel-mueller	2021-03-14
5017709	jens-daniel-mueller	2021-03-11
85a5ed2	jens-daniel-mueller	2021-03-10
7b672f7	jens-daniel-mueller	2021-01-11
33ba23c	jens-daniel-mueller	2021-01-07
318609d	jens-daniel-mueller	2020-12-23
6949b06	jens-daniel-mueller	2020-12-23
0aa2b50	jens-daniel-mueller	2020-12-23
2886da0	jens-daniel-mueller	2020-12-19
02f0ee9	jens-daniel-mueller	2020-12-18
158fe26	jens-daniel-mueller	2020-12-15
3ebff89	jens-daniel-mueller	2020-12-12
2fd0a2a	jens-daniel-mueller	2020-12-11
24a632f	jens-daniel-mueller	2020-12-07
6a8004b	jens-daniel-mueller	2020-12-07
70bf1a5	jens-daniel-mueller	2020-12-07
7555355	jens-daniel-mueller	2020-12-07
143d6fa	jens-daniel-mueller	2020-12-07
37e9dac	jens-daniel-mueller	2020-12-02
7c25f7a	jens-daniel-mueller	2020-12-02
d5c5378	jens-daniel-mueller	2020-12-02
083b3b0	jens-daniel-mueller	2020-12-02
0ff728b	jens-daniel-mueller	2020-12-01
b02b7a4	jens-daniel-mueller	2020-12-01
196be51	jens-daniel-mueller	2020-11-30

ggsave(path = path_version_figures,
       filename = "data_distribution_era.png",
       height = 8,
       width = 5)

4.8 Model vs observation

variables <-
  c(
    "temp",
    "sal",
    "gamma",
    "tco2",
    "talk",
    "phosphate",
    "oxygen",
    "aou",
    "nitrate",
    "silicate"
  )

for (i_var in variables) {
  #  i_var <- variables[1]
  
  p_prop_prop(df = GLODAP,
              var1 = i_var,
              var2 = paste0(i_var, "_model"))
  
}

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] gt_0.2.2        lubridate_1.7.9 ggforce_0.3.3   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_1.1.3     tibble_3.1.3    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               viridisLite_0.3.0        jsonlite_1.7.1          
 [4] here_0.1                 modelr_0.1.8             assertthat_0.2.1        
 [7] highr_0.8                blob_1.2.1               cellranger_1.1.0        
[10] yaml_2.2.1               pillar_1.6.2             backports_1.1.10        
[13] lattice_0.20-41          glue_1.4.2               RcppEigen_0.3.3.7.0     
[16] digest_0.6.27            RColorBrewer_1.1-2       promises_1.1.1          
[19] polyclip_1.10-0          checkmate_2.0.0          rvest_0.3.6             
[22] colorspace_2.0-2         htmltools_0.5.0          httpuv_1.5.4            
[25] Matrix_1.2-18            pkgconfig_2.0.3          broom_0.7.5             
[28] haven_2.3.1              scales_1.1.1             tweenr_1.0.2            
[31] whisker_0.4              later_1.2.0              git2r_0.27.1            
[34] generics_0.1.0           farver_2.0.3             ellipsis_0.3.2          
[37] withr_2.3.0              cli_3.0.1                magrittr_1.5            
[40] crayon_1.3.4             readxl_1.3.1             evaluate_0.14           
[43] fs_1.5.0                 fansi_0.4.1              MASS_7.3-53             
[46] xml2_1.3.2               RcppArmadillo_0.10.1.2.0 tools_4.0.3             
[49] data.table_1.14.0        hms_0.5.3                lifecycle_1.0.0         
[52] munsell_0.5.0            reprex_0.3.0             compiler_4.0.3          
[55] rlang_0.4.10             grid_4.0.3               rstudioapi_0.13         
[58] labeling_0.4.2           rmarkdown_2.10           gtable_0.3.0            
[61] DBI_1.1.0                R6_2.5.0                 knitr_1.33              
[64] utf8_1.1.4               rprojroot_2.0.2          stringi_1.5.3           
[67] parallel_4.0.3           Rcpp_1.0.5               vctrs_0.3.8             
[70] dbplyr_1.4.4             tidyselect_1.1.0         xfun_0.25