Mapping cant

workflowr

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Last updated: 2020-11-26

Checks: 7 0

Knit directory: Cant_eMLR/

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

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R Markdown file: up-to-date

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

Environment: empty

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

Seed: set.seed(20200707)

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

Session information: recorded

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

Cache: none

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

File paths: relative

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

Repository version: fdd65b6

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 fdd65b6. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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

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

Untracked files:
    Untracked:  code/biogeochemical_functions.R
    Untracked:  code/test_scripts/analysis_previous_studies.Rmd
    Untracked:  code/test_scripts/read_World_Ocean_Atlas_2013_Clement.Rmd
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1981-07-14_n_2129_cruise_237_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1983-01-10_n_1241_cruise_238_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1989-08-18_n_483_cruise_371_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-06-25_n_242_cruise_618_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-04-26_n_20_cruise_648_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-06-14_n_1478_cruise_259_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-08-25_n_807_cruise_261_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2002-06-27_n_185_cruise_263_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-10-10_n_107_cruise_633_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-11-03_n_978_cruise_265_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-07-13_n_173_cruise_635_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-10-16_n_161_cruise_2028_.png
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    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-11-10_n_191_cruise_1073_.png
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    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-04-20_n_263_cruise_1103_.png
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    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2017-11-16_n_134_cruise_2063_.png
    Untracked:  output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2018-10-09_n_158_cruise_2068_.png

Unstaged changes:
    Modified:   analysis/eMLR_assumption_testing.Rmd
    Modified:   analysis/eMLR_model_fitting.Rmd
    Modified:   code/mapping_functions.R
    Modified:   code/plotting_functions.R
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1981-07-14_n_2095_cruise_237_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1983-01-12_n_1184_cruise_238_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1983-11-25_n_409_cruise_239_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1984-07-22_n_272_cruise_223_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1986-03-13_n_1437_cruise_370_.png
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    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1988-09-11_n_3171_cruise_242_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1989-02-17_n_59_cruise_621_.png
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    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1989-08-18_n_319_cruise_371_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1990-02-18_n_548_cruise_28_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1991-05-01_n_255_cruise_679_.png
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    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1994-01-27_n_858_cruise_459_.png
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    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-05-13_n_1438_cruise_252_.png
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    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-11-18_n_697_cruise_256_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-12-26_n_1346_cruise_257_.png
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    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-03-07_n_1135_cruise_374_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-05-01_n_518_cruise_334_.png
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    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-06-24_n_184_cruise_618_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-09-09_n_554_cruise_68_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-09-26_n_85_cruise_40_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-11-17_n_738_cruise_258_.png
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    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-06-07_n_44_cruise_448_.png
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    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-01-25_n_2240_cruise_350_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-01-25_n_59_cruise_558_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-03-08_n_67_cruise_494_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-04-28_n_60_cruise_559_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-05-25_n_894_cruise_683_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-05-31_n_251_cruise_168_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-06-11_n_1558_cruise_495_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-07-17_n_66_cruise_599_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-09-14_n_1839_cruise_266_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-09-21_n_503_cruise_666_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-09-30_n_178_cruise_496_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-10-25_n_69_cruise_600_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-12-09_n_2670_cruise_497_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-01-24_n_68_cruise_561_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-03-08_n_1719_cruise_306_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-04-25_n_38_cruise_562_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-06-04_n_589_cruise_25_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-06-16_n_1_cruise_602_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-06-21_n_968_cruise_498_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-07-11_n_37_cruise_603_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-10-26_n_68_cruise_604_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-01-23_n_85_cruise_564_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-02-28_n_1678_cruise_352_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-03-09_n_1058_cruise_501_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-04-11_n_1995_cruise_353_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-04-30_n_63_cruise_565_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-05-30_n_632_cruise_327_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-07-03_n_47_cruise_606_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-07-31_n_33_cruise_607_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-08-14_n_1212_cruise_502_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-09-16_n_486_cruise_667_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-09-18_n_299_cruise_503_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-10-30_n_1828_cruise_504_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-10-31_n_63_cruise_566_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-12-07_n_1654_cruise_505_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-01-08_n_608_cruise_74_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-01-16_n_3265_cruise_345_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-02-01_n_79_cruise_608_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-02-21_n_1666_cruise_354_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-03-02_n_996_cruise_385_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-03-15_n_936_cruise_19_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-04-06_n_846_cruise_75_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-04-28_n_57_cruise_568_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-05-28_n_426_cruise_171_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-06-22_n_880_cruise_394_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-10-21_n_363_cruise_506_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-01-07_n_345_cruise_674_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-02-16_n_673_cruise_675_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-02-27_n_1170_cruise_84_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-03-29_n_1074_cruise_676_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-04-17_n_3611_cruise_355_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-05-18_n_2666_cruise_507_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-05-23_n_317_cruise_172_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-07-11_n_64_cruise_635_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-08-02_n_127_cruise_26_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-11-10_n_319_cruise_63_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-11-18_n_160_cruise_1059_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-01-01_n_4235_cruise_273_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-01-25_n_935_cruise_699_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-03-30_n_2343_cruise_346_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-04-02_n_387_cruise_703_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-05-21_n_273_cruise_173_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-05-26_n_168_cruise_1085_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-06-19_n_847_cruise_395_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-06-26_n_157_cruise_1063_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-07-25_n_1356_cruise_609_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-08-19_n_88_cruise_1064_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-10-06_n_72_cruise_2028_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-11-15_n_87_cruise_2029_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-12-22_n_1308_cruise_20_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-01-17_n_108_cruise_1065_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-01-30_n_270_cruise_1087_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-02-18_n_121_cruise_1066_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-03-21_n_2158_cruise_295_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-05-18_n_527_cruise_174_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-06-25_n_250_cruise_1067_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-07-07_n_2466_cruise_517_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-10-08_n_896_cruise_347_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-10-20_n_105_cruise_2031_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-01-28_n_253_cruise_1090_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-02-06_n_591_cruise_1002_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-02-19_n_242_cruise_1069_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-04-01_n_826_cruise_329_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-04-15_n_111_cruise_2033_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-05-01_n_1404_cruise_330_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-06-07_n_152_cruise_1029_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-06-26_n_388_cruise_1092_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-07-05_n_718_cruise_1031_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-07-20_n_793_cruise_1071_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-08-14_n_1250_cruise_518_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-11-25_n_77_cruise_1073_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-12-05_n_231_cruise_2071_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-12-12_n_118_cruise_1074_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-12-15_n_828_cruise_1050_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-01-23_n_902_cruise_1051_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-01-29_n_369_cruise_1093_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-02-19_n_221_cruise_1076_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-03-14_n_222_cruise_2072_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-05-02_n_2819_cruise_1035_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-05-06_n_298_cruise_2073_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-06-09_n_233_cruise_1078_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-07-24_n_678_cruise_1079_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-08-21_n_883_cruise_1096_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-09-02_n_2030_cruise_1041_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-10-11_n_140_cruise_2035_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-12-06_n_137_cruise_2074_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-01-11_n_1770_cruise_1042_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-01-24_n_288_cruise_2075_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-02-22_n_253_cruise_2038_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-03-13_n_187_cruise_2076_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-04-18_n_2219_cruise_1036_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-04-29_n_78_cruise_2039_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-05-05_n_288_cruise_2077_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-05-18_n_272_cruise_2040_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-06-16_n_195_cruise_2078_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-07-08_n_374_cruise_1098_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-07-25_n_403_cruise_2041_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-08-03_n_1705_cruise_1053_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-08-10_n_726_cruise_1099_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-11-24_n_82_cruise_2079_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-12-11_n_536_cruise_1004_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-01-19_n_65_cruise_2043_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-01-29_n_315_cruise_2080_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-02-14_n_234_cruise_2044_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-03-04_n_215_cruise_2081_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-03-25_n_17_cruise_1017_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-04-19_n_185_cruise_1103_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-04-20_n_96_cruise_2045_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-05-02_n_230_cruise_2083_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-05-04_n_874_cruise_1043_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-05-12_n_368_cruise_1027_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-05-17_n_141_cruise_2046_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-05-17_n_689_cruise_1011_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-06-09_n_1589_cruise_1044_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-06-13_n_281_cruise_2084_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-07-20_n_445_cruise_2047_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-08-16_n_817_cruise_1100_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2015-11-20_n_106_cruise_2086_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-01-03_n_663_cruise_1054_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-01-16_n_78_cruise_2049_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-01-25_n_287_cruise_2087_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-02-15_n_381_cruise_2050_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-03-01_n_1359_cruise_1046_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-03-04_n_230_cruise_2088_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-04-13_n_106_cruise_2051_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-05-04_n_307_cruise_2090_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-05-16_n_146_cruise_2052_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-05-31_n_2080_cruise_1020_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-06-16_n_263_cruise_2091_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-06-24_n_104_cruise_2053_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-07-05_n_837_cruise_2011_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-07-21_n_1102_cruise_1101_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-08-13_n_290_cruise_2054_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-09-25_n_160_cruise_2055_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-11-20_n_103_cruise_2056_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2016-12-25_n_3975_cruise_1045_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2017-01-12_n_103_cruise_2093_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2017-01-30_n_368_cruise_2057_.png
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---

1 Libraries

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

library(seacarb)

2 Predictor fields

Currently, we use combined predictor fields:

• WOA18: S, T, and derived variables
• GLODAP16: Oxygen, PO4, NO3, Silicate, and derived variables

predictors <- 
    read_csv(here::here("data/mapping",
                         "W18_st_G16_opsn.csv"))

predictors_surface <- 
    read_csv(here::here("data/mapping",
                         "W18_st_G16_opsn_surface.csv"))

3 Atm. pCO2

co2_atm_tref <-
  read_csv(here::here(
    "data/interim",
    "co2_atm_tref.csv"
  ))

4 Load MLR models

lm_all_wide <-
  read_csv(here::here("data/eMLR",
                       "lm_all_wide.csv"))

5 Merge MLRs + climatologies

lm_all_wide <- lm_all_wide %>% 
  mutate(model = str_remove(model, "Cstar ~ "))
         
cant <- full_join(predictors, lm_all_wide)

rm(predictors, lm_all_wide)

6 Map cant

6.1 Deep water

6.2 Apply MLRs to predictor

cant <- b_cant(cant)

cant <- cant %>%
  mutate(cant_pos = if_else(cant < 0, 0, cant))

cant <- b_cant_predictor(cant)

6.2.1 Sections by model

Zonal sections plots are produced for every 20° longitude, each era and for all models individually and can be downloaded here.

for (i_eras in unique(cant$eras)) {
  # i_eras <- unique(cant$eras)[2]
  cant_eras <- cant %>%
    filter(eras == i_eras)
  
  for (i_lon in seq(20.5, 360, 20)) {
    # i_lon <- seq(20.5, 360, 20)[7]
    cant_eras_lon <- cant_eras %>%
      filter(lon == i_lon)
    
    limits = max(abs(cant_eras_lon$cant)) * c(-1,1)
    
    cant_eras_lon %>%
      ggplot(aes(lat, depth, col = cant)) +
      geom_point() +
      scale_color_scico(
        name = "cant",
        palette = "vik",
        limit = limits
      ) +
      scale_y_reverse(limits = c(parameters$inventory_depth, NA)) +
      scale_x_continuous(limits = c(-75, 65)) +
      guides(fill = guide_colorsteps(barheight = unit(10, "cm"))) +
      labs(title = paste("eras:", i_eras,
                         "| lon:", i_lon,
                         "|", parameters$Version_ID)) +
      facet_wrap( ~ model, ncol = 5)
    
    ggsave(
      here::here(
        "output/figure/mapping",
        paste(i_eras,
              "lon",
              i_lon,
              "model_cant.png",
              sep = "_")
      ),
      width = 17,
      height = 9
    )
    
  }
}

6.3 Surface water

As outlined in Gruber et al. (2019), a transient equilibrium approach was applied to estimate cant in surface waters, assuming that the CO₂ system in these waters has followed the increase in atmospheric CO₂ closely.

Using eq 10.2.16 from OBD, the change in anthropogenic CO₂ in the upper ocean was computed as:

_tC_ant,eq(t2,ref − t1,ref) = 1∕γ ⋅ DIC/pCO2 ⋅ (pCO2atm (t2ref)− pCO2atm (t1ref))

, where DIC and pCO₂ are the in situ values, where γ is the buffer (Revelle) factor and where we evaluated the right-hand side using seacarb employing the Mehrbach constants as refitted by Dickson and Millero using the climatological values for temperature, salinity, DIC and Alk.

6.3.1 pCO₂ climatology

# calculate pCO2 from talk and tco2 climatology
predictors_surface <- predictors_surface %>% 
  mutate(pCO2 = carb(flag = 15,
                     var1 = TAlk*1e-6,
                     var2 = TCO2*1e-6,
                     S = sal,
                     T = tem,
                     P = depth/10,
                     Pt = phosphate*1e-6,
                     Sit = silicate*1e-6,
                     k1k2 = "l")$pCO2)

p_map_climatology(
  df = predictors_surface,
  var = "pCO2")

p_section_climatology_regular(
  df = predictors_surface,
  var = "pCO2")

6.3.2 Revelle factor

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

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

p_section_climatology_regular(
  df = predictors_surface,
  var = "rev_fac")

6.3.3 C_ant

# calculate increase in atm pCO2 between eras
co2_atm_tref <- co2_atm_tref %>% 
  arrange(pCO2_tref) %>% 
  mutate(d_pCO2_tref = pCO2_tref - lag(pCO2_tref)) %>% 
  drop_na() %>% 
  mutate(eras = c("JGOFS_GO", "GO_new")) %>% 
  select(eras, d_pCO2_tref)

cant_surface <- full_join(predictors_surface, co2_atm_tref,
                          by = character())

# calculate cant
cant_surface <- cant_surface %>% 
  mutate(cant = (1 / rev_fac) * (TCO2 / pCO2) * d_pCO2_tref)

# calculate positive cant
cant_surface <- cant_surface %>%
  mutate(cant_pos = if_else(cant < 0, 0, cant))

p_map_climatology(
  df = cant_surface,
  var = "cant")

p_section_climatology_regular(
  df = cant_surface,
  var = "cant")

6.4 Mean cant fields

Mean and sd are calculated for cant in each grid cell (XYZ), basin and era combination. Calculations are performed for all cant values vs positive values only. This averaging step summarizes the information derived from ten best fitting MLRs.

6.4.1 Deep water averaging

cant_predictor_average <- m_cant_predictor_model_average(cant)
cant_predictor_average <- m_cut_gamma(cant_predictor_average, "gamma")

cant_average <- m_cant_model_average(cant)
rm(cant)

6.4.2 Surface water averaging

cant_surface_average <- m_cant_model_average(cant_surface)
rm(cant_surface)

6.4.3 Join surface and deep water

cant_average <- full_join(cant_average, cant_surface_average)
rm(cant_surface_average)

cant_average <- m_cut_gamma(cant_average, "gamma")

6.5 Mean cant sections

For each basin and era combination, the zonal mean cant is calculated, again for all vs positive only values. Likewise, sd is calculated for the averaging of the mean basin fields.

cant_average <- left_join(cant_average,
                          basinmask %>% select(-basin))

cant_average_zonal <- m_cant_zonal_mean(cant_average)
cant_average_zonal <- m_cut_gamma(cant_average_zonal, "gamma_mean")

6.6 Mean cant sections by coefficient

For each basin and era combination, the zonal mean cant is calculated by model coefficient.

cant_predictor_average <- full_join(cant_predictor_average,
                                basinmask %>% select(-basin))

cant_predictor_average_zonal <-
  m_cant_predictor_zonal_mean(cant_predictor_average)

cant_predictor_average_zonal <-
  m_cut_gamma(cant_predictor_average_zonal, "gamma")

6.7 Inventory calculation

To calculate cant column inventories, we:

1. Multiple layer thickness with cant concentration to get a layer inventory
2. For each horizontal grid cell and era, sum cant layer inventories from 150 - 3000 m

Step 2 is performed again for all cant and positive cant values only

cant_inv <- m_cant_inv(cant_average)

7 Write csv

# cant %>%
#     write_csv(here::here("data/output",
#                          "cant.csv"))

cant_average %>%
    write_csv(here::here("data/output",
                         "cant_3d.csv"))

cant_predictor_average %>%
    write_csv(here::here("data/output",
                         "cant_predictor_3d.csv"))

cant_average_zonal %>%
    write_csv(here::here("data/output",
                         "cant_zonal.csv"))

cant_predictor_average_zonal %>%
    write_csv(here::here("data/output",
                         "cant_predictor_zonal.csv"))

cant_inv %>%
    write_csv(here::here("data/output",
                         "cant_inv.csv"))

Session information

sessionInfo()

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

Matrix products: default

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

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

other attached packages:
 [1] seacarb_3.2.13  oce_1.2-0       gsw_1.0-5       testthat_2.3.2 
 [5] metR_0.7.0      scico_1.2.0     patchwork_1.0.1 collapse_1.3.2 
 [9] forcats_0.5.0   stringr_1.4.0   dplyr_1.0.0     purrr_0.3.4    
[13] readr_1.3.1     tidyr_1.1.0     tibble_3.0.3    ggplot2_3.3.2  
[17] tidyverse_1.3.0 workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] httr_1.4.2        viridisLite_0.3.0 jsonlite_1.7.0    here_0.1         
 [5] modelr_0.1.8      Formula_1.2-3     assertthat_0.2.1  blob_1.2.1       
 [9] cellranger_1.1.0  yaml_2.2.1        pillar_1.4.6      backports_1.1.8  
[13] lattice_0.20-41   glue_1.4.1        digest_0.6.25     promises_1.1.1   
[17] checkmate_2.0.0   rvest_0.3.6       colorspace_1.4-1  sandwich_2.5-1   
[21] htmltools_0.5.0   httpuv_1.5.4      Matrix_1.2-18     pkgconfig_2.0.3  
[25] broom_0.7.0       haven_2.3.1       xtable_1.8-4      scales_1.1.1     
[29] whisker_0.4       later_1.1.0.1     git2r_0.27.1      farver_2.0.3     
[33] generics_0.0.2    ellipsis_0.3.1    withr_2.2.0       cli_2.0.2        
[37] magrittr_1.5      crayon_1.3.4      readxl_1.3.1      evaluate_0.14    
[41] fs_1.4.2          fansi_0.4.1       xml2_1.3.2        tools_4.0.2      
[45] data.table_1.13.0 hms_0.5.3         lifecycle_0.2.0   munsell_0.5.0    
[49] reprex_0.3.0      isoband_0.2.2     compiler_4.0.2    lfe_2.8-5.1      
[53] rlang_0.4.7       grid_4.0.2        rstudioapi_0.11   labeling_0.3     
[57] rmarkdown_2.3     gtable_0.3.0      DBI_1.1.0         R6_2.4.1         
[61] zoo_1.8-8         lubridate_1.7.9   knitr_1.30        rprojroot_1.3-2  
[65] stringi_1.4.6     parallel_4.0.2    Rcpp_1.0.5        vctrs_0.3.2      
[69] dbplyr_1.4.4      tidyselect_1.1.0  xfun_0.16