Last updated: 2020-11-20

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.

R Markdown file: up-to-date

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Environment: empty

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Seed: set.seed(20200707)

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Session information: recorded

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Cache: none

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File paths: relative

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Repository version: 1585269

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The results in this page were generated with repository version 1585269. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
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    Ignored:    data/auxillary/
    Ignored:    data/eMLR/
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    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-05-01_n_518_cruise_334_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-06-07_n_1030_cruise_288_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-06-25_n_242_cruise_618_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-09-09_n_552_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-04-26_n_20_cruise_648_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-05-26_n_1040_cruise_160_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-05-27_n_309_cruise_42_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-06-14_n_1462_cruise_259_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-07-30_n_1132_cruise_260_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-08-25_n_798_cruise_261_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-11-22_n_211_cruise_464_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-12-20_n_514_cruise_434_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-02-11_n_1024_cruise_341_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-03-14_n_196_cruise_69_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-06-07_n_44_cruise_448_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-06-28_n_52_cruise_449_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-08-03_n_187_cruise_450_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-10-09_n_33_cruise_409_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-11-24_n_251_cruise_465_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-01-07_n_120_cruise_466_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-05-17_n_107_cruise_467_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-05-31_n_338_cruise_461_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-06-23_n_381_cruise_46_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-09-05_n_89_cruise_468_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-10-14_n_33_cruise_410_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-01-20_n_186_cruise_472_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-05-22_n_433_cruise_24_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-10-14_n_26_cruise_411_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-10-16_n_380_cruise_437_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-10-26_n_605_cruise_82_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-06-15_n_1143_cruise_83_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-06-23_n_381_cruise_476_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-08-14_n_870_cruise_477_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-09-04_n_32_cruise_478_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-09-12_n_392_cruise_438_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-11-17_n_912_cruise_70_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2002-04-01_n_46_cruise_682_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2002-05-29_n_26_cruise_706_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2002-06-27_n_147_cruise_263_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2002-06-28_n_769_cruise_392_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-03-13_n_768_cruise_484_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-07-03_n_14_cruise_591_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-07-23_n_20_cruise_592_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-08-10_n_1153_cruise_56_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-09-07_n_2722_cruise_486_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-10-06_n_1055_cruise_264_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-10-10_n_102_cruise_633_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-11-03_n_976_cruise_265_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-11-19_n_1221_cruise_487_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-01-01_n_1682_cruise_488_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-01-23_n_13_cruise_593_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-04-06_n_61_cruise_489_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-04-22_n_913_cruise_695_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-04-29_n_59_cruise_556_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-05-22_n_202_cruise_167_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-05-26_n_10_cruise_463_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-06-20_n_14_cruise_594_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-06-22_n_806_cruise_393_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-07-12_n_63_cruise_595_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-07-20_n_3228_cruise_272_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-08-17_n_956_cruise_490_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-10-23_n_83_cruise_492_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-10-27_n_59_cruise_596_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-11-27_n_926_cruise_493_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-01-10_n_691_cruise_72_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-01-24_n_14_cruise_597_.png
    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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-05-25_n_890_cruise_683_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-05-30_n_242_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-09-14_n_1837_cruise_266_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-09-21_n_499_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-12-08_n_2641_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-06-04_n_587_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-02-28_n_1671_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-05-31_n_600_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-08-14_n_1209_cruise_502_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-09-16_n_478_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-01-08_n_551_cruise_74_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-01-16_n_3261_cruise_345_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-02-01_n_79_cruise_608_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-02-21_n_1640_cruise_354_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-03-02_n_996_cruise_385_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-03-15_n_927_cruise_19_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-04-06_n_841_cruise_75_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-04-28_n_57_cruise_568_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-05-28_n_416_cruise_171_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-06-22_n_868_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-02-16_n_672_cruise_675_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-02-27_n_1170_cruise_84_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-03-29_n_1063_cruise_676_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-04-17_n_3605_cruise_355_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-05-18_n_2663_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_2009-07-12_n_145_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-11-18_n_158_cruise_1059_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-01-01_n_4235_cruise_273_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-01-25_n_932_cruise_699_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-03-30_n_2340_cruise_346_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-04-03_n_377_cruise_703_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-05-21_n_266_cruise_173_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-05-26_n_168_cruise_1085_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-06-19_n_842_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_2010-10-16_n_161_cruise_2028_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-11-15_n_87_cruise_2029_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-12-22_n_1297_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-03-21_n_2140_cruise_295_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-05-18_n_516_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-10-08_n_887_cruise_347_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-10-26_n_214_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_2012-04-03_n_1103_cruise_329_.png
    Modified:   output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-04-15_n_111_cruise_2033_.png
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-05-01_n_1390_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
    Deleted:    output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-07-05_n_715_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
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1 Libraries

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

library(marelac)
library(lubridate)

2 Required data

Required are:

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

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

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

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

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

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

3 C*

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

organic matter formation and respiration
calcification and calcium carbonate dissolution

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

3.1 Stoichiometric ratios

rCP <- 117
rNP <- 16

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

C/P: 117
N/P: 16

3.2 Calculation

C* is calculated as:

print("Cstar = tco2  + rCP_phosphate  + talk_05  + rNP_phosphate_05")

[1] "Cstar = tco2  + rCP_phosphate  + talk_05  + rNP_phosphate_05"

GLODAP <- GLODAP %>% 
  mutate(rCP_phosphate = -rCP * phosphate,
         talk_05 = -0.5 * talk,
         rNP_phosphate_05 = -0.5 * rNP * phosphate,
         Cstar = tco2  + rCP_phosphate  + talk_05  + rNP_phosphate_05)

rm(rCP, rNP)

4 PO₄* calculation

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

GLODAP <- GLODAP %>% 
  mutate(phosphate_star = phosphate + (oxygen / 170)  - 1.95)

5 Reference year adjustment

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

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

5.1 Merge data sets

5.1.1 GLODAP + Cant

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

S04_cant_3d_obs <- S04_cant_3d_obs %>%
  group_by(lon, lat) %>% 
  mutate(n = n()) %>% 
  ungroup()

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

rm(S04_cant_3d, GLODAP_obs_grid)

GLODAP_cant_obs <- full_join(GLODAP, S04_cant_3d_obs)

rm(GLODAP, S04_cant_3d_obs)

GLODAP_cant_obs <- GLODAP_cant_obs %>%
  group_by(lon, lat) %>% 
  mutate(n = mean(n, na.rm = TRUE)) %>% 
  ungroup()

The mapped Cant product was merged with GLODAP observation by:

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

# GLODAP_cant_obs <- full_join(GLODAP_cant_obs, S04_cant_3d_obs_nr)

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

# GLODAP_cant_obs_set <- GLODAP_cant_obs %>%
#   filter(n_cant == 1) %>% 
#   group_by(lat, lon) %>%
#   arrange(depth) %>%
#   mutate(cant_pos_int = mean(cant, na.rm = TRUE)) %>%
#   ungroup()

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

# remove cant data at grid cells without observations

GLODAP <- GLODAP_cant_obs %>%
  filter(!is.na(Cstar)) %>%
  mutate(cant_pos = cant_pos_int) %>%
  select(-cant_pos_int, n)

rm(GLODAP_cant_obs)

5.1.2 GLODAP + atm. pCO₂

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

GLODAP <- left_join(GLODAP, co2_atm)

5.2 Calculate adjustment

Calculate Cant for tref = 2007 by applying alpha = 0.28 to the estimate of Sabine et al. (2004).

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

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

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

co2_atm_tref <- right_join(co2_atm, tref) %>% 
  select(-year) %>% 
  rename(pCO2_tref = pCO2)

GLODAP <- full_join(GLODAP, co2_atm_tref)

rm(co2_atm, tref)


GLODAP <- GLODAP %>%
  mutate(alpha = (tref - min(tref)) * (0.28 / 13),
         cant_pos = cant_pos * (1 + alpha),
         Cstar_tref_delta =
           ((pCO2 - pCO2_tref) / (pCO2_tref - 280)) * cant_pos,
         Cstar_tref = Cstar - Cstar_tref_delta)

5.3 Control plots

5.3.1 Histogram

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

5.3.2 Time series

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

GLODAP <- GLODAP %>% 
  select(-c(alpha))

6 Selected section plots

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

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

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

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

lat_section +
  geom_point(aes(col = tco2))

lat_section +
  geom_point(aes(col = rCP_phosphate))

lat_section +
  geom_point(aes(col = talk_05))

lat_section +
  geom_point(aes(col = rNP_phosphate_05))

lat_section +
  geom_point(aes(col = Cstar))

lat_section +
  geom_point(aes(col = -Cstar_tref_delta))

rm(lat_section, GLODAP_cruise)

GLODAP <- GLODAP %>% 
  select(-c(rCP_phosphate:Cstar, cant_pos:Cstar_tref_delta))

7 Isoneutral slabs

The following boundaries for isoneutral slabs were defined:

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

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

GLODAP_Atl <- GLODAP %>% 
  filter(basin == "Atlantic") %>% 
  mutate(gamma_slab = cut(gamma, parameters$slabs_Atl))

GLODAP_Ind_Pac <- GLODAP %>% 
  filter(basin == "Indo-Pacific") %>% 
  mutate(gamma_slab = cut(gamma, parameters$slabs_Ind_Pac))

GLODAP <- bind_rows(GLODAP_Atl, GLODAP_Ind_Pac)

rm(GLODAP_Atl, GLODAP_Ind_Pac)

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

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

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

rm(lat_section, GLODAP_cruise)

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

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

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

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

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

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

GLODAP_cruise <- calculate_gamma(GLODAP_cruise)

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

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

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

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

rm(lat_section, GLODAP_cruise, cruises_meridional)

8 Observations coverage

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

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

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

9 Individual cruise sections

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

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

GLODAP <- full_join(GLODAP, cruises)

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

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

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


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

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

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

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

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

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

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

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

lon_Cstar <- lon_section+
  geom_point(aes(col=Cstar_tref))


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

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

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

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

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

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

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

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

lat_Cstar <- lat_section+
  geom_point(aes(col=Cstar_tref))

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

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

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

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

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

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

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

hist_Cstar <- GLODAP_cruise %>%
  ggplot(aes(Cstar_tref)) +
  geom_histogram()

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

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

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

}

10 Write files

GLODAP <- GLODAP %>% 
  rename(Cstar = Cstar_tref)

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

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

sessionInfo()

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

Matrix products: default

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

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

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

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

eMLR - data preparation

Jens Daniel Müller

20 November, 2020

1 Libraries

2 Required data

3 C*

3.1 Stoichiometric ratios

3.2 Calculation

4 PO₄* calculation

5 Reference year adjustment

5.1 Merge data sets

5.1.1 GLODAP + Cant

5.1.2 GLODAP + atm. pCO₂

5.2 Calculate adjustment

5.3 Control plots

5.3.1 Histogram

5.3.2 Time series

6 Selected section plots

7 Isoneutral slabs

8 Observations coverage

9 Individual cruise sections

10 Write files

eMLR - data preparation

Jens Daniel Müller

20 November, 2020

1 Libraries

2 Required data

3 C*

3.1 Stoichiometric ratios

3.2 Calculation

4 PO4* calculation

5 Reference year adjustment

5.1 Merge data sets

5.1.1 GLODAP + Cant

5.1.2 GLODAP + atm. pCO2

5.2 Calculate adjustment

5.3 Control plots

5.3.1 Histogram

5.3.2 Time series

6 Selected section plots

7 Isoneutral slabs

8 Observations coverage

9 Individual cruise sections

10 Write files

4 PO₄* calculation

5.1.2 GLODAP + atm. pCO₂