eMLR - data preparation
Jens Daniel Müller
08 September, 2020
Last updated: 2020-09-08
Checks: 7 0
Knit directory: Cant_eMLR/
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Ignored files:
Ignored: .Rproj.user/
Ignored: analysis/figure/
Ignored: data/GLODAPv1_1/
Ignored: data/GLODAPv2_2016b_MappedClimatologies/
Ignored: data/GLODAPv2_2020/
Ignored: data/Gruber_2019/
Ignored: data/WOCE/
Ignored: data/World_Ocean_Atlas_2013_Clement/
Ignored: data/World_Ocean_Atlas_2018/
Ignored: data/eMLR/
Ignored: data/mapping/
Ignored: data/pCO2_atmosphere/
Ignored: dump/
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Unstaged changes:
Modified: analysis/_site.yml
Modified: analysis/analysis_this_study.Rmd
Modified: analysis/config_nomenclature.Rmd
Modified: analysis/config_parameterization.Rmd
Modified: analysis/eMLR_assumption_testing.Rmd
Modified: analysis/eMLR_model_fitting.Rmd
Modified: analysis/mapping_cant_calculation.Rmd
Modified: analysis/mapping_predictor_preparation.Rmd
Modified: analysis/read_CO2_atm.Rmd
Modified: analysis/read_GLODAPv2_2016_MappedClimatologies.Rmd
Modified: analysis/read_GLODAPv2_2020.Rmd
Modified: analysis/read_Gruber_2019_Cant.Rmd
Modified: analysis/read_Sabine_2004_Cant.Rmd
Modified: analysis/read_World_Ocean_Atlas_2013_Clement.Rmd
Modified: code/plotting_functions.R
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1981-07-14_n_2108_cruise_237_.png
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Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1994-10-11_n_765_cruise_102_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1994-12-28_n_1422_cruise_249_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-01-10_n_58_cruise_441_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-01-18_n_709_cruise_67_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-01-29_n_654_cruise_361_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-02-13_n_1804_cruise_250_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-03-12_n_211_cruise_362_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-03-29_n_1450_cruise_251_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-05-13_n_1431_cruise_252_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-06-26_n_1064_cruise_253_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-08-01_n_1569_cruise_254_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-09-02_n_341_cruise_431_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-09-21_n_1384_cruise_255_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-10-10_n_1383_cruise_339_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-11-18_n_684_cruise_256_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1995-12-26_n_1338_cruise_257_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-02-12_n_1867_cruise_280_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-03-07_n_1097_cruise_374_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-06-05_n_733_cruise_288_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-09-09_n_549_cruise_68_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1996-11-17_n_738_cruise_258_.png
Modified: 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_1028_cruise_160_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-05-27_n_307_cruise_42_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-06-14_n_1454_cruise_259_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-07-30_n_1096_cruise_260_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-08-25_n_770_cruise_261_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1997-11-22_n_209_cruise_464_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-02-11_n_635_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
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-06-28_n_38_cruise_449_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-10-09_n_33_cruise_409_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1998-11-24_n_250_cruise_465_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-05-17_n_90_cruise_467_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-05-31_n_324_cruise_461_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-09-05_n_87_cruise_468_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_1999-10-14_n_33_cruise_410_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-01-20_n_179_cruise_472_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-05-22_n_431_cruise_24_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-10-14_n_26_cruise_411_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-10-16_n_375_cruise_437_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2000-10-26_n_603_cruise_82_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-06-15_n_1120_cruise_83_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-06-23_n_361_cruise_476_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-08-14_n_814_cruise_477_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-09-04_n_31_cruise_478_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-09-12_n_390_cruise_438_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2001-11-17_n_898_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_146_cruise_263_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-03-14_n_647_cruise_484_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-08-10_n_1036_cruise_56_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-09-07_n_2595_cruise_486_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-10-06_n_1050_cruise_264_.png
Modified: 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_975_cruise_265_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2003-11-19_n_1218_cruise_487_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-01-02_n_1630_cruise_488_.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_2004-04-23_n_801_cruise_695_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-05-22_n_200_cruise_167_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-05-26_n_9_cruise_463_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-07-20_n_3224_cruise_272_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-08-18_n_876_cruise_490_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2004-10-22_n_81_cruise_492_.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_682_cruise_72_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-01-25_n_2237_cruise_350_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-03-08_n_66_cruise_494_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-05-25_n_889_cruise_683_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-05-30_n_240_cruise_168_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-06-11_n_1490_cruise_495_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-09-14_n_1833_cruise_266_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-09-21_n_499_cruise_666_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-09-30_n_175_cruise_496_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2005-12-09_n_2541_cruise_497_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-03-09_n_1553_cruise_306_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-06-16_n_1_cruise_602_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2006-06-22_n_844_cruise_498_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-02-28_n_1668_cruise_352_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-03-09_n_1006_cruise_501_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-04-11_n_1914_cruise_353_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-05-31_n_600_cruise_327_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-08-14_n_1167_cruise_502_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-09-16_n_477_cruise_667_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-09-18_n_299_cruise_503_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-10-30_n_1748_cruise_504_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2007-12-07_n_1627_cruise_505_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-01-09_n_543_cruise_74_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-01-17_n_2443_cruise_345_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-02-20_n_1284_cruise_354_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-03-02_n_957_cruise_385_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-03-14_n_846_cruise_19_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-04-06_n_820_cruise_75_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-05-28_n_411_cruise_171_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2008-10-21_n_311_cruise_506_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-01-07_n_343_cruise_674_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-02-16_n_652_cruise_675_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-02-27_n_1162_cruise_84_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-03-29_n_1062_cruise_676_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-04-17_n_3549_cruise_355_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-05-18_n_2644_cruise_507_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-05-23_n_312_cruise_172_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-07-13_n_143_cruise_635_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-08-02_n_120_cruise_26_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-11-10_n_316_cruise_63_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2009-12-27_n_2668_cruise_273_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-01-25_n_928_cruise_699_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-03-30_n_2265_cruise_346_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-04-03_n_367_cruise_703_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-05-26_n_161_cruise_1085_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-06-26_n_157_cruise_1063_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-07-26_n_1203_cruise_609_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-08-19_n_80_cruise_1064_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-10-17_n_136_cruise_2028_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-11-15_n_83_cruise_2029_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2010-12-22_n_1296_cruise_20_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-01-17_n_107_cruise_1065_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-01-30_n_269_cruise_1087_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-02-18_n_116_cruise_1066_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-03-21_n_1930_cruise_295_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-05-18_n_510_cruise_174_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-06-25_n_249_cruise_1067_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-07-07_n_2107_cruise_517_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-10-09_n_617_cruise_347_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2011-10-26_n_204_cruise_2031_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-02-06_n_144_cruise_1090_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-02-06_n_586_cruise_1002_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-02-19_n_235_cruise_1069_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-04-04_n_1059_cruise_329_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-04-15_n_99_cruise_2033_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-05-01_n_1379_cruise_330_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-06-07_n_141_cruise_1029_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-06-26_n_386_cruise_1092_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-07-20_n_784_cruise_1071_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-08-15_n_1114_cruise_518_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-11-12_n_161_cruise_1073_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-12-05_n_200_cruise_2071_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-12-12_n_113_cruise_1074_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2012-12-15_n_775_cruise_1050_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-01-23_n_823_cruise_1051_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-01-29_n_350_cruise_1093_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-02-19_n_217_cruise_1076_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-03-14_n_208_cruise_2072_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-05-03_n_2792_cruise_1035_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-05-06_n_288_cruise_2073_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-06-09_n_213_cruise_1078_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-07-23_n_668_cruise_1079_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-08-21_n_830_cruise_1096_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-09-03_n_1824_cruise_1041_.png
Modified: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-10-11_n_140_cruise_2035_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-11-09_n_121_cruise_2036_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2013-12-06_n_135_cruise_2074_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-01-12_n_1650_cruise_1042_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-01-24_n_281_cruise_2075_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-02-22_n_251_cruise_2038_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-03-13_n_183_cruise_2076_.png
Deleted: output/figure/eMLR/data_preparation/all_cruises_clean/GLODAP_cruise_date_2014-04-18_n_2200_cruise_1036_.png
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library(tidyverse)
library(patchwork)
library(lubridate)1 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/GLODAPv2_2020/_summarized_data_files",
"GLODAPv2.2020_clean.csv"
)
)
GLODAP_obs_grid <-
read_csv(
here::here(
"data/GLODAPv2_2020/_summarized_data_files",
"GLODAPv2.2020_clean_obs_grid.csv"
)
)
Cant_clim <-
read_csv(
here::here(
"data/GLODAPv2_2016b_MappedClimatologies/_summarized_files",
"Cant.csv"
)
)
co2_atm <-
read_csv(here::here(
"data/pCO2_atmosphere/_summarized_data_files",
"co2_atm.csv"
))Cant_clim <- Cant_clim %>%
rename(cant = Cant)2 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.
2.1 Stoichiometric ratios
rCP <- 117
rNP <- 16The stoichiometric nutrient ratios for the production and mineralization of organic matter were set to:
- C/P: 117
- N/P: 16
2.2 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)3 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)4 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).
4.1 Merge data sets
4.1.1 GLODAP + Cant
Cant_clim_obs <- left_join(GLODAP_obs_grid, Cant_clim)
Cant_clim_obs <- Cant_clim_obs %>%
group_by(lon, lat) %>%
mutate(n = n()) %>%
ungroup()
# Cant_clim_obs %>%
# filter(n <= 1) %>%
# ggplot(aes(lon,lat)) +
# geom_point(data = GLODAP_obs_grid, aes(lon, lat)) +
# geom_point(col = "red")
rm(Cant_clim, GLODAP_obs_grid)
GLODAP_Cant_obs <- full_join(GLODAP, Cant_clim_obs)
rm(GLODAP, Cant_clim_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, Cant_clim_obs_nr)
GLODAP_Cant_obs <- GLODAP_Cant_obs %>%
filter(n > 1) %>%
group_by(lat, lon) %>%
arrange(depth) %>%
mutate(cant_int = approxfun(depth, cant, rule = 2)(depth)) %>%
ungroup()
# GLODAP_Cant_obs_set <- GLODAP_Cant_obs %>%
# filter(n_cant == 1) %>%
# group_by(lat, lon) %>%
# arrange(depth) %>%
# mutate(cant_int = mean(cant, na.rm = TRUE)) %>%
# ungroup()
ggplot() +
geom_path(
data = GLODAP_Cant_obs %>%
filter(lat == 48.5, lon == 165.5,!is.na(cant)) %>%
arrange(depth),
aes(cant, depth, col = "mapped")
) +
geom_point(
data = GLODAP_Cant_obs %>%
filter(lat == 48.5, lon == 165.5,!is.na(cant)) %>%
arrange(depth),
aes(cant, depth, col = "mapped")
) +
geom_point(
data = GLODAP_Cant_obs %>%
filter(lat == 48.5, lon == 165.5, date == ymd("2018-06-27")),
aes(cant_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 = cant_int) %>%
select(-cant_int, n)
rm(GLODAP_Cant_obs)4.1.2 GLODAP + atm. pCO2
GLODAP observations were merged with mean annual atmospheric pCO2 levels by year.
GLODAP <- left_join(GLODAP, co2_atm)4.2 Calculate adjustment
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, co2_atm_tref, tref)
GLODAP <- GLODAP %>%
mutate(Cstar_tref_delta =
((pCO2 - pCO2_tref) / (pCO2_tref - 280)) * cant,
Cstar_tref = Cstar - Cstar_tref_delta)4.3 Control plots
4.3.1 Histogram
GLODAP %>%
ggplot(aes(Cstar_tref_delta)) +
geom_histogram()
4.3.2 Time series
GLODAP %>%
sample_n(1e4) %>%
ggplot(aes(year, Cstar_tref_delta, col = cant)) +
geom_point() +
scale_color_viridis_c() +
labs(title = "random subsample 1e4")
5 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$cruises_meridional)GLODAP_cruise %>%
arrange(date) %>%
ggplot(aes(lon, lat)) +
geom_raster(data = landmask,
aes(lon, lat), fill = "grey80") +
geom_path() +
geom_point(aes(col = date)) +
coord_quickmap(expand = 0) +
scale_color_viridis_c(trans = "date") +
labs(title = paste("Cruise year:", mean(GLODAP_cruise$year))) +
theme(axis.title = element_blank())
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:Cstar_tref_delta))6 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)7 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)
8 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 <- GLODAP_cruise %>%
ggplot(aes(lon, lat)) +
geom_raster(data = landmask,
aes(lon, lat), fill = "grey80") +
geom_point(aes(col=date)) +
coord_quickmap(expand = FALSE) +
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))
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))
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)) +
geom_histogram()
(map /
((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,
lon_section, lat_section,
lat_tco2, lat_talk, lat_phosphate, lon_tco2, lon_talk, lon_phosphate,
GLODAP_cruise, cruises_cruise)
}9 Write file
GLODAP <- GLODAP %>%
rename(Cstar = Cstar_tref)
GLODAP %>% write_csv(here::here("data/GLODAPv2_2020/_summarized_data_files",
"GLODAP_MLR_fitting_ready.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 patchwork_1.0.1 forcats_0.5.0 stringr_1.4.0
[5] dplyr_1.0.0 purrr_0.3.4 readr_1.3.1 tidyr_1.1.0
[9] tibble_3.0.3 ggplot2_3.3.2 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 here_0.1 assertthat_0.2.1 rprojroot_1.3-2
[5] digest_0.6.25 R6_2.4.1 cellranger_1.1.0 backports_1.1.8
[9] reprex_0.3.0 evaluate_0.14 httr_1.4.2 pillar_1.4.6
[13] rlang_0.4.7 readxl_1.3.1 rstudioapi_0.11 whisker_0.4
[17] blob_1.2.1 rmarkdown_2.3 labeling_0.3 munsell_0.5.0
[21] broom_0.7.0 compiler_4.0.2 httpuv_1.5.4 modelr_0.1.8
[25] xfun_0.16 pkgconfig_2.0.3 htmltools_0.5.0 tidyselect_1.1.0
[29] fansi_0.4.1 viridisLite_0.3.0 crayon_1.3.4 dbplyr_1.4.4
[33] withr_2.2.0 later_1.1.0.1 grid_4.0.2 jsonlite_1.7.0
[37] gtable_0.3.0 lifecycle_0.2.0 DBI_1.1.0 git2r_0.27.1
[41] magrittr_1.5 scales_1.1.1 cli_2.0.2 stringi_1.4.6
[45] farver_2.0.3 fs_1.4.2 promises_1.1.1 xml2_1.3.2
[49] ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.2 RColorBrewer_1.1-2
[53] tools_4.0.2 glue_1.4.1 hms_0.5.3 yaml_2.2.1
[57] colorspace_1.4-1 rvest_0.3.6 knitr_1.29 haven_2.3.1