2018-02-21 11:52:31 +01:00
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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2019-01-02 23:24:07 +01:00
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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2018-02-21 11:52:31 +01:00
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# #
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# LICENCE #
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2019-01-02 23:24:07 +01:00
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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2018-02-21 11:52:31 +01:00
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# #
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2019-01-02 23:24:07 +01:00
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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2019-04-05 18:47:39 +02:00
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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2018-02-21 11:52:31 +01:00
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# ==================================================================== #
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2018-09-01 21:19:46 +02:00
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globalVariables(c(".",
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2018-09-24 23:33:29 +02:00
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"..property",
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2019-05-10 16:44:59 +02:00
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"ab",
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"abbreviations",
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2018-09-01 21:19:46 +02:00
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"antibiotic",
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"Antibiotic",
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"antibiotics",
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2019-01-17 12:08:04 +01:00
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"atc",
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2018-09-24 23:33:29 +02:00
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"authors",
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2018-10-01 11:39:43 +02:00
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"Becker",
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2019-04-05 18:47:39 +02:00
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"CNS_CPS",
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2018-09-01 21:19:46 +02:00
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"cnt",
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2019-02-20 00:04:48 +01:00
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"col_id",
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2018-09-01 21:19:46 +02:00
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"count",
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2018-10-01 11:39:43 +02:00
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"count.x",
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"count.y",
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2018-09-01 21:19:46 +02:00
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"cum_count",
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"cum_percent",
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"date_lab",
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2018-10-01 14:44:40 +02:00
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"diff.percent",
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2018-09-01 21:19:46 +02:00
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"fctlvl",
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2019-01-29 20:38:45 +01:00
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"First name",
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2018-09-01 21:19:46 +02:00
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"first_isolate_row_index",
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"Freq",
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2018-09-24 23:33:29 +02:00
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"fullname",
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2019-02-27 17:39:39 +01:00
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"fullname_lower",
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2018-09-01 21:19:46 +02:00
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"genus",
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"gramstain",
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2018-11-16 22:28:55 +01:00
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"index",
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2019-02-27 19:02:47 +01:00
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"input",
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2019-04-05 18:47:39 +02:00
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"Interpretation",
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2018-09-01 21:19:46 +02:00
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"item",
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"key_ab",
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"key_ab_lag",
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"key_ab_other",
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2019-02-20 00:04:48 +01:00
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"kingdom",
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2019-01-17 12:08:04 +01:00
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"labs",
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2018-10-01 11:39:43 +02:00
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"Lancefield",
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2019-05-10 16:44:59 +02:00
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"lang",
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2019-01-29 20:38:45 +01:00
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"Last name",
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2018-09-16 22:11:17 +02:00
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"lbl",
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2019-05-10 16:44:59 +02:00
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"lookup",
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2018-09-01 21:19:46 +02:00
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"median",
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"mic",
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"microorganisms",
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2019-01-21 15:53:01 +01:00
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"microorganisms.codes",
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2018-09-24 23:33:29 +02:00
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"microorganisms.old",
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2018-10-31 12:10:49 +01:00
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"microorganisms.oldDT",
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2019-01-17 12:08:04 +01:00
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"microorganisms.prevDT",
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"microorganisms.unprevDT",
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"microorganismsDT",
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2018-09-01 21:19:46 +02:00
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"mo",
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2018-09-24 23:33:29 +02:00
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"mo.old",
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2019-01-02 23:24:07 +01:00
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"more_than_episode_ago",
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2019-05-10 16:44:59 +02:00
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"MPM",
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2018-09-01 21:19:46 +02:00
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"n",
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2018-09-24 23:33:29 +02:00
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"name",
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2019-03-28 22:05:03 +01:00
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"new",
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2018-09-01 21:19:46 +02:00
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"observations",
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2019-01-17 12:08:04 +01:00
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"observed",
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"official",
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2019-03-28 22:05:03 +01:00
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"old",
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2018-09-01 21:19:46 +02:00
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"other_pat_or_mo",
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2019-03-28 22:05:03 +01:00
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"package_v",
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2018-09-01 21:19:46 +02:00
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"Pasted",
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"patient_id",
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2019-02-20 00:04:48 +01:00
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"phylum",
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2019-04-05 18:47:39 +02:00
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"plural",
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2018-09-16 16:43:29 +02:00
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"prevalence",
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2019-02-20 00:04:48 +01:00
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"prevalent",
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2019-03-18 14:29:41 +01:00
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"property",
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2018-10-23 14:59:36 +02:00
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"psae",
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2018-09-01 21:19:46 +02:00
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"R",
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"real_first_isolate",
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2019-01-17 12:08:04 +01:00
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"ref",
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2019-04-05 18:47:39 +02:00
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"reference.rule",
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"reference.rule_group",
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2019-05-10 16:44:59 +02:00
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"rsi",
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2019-04-05 18:47:39 +02:00
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"rule_group",
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"rule_name",
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2018-09-01 21:19:46 +02:00
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"S",
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2019-01-17 12:08:04 +01:00
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"se_max",
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"se_min",
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2018-09-01 21:19:46 +02:00
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"septic_patients",
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2019-01-29 20:38:45 +01:00
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"Sex",
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2018-09-27 23:23:48 +02:00
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"shortname",
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2018-09-01 21:19:46 +02:00
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"species",
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2019-03-26 14:24:03 +01:00
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"species_id",
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2019-03-26 14:42:56 +01:00
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"subspecies",
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2019-05-10 16:44:59 +02:00
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"synonyms",
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2019-01-17 12:08:04 +01:00
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"trade_name",
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2019-05-10 16:44:59 +02:00
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"trans",
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2019-01-17 12:08:04 +01:00
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"transmute",
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2018-09-24 23:33:29 +02:00
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"tsn",
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"tsn_new",
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2019-04-05 18:47:39 +02:00
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"txt",
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2018-09-01 21:19:46 +02:00
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"value",
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2018-09-16 22:11:17 +02:00
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"Value",
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2019-03-15 20:15:56 +01:00
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"x",
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2018-09-24 23:33:29 +02:00
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"y",
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"year"))
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