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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2020-07-08 14:48:06 +02:00
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# https://github.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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2020-01-05 17:22:09 +01:00
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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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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2020-01-05 17:22:09 +01:00
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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2020-07-08 14:48:06 +02:00
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# Visit our website for more info: https://msberends.github.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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2019-09-25 15:43:22 +02:00
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"ab_txt",
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2019-05-10 16:44:59 +02:00
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"abbreviations",
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2020-03-08 11:18:59 +01:00
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"angle",
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2018-09-01 21:19:46 +02:00
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"antibiotic",
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2020-02-14 20:03:43 +01:00
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"antibiotics",
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2020-05-16 20:08:21 +02:00
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"atc_group1",
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"atc_group2",
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2019-04-05 18:47:39 +02:00
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"CNS_CPS",
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2020-05-16 20:08:21 +02:00
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"code",
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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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2018-09-01 21:19:46 +02:00
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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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2019-07-02 16:48:52 +02:00
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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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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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2019-12-22 11:43:38 +01:00
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"g_species",
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2018-09-01 21:19:46 +02:00
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"genus",
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2020-05-16 20:08:21 +02:00
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"gr",
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2018-09-01 21:19:46 +02:00
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"gramstain",
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2019-08-12 15:34:49 +02:00
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"group",
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2020-03-08 11:18:59 +01:00
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"hjust",
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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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2019-06-13 16:40:35 +02:00
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"interpretation",
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2019-06-27 11:57:45 +02:00
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"isolates",
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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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2019-09-22 12:41:45 +02:00
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"kingdom_index",
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2019-05-10 16:44:59 +02:00
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"lang",
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2019-07-02 16:48:52 +02:00
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"Last name",
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2019-05-10 16:44:59 +02:00
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"lookup",
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2019-06-27 11:57:45 +02:00
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"mdr",
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2019-10-26 22:21:26 +02:00
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"MDRO",
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2018-09-01 21:19:46 +02:00
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"median",
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"microorganisms",
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2019-09-23 20:55:54 +02:00
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"microorganisms.codes",
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2020-02-14 20:03:43 +01:00
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"microorganisms.old",
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2019-06-27 11:57:45 +02:00
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"missing_names",
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2018-09-01 21:19:46 +02:00
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"mo",
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2020-05-16 20:08:21 +02:00
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"mo_new",
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"mo_old",
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2019-06-27 11:57:45 +02:00
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"mono_count",
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2019-01-02 23:24:07 +01:00
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"more_than_episode_ago",
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2019-06-27 11:57:45 +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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2019-08-09 14:28:46 +02:00
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"newvar_date",
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"newvar_genus_species",
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"newvar_mo",
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"newvar_patient_id",
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"newvar_row_index",
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"newvar_row_index_sorted",
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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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2019-03-28 22:05:03 +01:00
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"old",
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2019-09-18 15:46:09 +02:00
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"old_name",
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2018-09-01 21:19:46 +02:00
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"other_pat_or_mo",
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2019-09-16 12:00:56 +02:00
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"package_version",
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2018-09-01 21:19:46 +02:00
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"patient_id",
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2019-06-12 16:08:20 +02:00
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"pattern",
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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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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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2020-02-14 20:03:43 +01:00
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"rsi_translation",
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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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2019-06-27 11:57:45 +02:00
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"second",
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2019-01-29 20:38:45 +01:00
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"Sex",
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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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2019-08-25 23:25:12 +02:00
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"total",
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2019-04-05 18:47:39 +02:00
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"txt",
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2019-09-16 12:00:56 +02:00
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"uncertainty_level",
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2018-09-01 21:19:46 +02:00
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"value",
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2020-03-08 11:18:59 +01:00
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"varname",
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2019-09-16 12:00:56 +02:00
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"x",
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2019-06-27 11:57:45 +02:00
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"xdr",
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2020-03-08 11:18:59 +01:00
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"xvar",
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2018-09-24 23:33:29 +02:00
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"y",
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2020-03-08 11:18:59 +01:00
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"year",
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"yvar"))
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