2018-02-21 11:52:31 +01:00
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# ==================================================================== #
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# TITLE #
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2021-02-02 23:57:35 +01:00
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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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# 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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2021-12-23 18:56:28 +01:00
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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2020-10-08 11:16:03 +02:00
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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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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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: 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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2021-03-11 21:42:30 +01:00
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# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and rsi_translation
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# (sourcing "data-raw/_internals.R" will process the TSV file)
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EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(version_txt = "v11.0",
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year = 2021,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/clinical_breakpoints/"),
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"10.0" = list(version_txt = "v10.0",
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year = 2020,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/"))
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EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
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year = 2016,
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title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
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"3.2" = list(version_txt = "v3.2",
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year = 2020,
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title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
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2021-11-28 23:01:26 +01:00
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url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
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"3.3" = list(version_txt = "v3.3",
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year = 2021,
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title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
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SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
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current_source = "US Edition of SNOMED CT from 1 September 2020",
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current_version = 12,
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current_oid = "2.16.840.1.114222.4.11.1009",
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value_set_name = "Microorganism",
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url = "https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009")
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CATALOGUE_OF_LIFE <- list(
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year = 2019,
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version = "Catalogue of Life: {year} Annual Checklist",
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2021-11-29 10:38:38 +01:00
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url_CoL = "http://www.catalogueoflife.org",
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2021-03-11 21:42:30 +01:00
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url_LPSN = "https://lpsn.dsmz.de",
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2021-10-06 13:23:57 +02:00
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yearmonth_LPSN = "5 October 2021"
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)
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2020-12-17 16:22:25 +01:00
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globalVariables(c(".rowid",
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2020-08-26 15:34:12 +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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2021-05-17 11:26:12 +02:00
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"affect_ab_name",
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2021-02-21 23:19:40 +01:00
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"affect_mo_name",
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2020-03-08 11:18:59 +01:00
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"angle",
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2020-08-26 15:34:12 +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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2021-04-12 14:24:40 +02:00
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"base_ab",
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2020-05-16 20:08:21 +02:00
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"code",
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2021-02-25 12:31:12 +01:00
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"cols",
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"count",
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2020-07-08 22:55:17 +02:00
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"data",
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2021-02-25 12:31:12 +01:00
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"disk",
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2021-01-14 15:51:41 +01:00
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"dosage",
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2021-01-14 14:41:44 +01:00
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"dose",
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"dose_times",
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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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2019-08-12 15:34:49 +02:00
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"group",
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2020-12-13 13:44:04 +01:00
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"guideline",
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2020-03-08 11:18:59 +01:00
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"hjust",
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2019-02-27 19:02:47 +01:00
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"input",
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2020-08-26 15:34:12 +02:00
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"intrinsic_resistant",
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2019-06-27 11:57:45 +02:00
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"isolates",
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2019-05-10 16:44:59 +02:00
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"lang",
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2020-09-03 20:59:21 +02:00
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"language",
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2019-05-10 16:44:59 +02:00
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"lookup",
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2020-12-13 13:44:04 +01:00
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"method",
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2021-03-05 01:31:46 +01:00
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"mic",
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2021-02-25 12:31:12 +01:00
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"mic ",
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2020-08-26 15:34:12 +02:00
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"microorganism",
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2018-09-01 21:19:46 +02:00
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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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2018-09-01 21:19:46 +02:00
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"mo",
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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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2018-09-01 21:19:46 +02:00
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"observations",
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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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2019-06-12 16:08:20 +02:00
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"pattern",
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2018-09-01 21:19:46 +02:00
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"R",
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2021-12-14 22:39:23 +01:00
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"rank_index",
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2020-12-27 15:07:01 +01:00
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"reference.rule",
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2020-09-24 00:50:23 +02:00
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"reference.rule_group",
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"reference.version",
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"rowid",
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2021-03-05 01:31:46 +01:00
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"rsi",
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2021-02-25 12:31:12 +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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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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"species",
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2019-03-26 14:24:03 +01:00
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"species_id",
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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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2021-01-14 14:41:44 +01:00
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"type",
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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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"xvar",
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2020-11-24 11:47:54 +01:00
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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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