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AMR/R/globals.R

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first commit
2018-02-21 11:52:31 +01:00
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
big website update, licence txt update
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# SOURCE #
# https://gitlab.com/msberends/AMR #
first commit
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# #
# LICENCE #
big website update, licence txt update
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
first commit
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# #
big website update, licence txt update
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# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
new EUCAST rules algorithm
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
first commit
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# ==================================================================== #
new MOs, cleanup
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globalVariables(c(".",
first inclusion of ITIS data
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"..property",
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"antibiotic",
"Antibiotic",
"antibiotics",
select() fix for freq
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"atc",
first inclusion of ITIS data
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"authors",
authors from ITIS, diff for freq
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"Becker",
select() fix for freq
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"certe",
new EUCAST rules algorithm
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"CNS_CPS",
new MOs, cleanup
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"cnt",
Catalogue of life
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"col_id",
new MOs, cleanup
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"count",
authors from ITIS, diff for freq
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"count.x",
"count.y",
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"cum_count",
"cum_percent",
"date_lab",
renamed year columns to ref
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"diff.percent",
new MOs, cleanup
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"fctlvl",
website update
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"First name",
new MOs, cleanup
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"first_isolate_row_index",
"Freq",
first inclusion of ITIS data
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"fullname",
global var fix
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"fullname_lower",
new MOs, cleanup
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"genus",
"gramstain",
unit tests
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"index",
global var fix
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"input",
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"Interpretation",
new MOs, cleanup
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"item",
"key_ab",
"key_ab_lag",
"key_ab_other",
Catalogue of life
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"kingdom",
select() fix for freq
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"labs",
authors from ITIS, diff for freq
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"Lancefield",
website update
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"Last name",
add labels_rsi_count
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"lbl",
new MOs, cleanup
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"median",
"mic",
"microorganisms",
set_mo_source
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"microorganisms.codes",
first inclusion of ITIS data
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"microorganisms.old",
speed improvement as.mo, freq title
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"microorganisms.oldDT",
select() fix for freq
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"microorganisms.prevDT",
"microorganisms.unprevDT",
"microorganismsDT",
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"mo",
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"mo.old",
big website update, licence txt update
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"more_than_episode_ago",
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"n",
first inclusion of ITIS data
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"name",
v0.6.1
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"new",
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"observations",
select() fix for freq
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"observed",
"official",
v0.6.1
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"old",
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"other_pat_or_mo",
v0.6.1
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"package_v",
new MOs, cleanup
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"Pasted",
"patient_id",
Catalogue of life
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"phylum",
new EUCAST rules algorithm
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"plural",
added prevalence column and alterted as.mo algorith to use it, added ab_name as alias
2018-09-16 16:43:29 +02:00
"prevalence",
Catalogue of life
2019-02-20 00:04:48 +01:00
"prevalent",
DSMZ data
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"property",
fixes
2018-10-23 14:59:36 +02:00
"psae",
new MOs, cleanup
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"R",
"real_first_isolate",
select() fix for freq
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"ref",
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"reference.rule",
"reference.rule_group",
"rule_group",
"rule_name",
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"S",
select() fix for freq
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"se_max",
"se_min",
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"septic_patients",
website update
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"Sex",
speed improvement for as.mo, more old taxonomic names
2018-09-27 23:23:48 +02:00
"shortname",
new MOs, cleanup
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"species",
added Becker 2019
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"species_id",
ci fixes
2019-03-26 14:42:56 +01:00
"subspecies",
select() fix for freq
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"trade_name",
"transmute",
first inclusion of ITIS data
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"tsn",
"tsn_new",
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"txt",
select() fix for freq
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"umcg",
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"value",
add labels_rsi_count
2018-09-16 22:11:17 +02:00
"Value",
global var
2019-03-15 20:15:56 +01:00
"x",
first inclusion of ITIS data
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"y",
"year"))
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