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AMR/data-raw
History
Dr. Matthijs Berends f065945d7b
Update clinical breakpoints and fix some as.mo() bugs (#117) 
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
2023-06-22 15:10:59 +02:00
..
_language_update.R
documentation update
2023-05-27 10:39:22 +02:00
_pre_commit_hook.R
documentation update
2023-05-27 10:39:22 +02:00
ab.md5
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
AMR_intro.ai
bring back antibiogram(), without deps
2023-02-10 16:18:00 +01:00
antibiograms.html
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
antibiograms.pdf
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
antibiograms.Rmd
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
antibiotics.dta
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
antibiotics.feather
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
antibiotics.parquet
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
antibiotics.rds
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
antibiotics.sas
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
antibiotics.sav
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
antibiotics.txt
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
antibiotics.xlsx
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
antibiotics.xpt
add XPT files for SAS software
2023-05-12 10:07:55 +02:00
antivirals.dta
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
antivirals.feather
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
antivirals.parquet
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
antivirals.rds
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
antivirals.sas
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
antivirals.sav
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
antivirals.txt
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
antivirals.xlsx
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
antivirals.xpt
add XPT files for SAS software
2023-05-12 10:07:55 +02:00
av.md5
Implement extensive support for antiviral agents support (#77)
2022-11-13 08:46:10 +01:00
bacdive.csv
fix coercing NA to custom codes, fixes #107
2023-05-08 13:04:18 +02:00
bartlett_et_al_2022_human_pathogens.xlsx
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
clin_break.md5
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
clinical_breakpoints.dta
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
clinical_breakpoints.feather
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
clinical_breakpoints.parquet
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
clinical_breakpoints.rds
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
clinical_breakpoints.sas
fix mo_rank() for 'unknown' MOs
2023-04-20 15:20:41 +02:00
clinical_breakpoints.sav
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
clinical_breakpoints.txt
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
clinical_breakpoints.xlsx
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
clinical_breakpoints.xpt
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
create_survey_page.R
sort sir history
2023-01-23 15:01:21 +01:00
dosage.dta
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.feather
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.md5
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.parquet
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.rds
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.sas
expert rules 12.0
2022-11-14 15:20:39 +01:00
dosage.sav
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.txt
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.xlsx
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
dosage.xpt
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
Dosages_v_11.0_Breakpoint_Tables.xlsx
(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)
2021-01-12 22:08:04 +01:00
Dosages_v_12.0_Breakpoint_Tables.pdf
expert rules 12.0
2022-11-14 15:20:39 +01:00
Dosages_v_12.0_Breakpoint_Tables.xlsx
expert rules 12.0
2022-11-14 15:20:39 +01:00
Dosages_v_13.0_Breakpoint_Tables.pdf
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
Dosages_v_13.0_Breakpoint_Tables.xlsx
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
eucast_rules.tsv
unit tests
2022-12-20 22:18:50 +01:00
extractATCs.R
completely updated antibiotics
2022-10-30 14:31:45 +01:00
Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf
(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup
2021-11-28 23:01:26 +01:00
intrinsic_resistant.dta
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.feather
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.md5
(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling
2021-12-11 13:41:31 +01:00
intrinsic_resistant.parquet
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.rds
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.sas
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.sav
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.txt
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.xlsx
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.xpt
add XPT files for SAS software
2023-05-12 10:07:55 +02:00
intrinsicR.md5
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
logo.svg
(v1.7.1.9068) new logo, unit tests
2021-12-12 11:07:02 +01:00
Loinc.csv
completely updated antibiotics
2022-10-30 14:31:45 +01:00
loinc.R
documentation update
2023-05-27 10:39:22 +02:00
microorganisms.dta
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.feather
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.md5
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.parquet
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.rds
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.sas
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.sav
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.txt
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.xlsx
add oxygen tolerance
2023-05-11 21:56:27 +02:00
microorganisms.xpt
add XPT files for SAS software
2023-05-12 10:07:55 +02:00
mo.md5
language updates
2022-08-19 12:33:14 +02:00
poorman_prepend.R
documentation update
2023-05-27 10:39:22 +02:00
read_EUCAST.R
documentation update
2023-05-27 10:39:22 +02:00
reproduction_of_antibiotics.R
documentation update
2023-05-27 10:39:22 +02:00
reproduction_of_antivirals.R
documentation update
2023-05-27 10:39:22 +02:00
reproduction_of_clinical_breakpoints.R
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
reproduction_of_dosage.R
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
reproduction_of_example_isolates_unclean.R
documentation update
2023-05-27 10:39:22 +02:00
reproduction_of_intrinsic_resistant.R
documentation update
2023-05-27 10:39:22 +02:00
reproduction_of_microorganisms.R
documentation update
2023-05-27 10:39:22 +02:00
reproduction_of_poorman.R
fix for antibiograms on R < 3.5
2023-02-24 09:43:10 +01:00
salmonellae.R
documentation update
2023-05-27 10:39:22 +02:00
salmonellae.rds
use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi
2023-02-06 11:57:22 +01:00
salonella_fix.R
unit tests
2023-02-12 17:10:48 +01:00
SNOMED_PHVS_Microorganism_CDC_V12.txt
(v1.5.0.9041) SNOMED update
2021-03-11 21:42:30 +01:00
taxonomy0.rds
microorganisms update, added Salmonella groups
2022-12-16 16:10:43 +01:00
taxonomy1.rds
microorganisms update, added Salmonella groups
2022-12-16 16:10:43 +01:00
taxonomy2.rds
microorganisms update, added Salmonella groups
2022-12-16 16:10:43 +01:00
taxonomy3.rds
microorganisms update, added Salmonella groups
2022-12-16 16:10:43 +01:00
taxonomy_gbif.rds
updated taxonomy
2022-12-12 00:14:56 +01:00
taxonomy_lpsn.rds
updated taxonomy
2022-12-12 00:14:56 +01:00
toxoplasma.R
styled, unit test fix
2022-08-28 10:31:50 +02:00
translations.tsv
anaerobic codes
2023-04-17 11:26:19 +02:00
v_10.0_Breakpoint_Tables.xlsx
(v0.9.0.9022) inheritance fix
2020-02-10 14:18:15 +01:00
v_11.0_Breakpoint_Tables.xlsx
(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)
2021-01-12 22:08:04 +01:00
v_12.0_Breakpoint_Tables.xlsx
(v1.8.1.9007) website update
2022-05-11 10:10:31 +02:00
v_13.0_Breakpoint_Tables.xlsx
Update clinical breakpoints and fix some as.mo() bugs (#117)
2023-06-22 15:10:59 +02:00
whonet_bugfixes.R
(v1.7.1.9050) fix for as.mo
2021-10-05 14:00:35 +02:00