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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 08:06:12 +01:00
AMR/data-raw
2023-02-11 22:28:48 +01:00
..
_language_update.R support new mo codes 2022-12-27 15:16:15 +01:00
_pre_commit_hook.R sort sir history 2023-01-23 15:01:21 +01:00
ab.md5 fix antibiotics error 2022-10-30 21:05:46 +01:00
AMR_intro.ai bring back antibiogram(), without deps 2023-02-10 16:18:00 +01:00
antibiograms.html pm update, unit test fix? 2023-02-08 13:48:06 +01:00
antibiograms.Rmd pm update, unit test fix? 2023-02-08 13:48:06 +01:00
antibiotics.dta fix antibiotics error 2022-10-30 21:05:46 +01:00
antibiotics.feather fix antibiotics error 2022-10-30 21:05:46 +01:00
antibiotics.parquet fix antibiotics error 2022-10-30 21:05:46 +01:00
antibiotics.rds fix antibiotics error 2022-10-30 21:05:46 +01:00
antibiotics.sas fix antibiotics error 2022-10-30 21:05:46 +01:00
antibiotics.sav fix antibiotics error 2022-10-30 21:05:46 +01:00
antibiotics.txt fix antibiotics error 2022-10-30 21:05:46 +01:00
antibiotics.xlsx fix antibiotics error 2022-10-30 21:05:46 +01:00
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
av.md5 Implement extensive support for antiviral agents support (#77) 2022-11-13 08:46:10 +01:00
bartlett_et_al_2022_human_pathogens.xlsx Fixes for Salmonella 2022-12-17 14:31:33 +01:00
clin_break.md5 Replace RSI with SIR 2023-01-21 23:47:20 +01:00
clinical_breakpoints.dta Replace RSI with SIR 2023-01-21 23:47:20 +01:00
clinical_breakpoints.feather Replace RSI with SIR 2023-01-21 23:47:20 +01:00
clinical_breakpoints.parquet Replace RSI with SIR 2023-01-21 23:47:20 +01:00
clinical_breakpoints.rds Replace RSI with SIR 2023-01-21 23:47:20 +01:00
clinical_breakpoints.sas Replace RSI with SIR 2023-01-21 23:47:20 +01:00
clinical_breakpoints.sav Replace RSI with SIR 2023-01-21 23:47:20 +01:00
clinical_breakpoints.txt Replace RSI with SIR 2023-01-21 23:47:20 +01:00
clinical_breakpoints.xlsx Replace RSI with SIR 2023-01-21 23:47:20 +01:00
create_survey_page.R sort sir history 2023-01-23 15:01:21 +01:00
dosage.dta expert rules 12.0 2022-11-14 15:20:39 +01:00
dosage.feather expert rules 12.0 2022-11-14 15:20:39 +01:00
dosage.md5 expert rules 12.0 2022-11-14 15:20:39 +01:00
dosage.parquet expert rules 12.0 2022-11-14 15:20:39 +01:00
dosage.rds expert rules 12.0 2022-11-14 15:20:39 +01:00
dosage.sas expert rules 12.0 2022-11-14 15:20:39 +01:00
dosage.sav expert rules 12.0 2022-11-14 15:20:39 +01:00
dosage.txt expert rules 12.0 2022-11-14 15:20:39 +01:00
dosage.xlsx expert rules 12.0 2022-11-14 15:20:39 +01:00
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
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
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 support new mo codes 2022-12-27 15:16:15 +01:00
microorganisms.dta use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
microorganisms.feather use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
microorganisms.md5 use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
microorganisms.parquet use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
microorganisms.rds use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
microorganisms.sas use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
microorganisms.sav use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
microorganisms.txt use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
microorganisms.xlsx use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
mo.md5 language updates 2022-08-19 12:33:14 +02:00
poorman_prepend.R pm update, unit test fix? 2023-02-08 13:48:06 +01:00
read_EUCAST.R sort sir history 2023-01-23 15:01:21 +01:00
reproduction_of_antibiotics.R sort sir history 2023-01-23 15:01:21 +01:00
reproduction_of_antivirals.R sort sir history 2023-01-23 15:01:21 +01:00
reproduction_of_clinical_breakpoints.R Replace RSI with SIR 2023-01-21 23:47:20 +01:00
reproduction_of_dosage.R sort sir history 2023-01-23 15:01:21 +01:00
reproduction_of_example_isolates_unclean.R support new mo codes 2022-12-27 15:16:15 +01:00
reproduction_of_intrinsic_resistant.R Replace RSI with SIR 2023-01-21 23:47:20 +01:00
reproduction_of_microorganisms.R bring back antibiogram(), without deps 2023-02-10 16:18:00 +01:00
reproduction_of_poorman.R pm fixes 2023-02-08 16:51:41 +01:00
salmonellae.R use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +01:00
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 use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi 2023-02-06 11:57:22 +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
tinytest_1.3.1.tar.gz (v1.7.1.9033) dplyr grouping fix on windows? 2021-08-30 15:01:32 +02:00
toxoplasma.R styled, unit test fix 2022-08-28 10:31:50 +02:00
translations.tsv pm_bind_rows 2023-02-11 22:28:48 +01:00
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
whonet_bugfixes.R (v1.7.1.9050) fix for as.mo 2021-10-05 14:00:35 +02:00