AMR/data-raw
dr. M.S. (Matthijs) Berends 9bf7584d58 (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
..
AMR new logo.txt new logo 2024-02-25 14:20:43 +01:00
AMR_intro.ai update intro logo 2024-04-24 09:58:24 +02:00
AMR_vet.html support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
AMR_vet.qmd support veterinary MIC/disk translation 2024-02-24 15:16:52 +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
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
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
Loinc.csv prepare for CRAN 2023-10-20 14:51:48 +02:00
SNOMED_PHVS_Microorganism_CDC_V12.txt (v1.5.0.9041) SNOMED update 2021-03-11 21:42:30 +01:00
Species groups.xlsx new species groups, updated clinical breakpoints 2023-07-08 17:30:05 +02:00
_language_update.R fix `reference_df` endless loop 2023-06-26 13:52:02 +02:00
_pre_commit_checks.R (v2.1.1.9041) antibiotics update 2024-06-08 17:35:25 +02:00
ab.md5 (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
antibiograms.Rmd fix for antibiograms on R < 3.5 2023-02-24 09:43:10 +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
antibiotics.dta (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
antibiotics.feather (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
antibiotics.parquet (v2.1.1.9041) antibiotics update 2024-06-08 17:35:25 +02:00
antibiotics.rds (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
antibiotics.sav (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
antibiotics.txt (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
antibiotics.xlsx (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
antibiotics.xpt (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
antivirals.dta prepare for CRAN 2023-10-20 14:51:48 +02:00
antivirals.feather prepare for CRAN 2023-10-20 14:51:48 +02:00
antivirals.parquet prepare for CRAN 2023-10-20 14:51:48 +02:00
antivirals.rds prepare for CRAN 2023-10-20 14:51:48 +02:00
antivirals.sav prepare for CRAN 2023-10-20 14:51:48 +02:00
antivirals.txt prepare for CRAN 2023-10-20 14:51:48 +02:00
antivirals.xlsx prepare for CRAN 2023-10-20 14:51:48 +02:00
antivirals.xpt prepare for CRAN 2023-10-20 14:51:48 +02:00
av.md5 prepare for CRAN 2023-10-20 14:51:48 +02:00
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 (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
clinical_breakpoints.dta (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
clinical_breakpoints.feather (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
clinical_breakpoints.parquet (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
clinical_breakpoints.rds (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
clinical_breakpoints.sav (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
clinical_breakpoints.txt (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
clinical_breakpoints.xlsx (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
clinical_breakpoints.xpt (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +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.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
eucast_rules.tsv update MIC comparisons 2024-04-05 16:44:43 +02:00
extractATCs.R new Norwegian link 2024-03-03 23:24:57 +01:00
intrinsicR.md5 Fixes for Salmonella 2022-12-17 14:31:33 +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.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
logo.old.svg new logo 2024-02-25 14:20:43 +01:00
logo.svg new logo 2024-02-25 14:20:43 +01:00
loinc.R prepare for CRAN 2023-10-20 14:51:48 +02:00
microorganisms.codes.dta (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
microorganisms.codes.feather (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
microorganisms.codes.md5 (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
microorganisms.codes.parquet (v2.1.1.9047) unit test and index 2024-06-13 07:37:53 +02:00
microorganisms.codes.rds (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
microorganisms.codes.sav (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
microorganisms.codes.txt (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
microorganisms.codes.xlsx (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
microorganisms.codes.xpt new species groups, updated clinical breakpoints 2023-07-08 17:30:05 +02:00
microorganisms.dta Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.feather Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.dta Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.feather Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.md5 Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.parquet Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.rds Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.sav Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.txt Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.xlsx Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.groups.xpt new species groups, updated clinical breakpoints 2023-07-08 17:30:05 +02:00
microorganisms.md5 Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.parquet Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.rds Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.sav Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.txt Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.xlsx Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
microorganisms.xpt Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
mo.md5 language updates 2022-08-19 12:33:14 +02:00
organisms.rds (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
poorman_prepend.R fix `reference_df` endless loop 2023-06-26 13:52:02 +02:00
read_EUCAST.R fix `reference_df` endless loop 2023-06-26 13:52:02 +02:00
reproduction_of_antibiotics.R (v2.1.1.9041) antibiotics update 2024-06-08 17:35:25 +02:00
reproduction_of_antivirals.R new Norwegian link 2024-03-03 23:24:57 +01:00
reproduction_of_clinical_breakpoints.R (v2.1.1.9049) new 2024 breakpoints, add `AMO`, set NI instead of N 2024-06-14 22:39:01 +02:00
reproduction_of_dosage.R fix `reference_df` endless loop 2023-06-26 13:52:02 +02:00
reproduction_of_example_isolates_unclean.R fix `reference_df` endless loop 2023-06-26 13:52:02 +02:00
reproduction_of_intrinsic_resistant.R fix `reference_df` endless loop 2023-06-26 13:52:02 +02:00
reproduction_of_microorganisms.R rename pre-commit hook to pre-commit checks (no-check) 2024-04-23 10:55:48 +02:00
reproduction_of_microorganisms.groups.R Added C. freundii complex and Y. pseudotuberculosis complex 2023-07-14 10:49:06 +02:00
reproduction_of_poorman.R fix for antibiograms on R < 3.5 2023-02-24 09:43:10 +01:00
salmonellae.R fix `reference_df` endless loop 2023-06-26 13:52:02 +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
species groups.R new species groups, updated clinical breakpoints 2023-07-08 17:30:05 +02:00
taxonomy0.rds support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
taxonomy1.rds support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
taxonomy2.rds support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
taxonomy3.rds support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
taxonomy_gbif.rds support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
taxonomy_lpsn.rds support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
taxonomy_lpsn_missing.rds support veterinary MIC/disk translation 2024-02-24 15:16:52 +01:00
toxoplasma.R styled, unit test fix 2022-08-28 10:31:50 +02:00
translations.tsv (v2.1.1.9042) update translations and example isolates 2024-06-09 11:31:04 +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