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1bc2e04e1ca62dc85502456559c934ed908905e0
AMR/data-raw
History
dr. M.S. (Matthijs) Berends 1bc2e04e1c (v2.1.1.9058) fix hosts, add translations
2024-06-17 22:19:38 +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
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
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
(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
…
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
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
update MIC comparisons
2024-04-05 16:44:43 +02:00
extractATCs.R
new Norwegian link
2024-03-03 23:24:57 +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
…
intrinsic_resistant.feather
Fixes for Salmonella
2022-12-17 14:31:33 +01:00
intrinsic_resistant.md5
…
intrinsic_resistant.parquet
…
intrinsic_resistant.rds
…
intrinsic_resistant.sav
…
intrinsic_resistant.txt
…
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
…
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.csv
prepare for CRAN
2023-10-20 14:51:48 +02:00
loinc.R
prepare for CRAN
2023-10-20 14:51:48 +02:00
microorganisms.codes.dta
(v2.1.1.9051) fix VGS mo code
2024-06-16 11:28:56 +02:00
microorganisms.codes.feather
(v2.1.1.9051) fix VGS mo code
2024-06-16 11:28:56 +02:00
microorganisms.codes.md5
(v2.1.1.9051) fix VGS mo code
2024-06-16 11:28:56 +02:00
microorganisms.codes.parquet
(v2.1.1.9047) unit test and index
2024-06-13 07:37:53 +02:00
microorganisms.codes.rds
(v2.1.1.9051) fix VGS mo code
2024-06-16 11:28:56 +02:00
microorganisms.codes.sav
(v2.1.1.9051) fix VGS mo code
2024-06-16 11:28:56 +02:00
microorganisms.codes.txt
(v2.1.1.9051) fix VGS mo code
2024-06-16 11:28:56 +02:00
microorganisms.codes.xlsx
(v2.1.1.9051) fix VGS mo code
2024-06-16 11:28:56 +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
…
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.groups.R
Added C. freundii complex and Y. pseudotuberculosis complex
2023-07-14 10:49:06 +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_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
…
salonella_fix.R
…
SNOMED_PHVS_Microorganism_CDC_V12.txt
…
species groups.R
new species groups, updated clinical breakpoints
2023-07-08 17:30:05 +02:00
Species groups.xlsx
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_missing.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
toxoplasma.R
…
translations.tsv
(v2.1.1.9058) fix hosts, add translations
2024-06-17 22:19:38 +02:00
v_10.0_Breakpoint_Tables.xlsx
…
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
…
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
…