Files in msberends/AMR
Antimicrobial Resistance Data Analysis

.Rbuildignore

.github/ISSUE_TEMPLATE/1-bug-report.yml

.github/ISSUE_TEMPLATE/2-feature-request.yml

.github/ISSUE_TEMPLATE/config.yml

.github/prehooks/commit-msg

.github/prehooks/pre-commit

.github/workflows/check-current-testthat.yaml

.github/workflows/check-old-tinytest.yaml

.github/workflows/codecovr.yaml

.github/workflows/lintr.yaml

.github/workflows/publish-to-pypi.yml

.github/workflows/website.yaml

.gitignore

AMR.Rproj

CRAN-SUBMISSION

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md

PythonPackage/AMR/AMR.egg-info/PKG-INFO

PythonPackage/AMR/AMR.egg-info/SOURCES.txt

PythonPackage/AMR/AMR.egg-info/dependency_links.txt

PythonPackage/AMR/AMR.egg-info/requires.txt

PythonPackage/AMR/AMR.egg-info/top_level.txt

PythonPackage/AMR/AMR/__init__.py

PythonPackage/AMR/AMR/datasets.py

PythonPackage/AMR/AMR/functions.py

PythonPackage/AMR/README.md

PythonPackage/AMR/dist/amr-2.1.1.9183-py3-none-any.whl

PythonPackage/AMR/dist/amr-2.1.1.9183.tar.gz

PythonPackage/AMR/setup.py

R/aa_amr-package.R R/aa_globals.R R/aa_helper_functions.R R/aa_helper_pm_functions.R R/aa_options.R R/ab.R R/ab_from_text.R R/ab_property.R R/age.R R/amr_selectors.R R/antibiogram.R R/atc_online.R R/av.R R/av_from_text.R R/av_property.R R/availability.R R/bug_drug_combinations.R R/count.R R/custom_antimicrobials.R R/custom_eucast_rules.R R/custom_microorganisms.R R/data.R R/disk.R R/eucast_rules.R R/export_biosample.R R/first_isolate.R R/g.test.R R/get_episode.R R/ggplot_pca.R R/ggplot_sir.R R/guess_ab_col.R R/italicise_taxonomy.R R/join_microorganisms.R R/key_antimicrobials.R R/kurtosis.R R/like.R R/mdro.R R/mean_amr_distance.R R/mic.R R/mo.R R/mo_matching_score.R R/mo_property.R R/mo_source.R R/pca.R R/plotting.R R/proportion.R R/random.R R/resistance_predict.R R/sir.R R/sir_calc.R R/sir_df.R R/skewness.R

R/sysdata.rda

R/top_n_microorganisms.R R/translate.R R/vctrs.R R/whocc.R R/zz_deprecated.R R/zzz.R README.md

_pkgdown.yml

codecov.yml

cran-comments.md

data-raw/AMR intro.jpg

data-raw/AMR new logo.txt

data-raw/AMR_intro.ai

data-raw/AMR_vet.html

data-raw/AMR_vet.qmd

data-raw/AMRforRGPT.pdf

data-raw/AMRforRGPT.pptx

data-raw/AMRforRGPT.svg

data-raw/AMRforRGPT_python.pdf

data-raw/AMRforRGPT_python.pptx

data-raw/Dosages_v_11.0_Breakpoint_Tables.xlsx

data-raw/Dosages_v_12.0_Breakpoint_Tables.pdf

data-raw/Dosages_v_12.0_Breakpoint_Tables.xlsx

data-raw/Dosages_v_13.0_Breakpoint_Tables.pdf

data-raw/Dosages_v_13.0_Breakpoint_Tables.xlsx

data-raw/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf

data-raw/Loinc.csv

data-raw/Preference animal species groups.xlsx

data-raw/SNOMED_PHVS_Microorganism_CDC_V12.txt

data-raw/Species groups.xlsx

data-raw/_generate_GPT_knowledge_input.sh

data-raw/_generate_python_wrapper.sh

data-raw/_language_update.R data-raw/_pre_commit_checks.R

data-raw/ab.md5

data-raw/antibiotics.dta

data-raw/antibiotics.feather

data-raw/antibiotics.parquet

data-raw/antibiotics.rds

data-raw/antibiotics.sav

data-raw/antibiotics.txt

data-raw/antibiotics.xlsx

data-raw/antivirals.dta

data-raw/antivirals.feather

data-raw/antivirals.parquet

data-raw/antivirals.rds

data-raw/antivirals.sav

data-raw/antivirals.txt

data-raw/antivirals.xlsx

data-raw/av.md5

data-raw/bacdive.csv

data-raw/bartlett_et_al_2022_human_pathogens.xlsx

data-raw/clin_break.md5

data-raw/clinical_breakpoints.dta

data-raw/clinical_breakpoints.feather

data-raw/clinical_breakpoints.parquet

data-raw/clinical_breakpoints.rds

data-raw/clinical_breakpoints.sav

data-raw/clinical_breakpoints.txt

data-raw/clinical_breakpoints.xlsx

data-raw/create_survey_page.R

data-raw/dosage.dta

data-raw/dosage.feather

data-raw/dosage.md5

data-raw/dosage.parquet

data-raw/dosage.rds

data-raw/dosage.sav

data-raw/dosage.txt

data-raw/dosage.xlsx

data-raw/eucast_rules.tsv

data-raw/extractATCs.R

data-raw/gpt_training_text_v2.1.1.9183.txt

data-raw/intrinsicR.md5

data-raw/intrinsic_resistant.dta

data-raw/intrinsic_resistant.feather

data-raw/intrinsic_resistant.md5

data-raw/intrinsic_resistant.parquet

data-raw/intrinsic_resistant.rds

data-raw/intrinsic_resistant.sav

data-raw/intrinsic_resistant.txt

data-raw/intrinsic_resistant.xlsx

data-raw/logo.old.svg

data-raw/logo.svg

data-raw/loinc.R

data-raw/microorganisms.codes.dta

data-raw/microorganisms.codes.feather

data-raw/microorganisms.codes.md5

data-raw/microorganisms.codes.parquet

data-raw/microorganisms.codes.rds

data-raw/microorganisms.codes.sav

data-raw/microorganisms.codes.txt

data-raw/microorganisms.codes.xlsx

data-raw/microorganisms.dta

data-raw/microorganisms.feather

data-raw/microorganisms.groups.dta

data-raw/microorganisms.groups.feather

data-raw/microorganisms.groups.md5

data-raw/microorganisms.groups.parquet

data-raw/microorganisms.groups.rds

data-raw/microorganisms.groups.sav

data-raw/microorganisms.groups.txt

data-raw/microorganisms.groups.xlsx

data-raw/microorganisms.md5

data-raw/microorganisms.parquet

data-raw/microorganisms.rds

data-raw/microorganisms.sav

data-raw/microorganisms.txt

data-raw/microorganisms.xlsx

data-raw/mo.md5

data-raw/organisms.rds

data-raw/poorman_prepend.R data-raw/read_EUCAST.R data-raw/reproduction_of_antibiotics.R data-raw/reproduction_of_antivirals.R data-raw/reproduction_of_clinical_breakpoints.R data-raw/reproduction_of_dosage.R data-raw/reproduction_of_example_isolates_unclean.R data-raw/reproduction_of_intrinsic_resistant.R data-raw/reproduction_of_microorganisms.R data-raw/reproduction_of_microorganisms.groups.R data-raw/reproduction_of_poorman.R data-raw/salmonellae.R

data-raw/salmonellae.rds

data-raw/salonella_fix.R data-raw/species groups.R

data-raw/taxonomy0.rds

data-raw/taxonomy1.rds

data-raw/taxonomy1b.rds

data-raw/taxonomy1c.rds

data-raw/taxonomy2.rds

data-raw/taxonomy2b.rds

data-raw/taxonomy2c.rds

data-raw/taxonomy3.rds

data-raw/taxonomy3b.rds

data-raw/taxonomy_gbif.rds

data-raw/taxonomy_lpsn.rds

data-raw/taxonomy_lpsn_missing.rds

data-raw/taxonomy_mycobank.rds

data-raw/toxoplasma.R

data-raw/translations.tsv

data-raw/v_10.0_Breakpoint_Tables.xlsx

data-raw/v_11.0_Breakpoint_Tables.xlsx

data-raw/v_12.0_Breakpoint_Tables.xlsx

data-raw/v_13.0_Breakpoint_Tables.xlsx

data-raw/whonet_bugfixes.R

data-raw/wisca.xlsx

data-raw/wisca_params.xlsx

data/WHONET.rda

data/antibiotics.rda

data/antivirals.rda

data/clinical_breakpoints.rda

data/dosage.rda

data/example_isolates.rda

data/example_isolates_unclean.rda

data/intrinsic_resistant.rda

data/microorganisms.codes.rda

data/microorganisms.groups.rda

data/microorganisms.rda

index.md

inst/CITATION

inst/rstudio/addins.dcf

logo.svg

man/AMR-deprecated.Rd man/AMR-options.Rd man/AMR.Rd man/WHOCC.Rd man/WHONET.Rd man/ab_from_text.Rd man/ab_property.Rd man/add_custom_antimicrobials.Rd man/add_custom_microorganisms.Rd man/age.Rd man/age_groups.Rd man/antibiogram.Rd man/antibiotics.Rd man/antimicrobial_selectors.Rd man/as.ab.Rd man/as.av.Rd man/as.disk.Rd man/as.mic.Rd man/as.mo.Rd man/as.sir.Rd man/atc_online.Rd man/av_from_text.Rd man/av_property.Rd man/availability.Rd man/bug_drug_combinations.Rd man/clinical_breakpoints.Rd man/count.Rd man/custom_eucast_rules.Rd man/dosage.Rd man/eucast_rules.Rd man/example_isolates.Rd man/example_isolates_unclean.Rd man/export_ncbi_biosample.Rd

man/figures/mo_matching_score.png

man/first_isolate.Rd man/g.test.Rd man/get_episode.Rd man/ggplot_pca.Rd man/ggplot_sir.Rd man/guess_ab_col.Rd man/intrinsic_resistant.Rd man/italicise_taxonomy.Rd man/join.Rd man/key_antimicrobials.Rd man/kurtosis.Rd man/like.Rd man/mdro.Rd man/mean_amr_distance.Rd man/microorganisms.Rd man/microorganisms.codes.Rd man/microorganisms.groups.Rd man/mo_matching_score.Rd man/mo_property.Rd man/mo_source.Rd man/pca.Rd man/plot.Rd man/proportion.Rd man/random.Rd man/resistance_predict.Rd man/skewness.Rd man/top_n_microorganisms.Rd man/translate.Rd

pkgdown/assets/AMRforRGPT.svg

pkgdown/assets/AMRforRGPT_python.svg

pkgdown/assets/countries.png

pkgdown/assets/countries_large.png

pkgdown/assets/endorsement_clsi_eucast.jpg

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pkgdown/extra.js

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pkgdown/favicon/favicon-32x32.png

pkgdown/favicon/favicon.ico

tests/tinytest.R.old

vignettes/.gitignore

vignettes/AMR.Rmd vignettes/AMR_for_Python.Rmd vignettes/AMR_with_tidymodels.Rmd vignettes/EUCAST.Rmd vignettes/MDR.Rmd vignettes/PCA.Rmd vignettes/WHONET.Rmd

vignettes/benchmarks.Rmd.not

vignettes/datasets.Rmd vignettes/resistance_predict.Rmd vignettes/welcome_to_AMR.Rmd

msberends/AMR documentation built on March 5, 2025, 2:28 p.m.

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msberends/AMR
Antimicrobial Resistance Data Analysis

Files in msberends/AMR
Antimicrobial Resistance Data Analysis

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msberends/AMR Antimicrobial Resistance Data Analysis

Files in msberends/AMR Antimicrobial Resistance Data Analysis

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msberends/AMR
Antimicrobial Resistance Data Analysis

Files in msberends/AMR
Antimicrobial Resistance Data Analysis