AMR 2.1.1.9094__tar.gz

AMR-2.1.1.9094/AMR/__init__.py

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+from .datasets import example_isolates
+from .datasets import microorganisms
+from .datasets import antibiotics
+from .datasets import clinical_breakpoints
+from .functions import ab_from_text
+from .functions import ab_name
+from .functions import ab_cid
+from .functions import ab_synonyms
+from .functions import ab_tradenames
+from .functions import ab_group
+from .functions import ab_atc
+from .functions import ab_atc_group1
+from .functions import ab_atc_group2
+from .functions import ab_loinc
+from .functions import ab_ddd
+from .functions import ab_ddd_units
+from .functions import ab_info
+from .functions import ab_url
+from .functions import ab_property
+from .functions import add_custom_antimicrobials
+from .functions import clear_custom_antimicrobials
+from .functions import add_custom_microorganisms
+from .functions import clear_custom_microorganisms
+from .functions import age
+from .functions import age_groups
+from .functions import antibiogram
+from .functions import ab_class
+from .functions import ab_selector
+from .functions import aminoglycosides
+from .functions import aminopenicillins
+from .functions import antifungals
+from .functions import antimycobacterials
+from .functions import betalactams
+from .functions import carbapenems
+from .functions import cephalosporins
+from .functions import cephalosporins_1st
+from .functions import cephalosporins_2nd
+from .functions import cephalosporins_3rd
+from .functions import cephalosporins_4th
+from .functions import cephalosporins_5th
+from .functions import fluoroquinolones
+from .functions import glycopeptides
+from .functions import lincosamides
+from .functions import lipoglycopeptides
+from .functions import macrolides
+from .functions import nitrofurans
+from .functions import oxazolidinones
+from .functions import penicillins
+from .functions import polymyxins
+from .functions import quinolones
+from .functions import rifamycins
+from .functions import streptogramins
+from .functions import tetracyclines
+from .functions import trimethoprims
+from .functions import ureidopenicillins
+from .functions import administrable_per_os
+from .functions import administrable_iv
+from .functions import not_intrinsic_resistant
+from .functions import as_ab
+from .functions import is_ab
+from .functions import as_av
+from .functions import is_av
+from .functions import as_disk
+from .functions import is_disk
+from .functions import as_mic
+from .functions import is_mic
+from .functions import rescale_mic
+from .functions import as_mo
+from .functions import is_mo
+from .functions import mo_uncertainties
+from .functions import mo_renamed
+from .functions import mo_failures
+from .functions import mo_reset_session
+from .functions import mo_cleaning_regex
+from .functions import as_sir
+from .functions import is_sir
+from .functions import is_sir_eligible
+from .functions import sir_interpretation_history
+from .functions import atc_online_property
+from .functions import atc_online_groups
+from .functions import atc_online_ddd
+from .functions import atc_online_ddd_units
+from .functions import av_from_text
+from .functions import av_name
+from .functions import av_cid
+from .functions import av_synonyms
+from .functions import av_tradenames
+from .functions import av_group
+from .functions import av_atc
+from .functions import av_loinc
+from .functions import av_ddd
+from .functions import av_ddd_units
+from .functions import av_info
+from .functions import av_url
+from .functions import av_property
+from .functions import availability
+from .functions import bug_drug_combinations
+from .functions import count_resistant
+from .functions import count_susceptible
+from .functions import count_S
+from .functions import count_SI
+from .functions import count_I
+from .functions import count_IR
+from .functions import count_R
+from .functions import count_all
+from .functions import n_sir
+from .functions import count_df
+from .functions import custom_eucast_rules
+from .functions import eucast_rules
+from .functions import eucast_dosage
+from .functions import export_ncbi_biosample
+from .functions import first_isolate
+from .functions import filter_first_isolate
+from .functions import g_test
+from .functions import is_new_episode
+from .functions import ggplot_pca
+from .functions import ggplot_sir
+from .functions import geom_sir
+from .functions import theme_sir
+from .functions import labels_sir_count
+from .functions import guess_ab_col
+from .functions import italicise_taxonomy
+from .functions import italicize_taxonomy
+from .functions import inner_join_microorganisms
+from .functions import left_join_microorganisms
+from .functions import right_join_microorganisms
+from .functions import full_join_microorganisms
+from .functions import semi_join_microorganisms
+from .functions import anti_join_microorganisms
+from .functions import key_antimicrobials
+from .functions import all_antimicrobials
+from .functions import antimicrobials_equal
+from .functions import kurtosis
+from .functions import like
+from .functions import mdro
+from .functions import custom_mdro_guideline
+from .functions import brmo
+from .functions import mrgn
+from .functions import mdr_tb
+from .functions import mdr_cmi2012
+from .functions import eucast_exceptional_phenotypes
+from .functions import mean_amr_distance
+from .functions import amr_distance_from_row
+from .functions import mo_matching_score
+from .functions import mo_name
+from .functions import mo_fullname
+from .functions import mo_shortname
+from .functions import mo_subspecies
+from .functions import mo_species
+from .functions import mo_genus
+from .functions import mo_family
+from .functions import mo_order
+from .functions import mo_class
+from .functions import mo_phylum
+from .functions import mo_kingdom
+from .functions import mo_domain
+from .functions import mo_type
+from .functions import mo_status
+from .functions import mo_pathogenicity
+from .functions import mo_gramstain
+from .functions import mo_is_gram_negative
+from .functions import mo_is_gram_positive
+from .functions import mo_is_yeast
+from .functions import mo_is_intrinsic_resistant
+from .functions import mo_oxygen_tolerance
+from .functions import mo_is_anaerobic
+from .functions import mo_snomed
+from .functions import mo_ref
+from .functions import mo_authors
+from .functions import mo_year
+from .functions import mo_lpsn
+from .functions import mo_mycobank
+from .functions import mo_gbif
+from .functions import mo_rank
+from .functions import mo_taxonomy
+from .functions import mo_synonyms
+from .functions import mo_current
+from .functions import mo_group_members
+from .functions import mo_info
+from .functions import mo_url
+from .functions import mo_property
+from .functions import pca
+from .functions import resistance
+from .functions import susceptibility
+from .functions import sir_confidence_interval
+from .functions import proportion_R
+from .functions import proportion_IR
+from .functions import proportion_I
+from .functions import proportion_SI
+from .functions import proportion_S
+from .functions import proportion_df
+from .functions import sir_df
+from .functions import random_mic
+from .functions import random_disk
+from .functions import random_sir
+from .functions import resistance_predict
+from .functions import sir_predict
+from .functions import ggplot_sir_predict
+from .functions import skewness
+from .functions import reset_AMR_locale
+from .functions import translate_AMR

AMR-2.1.1.9094/AMR/datasets.py

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+BLUE = '\033[94m'
+GREEN = '\033[32m'
+RESET = '\033[0m'
+
+print(f"{BLUE}AMR:{RESET} Setting up R environment and AMR datasets...", flush=True)
+
+from rpy2 import robjects
+from rpy2.robjects import pandas2ri
+from rpy2.robjects.packages import importr, isinstalled
+import pandas as pd
+
+# Check if the R package is installed
+if not isinstalled('AMR'):
+    utils = importr('utils')
+    utils.install_packages('AMR')
+
+# Activate the automatic conversion between R and pandas DataFrames
+pandas2ri.activate()
+# example_isolates
+example_isolates = pandas2ri.rpy2py(robjects.r('''
+df <- AMR::example_isolates
+df[] <- lapply(df, function(x) {
+    if (inherits(x, c("Date", "POSIXt", "factor"))) {
+        as.character(x)
+    } else {
+        x
+    }
+})
+df
+'''))
+example_isolates['date'] = pd.to_datetime(example_isolates['date'])
+
+# microorganisms
+microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR::microorganisms, is.list)]'))
+antibiotics = pandas2ri.rpy2py(robjects.r('AMR::antibiotics[, !sapply(AMR::antibiotics, is.list)]'))
+clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints'))
+
+print(f"{BLUE}AMR:{RESET} {GREEN}Done.{RESET}", flush=True)