Man pages for msberends/AMR
Antimicrobial Resistance Data Analysis
| ab_from_text | Retrieve Antimicrobial Drug Names and Doses from Clinical... |
| ab_property | Get Properties of an Antibiotic |
| add_custom_antimicrobials | Add Custom Antimicrobials |
| add_custom_microorganisms | Add Custom Microorganisms |
| age | Age in Years of Individuals |
| age_groups | Split Ages into Age Groups |
| AMR | The 'AMR' Package |
| AMR-deprecated | Deprecated Functions |
| AMR-options | Options for the AMR package |
| antibiogram | Generate Traditional, Combination, Syndromic, or WISCA... |
| antibiotics | Data Sets with 607 Antimicrobial Drugs |
| antimicrobial_selectors | Antimicrobial Selectors |
| as.ab | Transform Input to an Antibiotic ID |
| as.av | Transform Input to an Antiviral Drug ID |
| as.disk | Transform Input to Disk Diffusion Diameters |
| as.mic | Transform Input to Minimum Inhibitory Concentrations (MIC) |
| as.mo | Transform Arbitrary Input to Valid Microbial Taxonomy |
| as.sir | Translate MIC and Disk Diffusion to SIR, or Clean Existing... |
| atc_online | Get ATC Properties from WHOCC Website |
| availability | Check Availability of Columns |
| av_from_text | Retrieve Antiviral Drug Names and Doses from Clinical Text |
| av_property | Get Properties of an Antiviral Drug |
| bug_drug_combinations | Determine Bug-Drug Combinations |
| clinical_breakpoints | Data Set with Clinical Breakpoints for SIR Interpretation |
| count | Count Available Isolates |
| custom_eucast_rules | Define Custom EUCAST Rules |
| dosage | Data Set with Treatment Dosages as Defined by EUCAST |
| eucast_rules | Apply EUCAST Rules |
| example_isolates | Data Set with 2 000 Example Isolates |
| example_isolates_unclean | Data Set with Unclean Data |
| export_ncbi_biosample | Export Data Set as NCBI BioSample Antibiogram |
| first_isolate | Determine First Isolates |
| get_episode | Determine Clinical or Epidemic Episodes |
| ggplot_pca | PCA Biplot with 'ggplot2' |
| ggplot_sir | AMR Plots with 'ggplot2' |
| g.test | _G_-test for Count Data |
| guess_ab_col | Guess Antibiotic Column |
| intrinsic_resistant | Data Set with Bacterial Intrinsic Resistance |
| italicise_taxonomy | Italicise Taxonomic Families, Genera, Species, Subspecies |
| join | Join microorganisms to a Data Set |
| key_antimicrobials | (Key) Antimicrobials for First Weighted Isolates |
| kurtosis | Kurtosis of the Sample |
| like | Vectorised Pattern Matching with Keyboard Shortcut |
| mdro | Determine Multidrug-Resistant Organisms (MDRO) |
| mean_amr_distance | Calculate the Mean AMR Distance |
| microorganisms | Data Set with 78 678 Taxonomic Records of Microorganisms |
| microorganisms.codes | Data Set with 4 971 Common Microorganism Codes |
| microorganisms.groups | Data Set with 521 Microorganisms In Species Groups |
| mo_matching_score | Calculate the Matching Score for Microorganisms |
| mo_property | Get Properties of a Microorganism |
| mo_source | User-Defined Reference Data Set for Microorganisms |
| pca | Principal Component Analysis (for AMR) |
| plot | Plotting Helpers for AMR Data Analysis |
| proportion | Calculate Antimicrobial Resistance |
| random | Random MIC Values/Disk Zones/SIR Generation |
| resistance_predict | Predict Antimicrobial Resistance |
| skewness | Skewness of the Sample |
| top_n_microorganisms | Filter Top _n_ Microorganisms |
| translate | Translate Strings from the AMR Package |
| WHOCC | WHOCC: WHO Collaborating Centre for Drug Statistics... |
| WHONET | Data Set with 500 Isolates - WHONET Example |
