Package: antibioticR 0.3.4

antibioticR: Analysis of Antibiotic Resistance Data

Antibiotic resistant bacteria are a serious threat to human health. This package aims to collect tools and functions to analyze environmental resistance data, especially minimal inhibitory concentration ('MIC') and inhibition zone diameters ('ZD').

Authors:Thomas Petzoldt

antibioticR_0.3.4.tar.gz
antibioticR_0.3.4.zip(r-4.7-any)antibioticR_0.3.4.zip(r-4.6-any)antibioticR_0.3.4.zip(r-4.5-any)
antibioticR_0.3.4.tgz(r-4.6-any)antibioticR_0.3.4.tgz(r-4.5-any)
antibioticR_0.3.4.tar.gz(r-4.7-any)antibioticR_0.3.4.tar.gz(r-4.6-any)
antibioticR_0.3.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
antibioticR/json (API)

# Install 'antibioticR' in R:

install.packages('antibioticR', repos = c('https://tpetzoldt.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tpetzoldt/antibioticr/issues

Datasets:

micdata - Minimum Inhibitory Concentration (MIC) Data

On CRAN:

3.54 score 7 stars 61 exports 21 dependencies

Last updated from:76d52990a1. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	155
source / vignettes	OK	213
linux-release	NOTE	178
macos-release	NOTE	130
macos-oldrel	NOTE	93
windows-devel	NOTE	109
windows-release	NOTE	101
windows-oldrel	NOTE	110
wasm-release	OK	129

Exports:abr_cumdens abr_cumdensquant abr_density abr_density.control abr_quantile AIC coef deviance df.residual diagnostics dunimix ecoff ECOFFinder ecoffinder_nls ecoffinder_startpar fit fit_en fit_enn fit_ennn fit_ennnn fit_ennnnn fit_n fit_nn fit_nnn fit_nnnn fit_nnnnn fit_unimix get_data logLik maxdens mixParmDf2parmlist models mx_compare mx_guess_components mx_intermediate mx_metafit mx_parmlist_select mx_parmlist_sort mx_plot mx_select mx_subset mx_wildtype mxObj obs parmList peakwindow plot pstart punimix reformat_eucast residuals results rsquared runimix startpar summary turnpoints unbin vcov weighted.sd zd_main_components

Dependencies:bbmle bdsmatrix cli evmix glue gsl lattice lifecycle magrittr MASS Matrix mvtnorm numDeriv plyr Rcpp reshape2 rlang SparseM stringi stringr vctrs

Analysis of Antibiotic Resistance Tests with Package antibioticR

Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2021-09-22
Started: 2018-07-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analysis of Antbiotic Resistance Data	antibioticR-package antibioticR
Classes of package 'antibioticR' ...	abr_baseclass abr_ecoffinder-class
Kernel Density Estimate for ZD and MIC data	abr_cumdens abr_cumdensquant abr_density abr_density.control maxdens
Normal Quantiles of Wild Type Population Identified with Ecoffinder	abr_quantile
Coercion Methods for 'mxObj' Univariate Mixture Objects	as.list,mxObj-method as.mxObj as.mxObj,list-method as.mxObj,vector-method as.vector,mxObj-method coerce
Diagnostics of Mixture Objects Fitted with 'mle2'	diagnostics diagnostics,mxMle-method
Univariate Mixtures of Exponential, Normal and Gamma Distributions	dunimix dunimix,numeric,list-method dunimix,numeric,mxObj-method punimix punimix,numeric,list-method punimix,numeric,mxObj-method runimix runimix,numeric,list-method runimix,numeric,mxObj-method
Launch antibioticR App ECOFFinder	ECOFFinder
Find Cutoff Value by Nonlinear Regression to Truncated Data	ecoffinder_nls
Start Values for ECOFFinder	ecoffinder_startpar
Methods for 'mxObj' Univariate Mixture Objects	AIC,mxMle-method coef,mxObj-method ecoff fit get_data get_data,mxMle-method logLik,mxMle-method models mxObj pstart pstart,mxObj-method rsquared startpar summary,mxMle-method vcov,mxMle-method
Fit of Normal and Exponential-Normal Mixtures to Binned Data	fit_en fit_enn fit_ennn fit_ennnn fit_ennnnn fit_n fit_nn fit_nnn fit_nnnn fit_nnnnn fit_unimix
Minimum Inhibitory Concentration (MIC) Data	micdata
Convert Parameters in data frame format to a paremeter list ...	mixParmDf2parmlist
Compare Fitted Mixture Distribution to Data	mx_compare
Initial Guess of Univariate Mixture Components	mx_guess_components
Fit Mixture Distribution to Data and Evaluate Results	mx_metafit
Sort and Select Distribution Components	mx_intermediate mx_parmlist_select mx_parmlist_sort mx_select mx_subset mx_wildtype
Plot Components of Mixture Distribution	mx_plot
Mixture Distribution Object Containing an 'mle2' fit as Subobject	mxMle-class
Class of Univariate Mixture Distribution Components and its Parameters	mxObj-class
Helper Classes	nls nls-class
Accessor Methods of Package 'antibioticR'.	coef,abr_baseclass-method deviance,abr_baseclass-method df.residual,abr_baseclass-method ecoff,abr_ecoffinder-method fit,abr_baseclass-method models,abr_ecoffinder-method obs obs,abr_baseclass-method residuals,abr_baseclass-method rsquared,abr_ecoffinder-method startpar,abr_ecoffinder-method
Convert Parameter Vector to List	parmList
Identify Peaks in Multimodal Density Curves and Time Series	peakwindow
Plot Fitted abrECOFFinder Object	plot,abr_ecoffinder,ANY-method
Reformat EUCAST crosstabe format into data base formats	reformat_eucast
Quantiles and Results of Mixture Objects Fitted with 'mle2'	results results,mxMle-method
Summary of an 'abr_ecoffinder' Object	summary,abr_baseclass-method summary,abr_ecoffinder-method
Find turning points (peaks or pits) Determine the number and the position of extrema (turning points, either peaks or pits) in a regular time series.	turnpoints
Unbin Data Frame	unbin
Weighted Standard Deviation	weighted.sd
Extract Main Components from Zone Diameter (ZD) Mixture Distribution	zd_main_components