Package: BHAI 0.99.2

Benedikt Zacher

BHAI: Estimate the Burden of Healthcare-Associated Infections

Provides an approach which is based on the methodology of the Burden of Communicable Diseases in Europe (BCoDE) and can be used for large and small samples such as individual countries. The Burden of Healthcare-Associated Infections (BHAI) is estimated in disability-adjusted life years, number of infections as well as number of deaths per year. Results can be visualized with various plotting functions and exported into tables.

Authors:Benedikt Zacher [aut, cre]

BHAI_0.99.2.tar.gz
BHAI_0.99.2.tar.gz(r-4.5-noble)BHAI_0.99.2.tar.gz(r-4.4-noble)
BHAI_0.99.2.tgz(r-4.4-emscripten)BHAI_0.99.2.tgz(r-4.3-emscripten)
BHAI.pdf |BHAI.html✨
BHAI/json (API)

# Install 'BHAI' in R:
install.packages('BHAI', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • eu_pps - Aggregated data of the ECDC PPS 2010-2011.
  • german_pps_conv - Aggregated data of the german PPS 2010-2011 (convenience sample).
  • hospital_discharges - Hospital discharges in Germany
  • length_of_stay - Average length of stay of survey patients in german PPS 2011
  • loi_pps - A list containing length of infections from all patients in the german PPS 2011 representative sample.
  • mccabe_life_exp - Named list containing remaining life expectancies for each McCabe score (NONFATAL, ULTFATAL, RAPFATAL).
  • mccabe_scores_distr - The observed McCabe scores (counts) for each infection, age and gender stratum from the ECDC PPS 2011-2012.
  • num_hai_patients - Number of cases for each infection in the german PPS 2011
  • num_hai_patients_by_stratum - Stratified number of cases for each infection in the german PPS 2011
  • num_hai_patients_by_stratum_prior - Stratified number of cases for each infection in the german PPS 2011 (convenience sample). This distribution is used as a Prior for the representative sample.
  • num_survey_patients - Number of survey patients in the german PPS 2011 (representative sample).
  • population - Population size of Germany in 2011.
  • sim_pps - Simulated/subsampled data sets from european PPS
  • sim_pps_bhai - BHAI with default options was applied to simulated/subsampled data sets from european PPS
  • sim_pps_bhai_prior - BHAI with prior was applied to simulated/subsampled data sets from european PPS
  • sim_pps_stratified - BHAI with stratified sampling was applied to simulated/subsampled data sets from european PPS

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

7 exports 0.23 score 29 dependencies 1 mentions 170 downloads

Last updated 5 years agofrom:1c9b40ccc1. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 01 2024
R-4.5-linuxOKSep 01 2024

Exports:bhaibhai.barplotbhai.circleplotbhai.prettyTablebhai.strataplotPPSsample.pps

Dependencies:clicodadplyrfansigenericsgluelatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackpillarpkgconfigplotrixprevtoincpurrrquantregR6rlangSparseMsurvivaltibbletidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Main function of the package to estimation of the burden of healthcare-associated infectionsbhai bhai,PPS,ANY-method bhai,PPS-method
BHAI:BHAI-package BHAI
Barplot of cases, deaths and DALYs.bhai.barplot
Summary plot of number of infections, deaths and DALYsbhai.circleplot
Create summary tablebhai.prettyTable
Stratified barplot of cases, deaths and DALYs.bhai.strataplot
Aggregated data of the ECDC PPS 2010-2011.eu_pps
Aggregated data of the german PPS 2010-2011 (convenience sample).german_pps_conv
Hospital discharges in Germany (2011)hospital_discharges
Average length of stay of survey patients in german PPS 2011 (representative sample)length_of_stay
A list containing length of infections from all patients in the german PPS 2011 representative sample.loi_pps
Named list containing remaining life expectancies for each McCabe score (NONFATAL, ULTFATAL, RAPFATAL).mccabe_life_exp
The observed McCabe scores (counts) for each infection, age and gender stratum from the ECDC PPS 2011-2012.mccabe_scores_distr
Number of cases for each infection in the german PPS 2011 (representative sample)num_hai_patients
Stratified number of cases for each infection in the german PPS 2011 (representative sample)num_hai_patients_by_stratum
Stratified number of cases for each infection in the german PPS 2011 (convenience sample). This distribution is used as a Prior for the representative sample.num_hai_patients_by_stratum_prior
Number of survey patients in the german PPS 2011 (representative sample).num_survey_patients
Population size of Germany in 2011.population
Create a PPS objectPPS
This class is a generic container for PPS data sets..PPS PPS-class
Simulate PPS datasample.pps
Simulated/subsampled data sets from european PPSsim_pps
BHAI with default options was applied to simulated/subsampled data sets from european PPSsim_pps_bhai
BHAI with prior was applied to simulated/subsampled data sets from european PPSsim_pps_bhai_prior
BHAI with stratified sampling was applied to simulated/subsampled data sets from european PPSsim_pps_stratified