Package: prevtoinc 0.12.0

Niklas Willrich

prevtoinc: Prevalence to Incidence Calculations for Point-Prevalence Studies in a Nosocomial Setting

Functions to simulate point prevalence studies (PPSs) of healthcare-associated infections (HAIs) and to convert prevalence to incidence in steady state setups. Companion package to the preprint Willrich et al., From prevalence to incidence - a new approach in the hospital setting; <doi:10.1101/554725> , where methods are explained in detail.

Authors:Niklas Willrich [aut, cre]

prevtoinc_0.12.0.tar.gz
prevtoinc_0.12.0.tar.gz(r-4.5-noble)prevtoinc_0.12.0.tar.gz(r-4.4-noble)
prevtoinc_0.12.0.tgz(r-4.4-emscripten)prevtoinc_0.12.0.tgz(r-4.3-emscripten)
prevtoinc.pdf |prevtoinc.html✨
prevtoinc/json (API)
NEWS

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

Peer review:

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

21 exports 0.23 score 17 dependencies 1 dependents 20 scripts 192 downloads

Last updated 5 years agofrom:abbb8c0e57. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-linuxNOTEAug 31 2024

Exports:A_to_X_distcalculate_CI_I_ppcalculate_Icalculate_I_mixedcalculate_I_rhamecalculate_I_smoothCI_np_bscreate_dist_veccreate_patient_history_addepmfgenerate_I_fastgeom_dist_fctlength_biased_distlength_unbiased_meanmonotone_smootherpois_dist_fctsimulate_incidence_statssimulate_incidence_stats_fastsimulate_pps_datasimulate_pps_fastX_to_A_dist

Dependencies:clidplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangtibbletidyselectutf8vctrswithr

Overview of the prevtoinc package

Niklas Willrich

Rendered fromprevtoinc_vignette.Rmdusingknitr::rmarkdownon Aug 31 2024.

Last update: 2019-06-18
Started: 2019-03-10

Readme and manuals

Help Manual

Help pageTopics
function to transform the distribution of stays to a fixed point to the distribution of the staying timesA_to_X_dist
Calculate confidence intervals for Grenander estimator of Ipp based on asymptoticscalculate_CI_I_pp
Function to calculate different estimators for I from PPS data.calculate_I
Function to calculate incidence from PPS data using a mix of two estimatorscalculate_I_mixed
Function to calculate incidence from PPS data using a Rhame-Sudderth like approach with estimates for x.loi and x.los supplied.calculate_I_rhame
Estimate the incidence based on PPS data using monotone estimators for the distribution of A.calculate_I_smooth
Function to calculate confidence intervals I.pp for gren estimator with bootstrap method based on Grenander estimatorCI_np_bs
Create vector of probabilities for a finite positive discrete distributioncreate_dist_vec
Function to simulate a single hospital bed trajectorycreate_patient_history_add
Calculate empirical probability mass function for a discrete positive distribution starting at 1epmf
Function to simulate PPS and data and calculate a number of estimatorsgenerate_I_fast
Probability mass function for a geometric distribution shifted by one and resulting expected value 8geom_dist_fct
Calculate length-biased distribution from discrete length-unbiased distribution starting at 1length_biased_dist
Calculate mean of length-unbiased distribution from discrete length-biased distribution starting at 1length_unbiased_mean
Calculate a monotone probability mass function estimatemonotone_smoother
Probability mass function for a Poisson distribution shifted by one and resulting expected value 8pois_dist_fct
prevtoinc:prevtoinc-package prevtoinc
Calculate theoretical values like x.los, x.loi and other characteristics of the patient populationsimulate_incidence_stats
Function to calculate theoretical value for x.loi and Isimulate_incidence_stats_fast
Function to simulate PPS datasimulate_pps_data
Faster method to generate data for PPS with only length of nosocomial infections as outputsimulate_pps_fast
Transform a distribution of times of stay to a distribution of staying-time up to observation point under assumption of steady state.X_to_A_dist