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-4.7-any)prevtoinc_0.12.0.tar.gz(r-4.6-any)
prevtoinc_0.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
prevtoinc/json (API)

# Install 'prevtoinc' in R:

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

On CRAN:

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

3.50 score 1 packages 21 scripts 242 downloads 21 exports 16 dependencies

Last updated from:abbb8c0e57. Checks:2 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	129
source / vignettes	OK	172
linux-release-x86_64	NOTE	141
wasm-release	OK	123

Exports:A_to_X_dist calculate_CI_I_pp calculate_I calculate_I_mixed calculate_I_rhame calculate_I_smooth CI_np_bs create_dist_vec create_patient_history_add epmf generate_I_fast geom_dist_fct length_biased_dist length_unbiased_mean monotone_smoother pois_dist_fct simulate_incidence_stats simulate_incidence_stats_fast simulate_pps_data simulate_pps_fast X_to_A_dist

Dependencies:cli dplyr generics glue lifecycle magrittr pillar pkgconfig purrr R6 rlang tibble tidyselect utf8 vctrs withr

Overview of the prevtoinc package

Rendered fromprevtoinc_vignette.Rmdusingknitr::rmarkdown

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

Citation

Readme and manuals

Help Manual

Help page	Topics
function to transform the distribution of stays to a fixed point to the distribution of the staying times	A_to_X_dist
Calculate confidence intervals for Grenander estimator of Ipp based on asymptotics	calculate_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 estimators	calculate_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 estimator	CI_np_bs
Create vector of probabilities for a finite positive discrete distribution	create_dist_vec
Function to simulate a single hospital bed trajectory	create_patient_history_add
Calculate empirical probability mass function for a discrete positive distribution starting at 1	epmf
Function to simulate PPS and data and calculate a number of estimators	generate_I_fast
Probability mass function for a geometric distribution shifted by one and resulting expected value 8	geom_dist_fct
Calculate length-biased distribution from discrete length-unbiased distribution starting at 1	length_biased_dist
Calculate mean of length-unbiased distribution from discrete length-biased distribution starting at 1	length_unbiased_mean
Calculate a monotone probability mass function estimate	monotone_smoother
Probability mass function for a Poisson distribution shifted by one and resulting expected value 8	pois_dist_fct
prevtoinc:	prevtoinc-package prevtoinc
Calculate theoretical values like x.los, x.loi and other characteristics of the patient population	simulate_incidence_stats
Function to calculate theoretical value for x.loi and I	simulate_incidence_stats_fast
Function to simulate PPS data	simulate_pps_data
Faster method to generate data for PPS with only length of nosocomial infections as output	simulate_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

Package: prevtoinc 0.12.0

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

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)