Package: xhaz 2.1.0

xhaz: Excess Hazard Modelling Considering Inappropriate Mortality Rates

Fits relative survival regression models with or without proportional excess hazards and with the additional possibility to correct for background mortality by one or more parameter(s). These models are relevant when the observed mortality in the studied group is not comparable to that of the general population or in population-based studies where the available life tables used for net survival estimation are insufficiently stratified. In the latter case, the proposed model by Touraine et al. (2020) <doi:10.1177/0962280218823234> can be used. The user can also fit a model that relaxes the proportional expected hazards assumption considered in the Touraine et al. excess hazard model. This extension was proposed by Mba et al. (2020) <doi:10.1186/s12874-020-01139-z> to allow non-proportional effects of the additional variable on the general population mortality. In non-population-based studies, researchers can identify non-comparability source of bias in terms of expected mortality of selected individuals. An excess hazard model correcting this selection bias is presented in Goungounga et al. (2019) <doi:10.1186/s12874-019-0747-3>. This class of model with a random effect at the cluster level on excess hazard is presented in Goungounga et al. (2023) <doi:10.1002/bimj.202100210>.

Authors:Juste Goungounga [aut, cre], Hadrien Charvat [aut], Darlin Mba [aut], Nathalie Graffeo [aut], Roch Giorgi [aut]

xhaz_2.1.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
xhaz/json (API)

# Install 'xhaz' in R:
install.packages('xhaz', repos = c('https://jgoungounga.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • breast - Simulated clinical trial data with non comparability bias in term of individuals expected hazard
  • ccr.mevents - Colorectum cancer data with multiple events
  • dataCancer - Simulated data with cause death information with non comparability bias in term of individuals expected hazard
  • rescaledData - Simulated data with cause death information with non comparability bias in term of individuals expected hazard
  • simuData - Simulated data with cause death information in long term follow-up setting without non comparability bias in term of individuals expected hazard

On CRAN:

Conda:

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

3.20 score 16 scripts 312 downloads 9 exports 22 dependencies

Last updated from:70e8f7d780. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK134
source / vignettesOK235
linux-releaseOK141
macos-releaseOK205
macos-oldrelOK224
windows-develOK121
windows-releaseOK101
windows-oldrelOK106
wasm-releaseOK104

Exports:as.predxhazas.predxhaz_listas.xhazduplicateexphazmexhazLTpred_listqbsxhaz

Dependencies:cligluegtoolslamWlatticelifecyclemagrittrMASSMatrixmexhaznumDerivoptimParallelRcppRcppParallelrlangstatmodstringistringrsurvexp.frsurvivalvctrsWriteXLS

Introduction to Excess Hazard Modelling Considering Inappropriate Mortality Rates
Introduction | Installation | Fitting an classical excess hazard regression model with a piecewise constant baseline hazard | Fitting an excess hazard regression model with a piecewise constant baseline hazard with background mortality corrected with proportional effect for race variable | Fitting an excess hazard regression model with a piecewise constant baseline hazard with background mortality corrected with non proportional effect for race variable | Plot of net survival and excess hazard for different models | License | Acknowledgments | session info

Last update: 2026-01-28
Started: 2022-09-07

How to implement a rescaled random-effects excess hazard regression model to handle situations involving inappropriate life tables.
Introduction | Installation | Fitting an classical excess hazard regression model with a cubic B-splines for the baseline hazard as in mexhaz | Fitting a rescaled excess hazard regression model with a cubic B-splines for the baseline hazard as in mexhaz | Fitting a random-effects excess hazard regression model with a cubic B-splines for the baseline hazard as in mexhaz | Fitting a rescaled random-effects excess hazard regression model with a cubic B-splines for the baseline hazard as in mexhaz | Plot of net survival and excess hazard for different models | License | Acknowledgments | Session Info

Last update: 2026-01-28
Started: 2024-06-30

Readme and manuals

Help Manual

Help pageTopics
anova.bsplines function used for likelihood-ratio Test of two models from xhaz functionanova.bsplines
anova.constant function used for likelihood-ratio Test of two models from xhaz functionanova.constant
anova.mexhazLT function used for likelihood-ratio Test of two models from mexhaz functionanova.mexhazLT
Coerce to predxhaz objectas.predxhaz
Coerce a generic list of models (and subgroups) to a predxhaz_listas.predxhaz_list
Coerce a fitted object to have '"xhaz"' as first classas.xhaz
Simulated clinical trial data with non comparability bias in term of individuals expected hazardbreast
colorectum cancer data with multiple eventsccr.mevents
Simulated data with cause death information with non comparability bias in term of individuals expected hazarddataCancer
duplicate functionduplicate
exphaz functionexphaz
mexhazLT functionmexhazAlpha mexhazLT
plot.bsplinesplot.bsplines
plots of excess hazard and net Survival from an 'predxhaz' objectplot.predxhaz
Plot predictions from several xhaz models (two-panel display)plot.predxhaz_list
Create a predxhaz_list from predxhaz objectspred_list
Predictions of excess hazard and net Survival from a 'bsplines' objectpredict.bsplines
Predictions of excess hazard and net Survival from an 'constant' objectpredict.constant
A print.bsplines Function used to print a object of class 'bsplines'print.bsplines
A print.constant Function used to print a object of class constantprint.constant
A print.predxhaz Function used to print a object of class predxhazprint.predxhaz
qbs functionqbs
Simulated data with cause death information with non comparability bias in term of individuals expected hazardrescaledData
Simulated data with cause death information in long term follow-up setting without non comparability bias in term of individuals expected hazardsimuData
A summary.bsplines Function used to print a object of class 'bsplines'summary.bsplines
A summary.constant Function used to print a object of class 'xhaz.constant'summary.constant
xhaz functionxhaz