Package: PHInfiniteEstimates 2.9.5

PHInfiniteEstimates: Tools for Inference in the Presence of a Monotone Likelihood

Proportional hazards estimation in the presence of a partially monotone likelihood has difficulties, in that finite estimators do not exist. These difficulties are related to those arising from logistic and multinomial regression. References for methods are given in the separate function documents. Supported by grant NSF DMS 1712839.

Authors:John E. Kolassa and Juan Zhang

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PHInfiniteEstimates/json (API)

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

Peer review:

Datasets:
  • voter.ml - Subset of British elections data used in (Kolassa 2016). Data are from (Sanders et al. 2007).

On CRAN:

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

27 exports 0.09 score 42 dependencies 338 downloads

Last updated 10 months agofrom:a592006509. Checks:OK: 7. Indexed: yes.

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Exports:aalenjohansenandersenplotarjasplotbestbetacheckcensorcheckresultscompareplotcompete.simulationconvertbaselineltolrconvertmtolconvertstomldrawdiagramfixcoxphgehan.wilcoxon.testheinzeschemperinferencelrapproximationsnetworknewllkpllkreduceLRsimcodesimultaneouscoveragesummarizefitssummarizetablesurvregpredicttestcox

Dependencies:clicodetoolscolorspacecoxphffansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclelpSolvemagrittrMASSMatrixmgcvmuhazmultcompmunsellmvtnormnlmenphpillarpkgconfigR6rbibutilsRColorBrewerRdpackrlangsandwichscalessurvivalTH.datatibbleutf8vctrsviridisLitewithrzoo

Readme and manuals

Help Manual

Help pageTopics
Calculate the Aalen-Johansen (1978) estimate in the Competing risk context. See Aalen, Odd O., and Søren Johansen. "An Empirical Transition Matrix for Non-Homogeneous Markov Chains Based on Censored Observations." Scandinavian Journal of Statistics 5, no. 3 (1978): 141-50. Accessed January 15, 2021. http://www.jstor.org/stable/4615704.aalenjohansen
Plot hazards for two strata for each time. At times with an event in one but not the other group, the fitted hazard remains constant, and so the plot is a step function. If hazards are proportional between strata, then the plot should be close to a straight line.andersenplot
Examine the potential role of treatment in treatment in a model already including sex. Straight lines that are not 45 degrees indicate the appropriateness of new variable as a linear effect.arjasplot
Newton Raphson Fitter for partial likelihoodbestbeta
Check how censoring impacts sampling properties of KM fit and log rank test.checkcensor
Produce a graphical assessment of Monte Carlo experiment on fidelity of proportional hazards regression to the uniform ideal.checkresults
Plot resuts of simcodecompareplot
Simulate from a competing risk model with correlated log normal errors, and plot various estimates.compete.simulation
Convert a baseline logit model data set, formatted in the long form as described in the documentation for mlogit.data from mlogit package, to a conditional logistic regression.convertbaselineltolr
Convert a polytomous regression to a conditional logistic regression.convertmtol
Convert a proportional hazards regression to a multinomial regression.convertstoml
Draw diagram for toy PH example.drawdiagram
Remove observations from a proportional hazards regression, and return the fit of the reduced model.fixcoxph
Perform Gehan's application to the Wilcoxon test for multiple samples, testing for equivalance of survival curve. See Klein and Moeschberger (1997) Survival Analysis (7.3.3) and pp. 193-194.gehan.wilcoxon.test
Simulate operating characteristics of repaired Cox regression and competitors.heinzeschemper
Perform inference on conditional sample space.inference
Assess the accuracy of the log rank statistic approximation to the true value, in the case without censoring. Provides plots of statistics, and empirical test level.lrapproximations
This function enumerates conditional sample spaces associated with logistic regression,network
Proportional hazards partial likelihood, using Breslow method for ties, excluding some observations.newllk
PHInfiniteEstimates: Tools for Proportional Hazards Estimation, and Inference on the Associate Parameters, when Other Parameters are Estimated at Infinity.PHInfiniteEstimates
Partial likelihood for proportional hazardspllk
Reduce a logistic regression with monotone likelihood to a conditional regression with double descending likelihood.reduceLR
Simulate Weibull survival data from a model, perform reduction to remove infinite estimates, and calculate p values.simcode
Calculate simultaneous coverage of pointwise confidence intervals.simultaneouscoverage
Summarize proportional hazards fitssummarizefits
Summarize the results of simulations investigating operating conditions for the data reduction method to avoid monotone likelihood. Files are of form "hsxxx", for xxx numerals.summarizetable
Fit survival probabilties from a survreg object.survregpredict
Test size of asymptotic Cox tests.testcox
Subset of British elections data used in (Kolassa 2016). Data are from (Sanders et al. 2007).voter.ml