Tools for Inference in the Presence of a Monotone Likelihood

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Documentation for package ‘PHInfiniteEstimates’ version 2.9.5

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aalenjohansen 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.
andersenplot 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.
arjasplot 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.
bestbeta Newton Raphson Fitter for partial likelihood
checkcensor Check how censoring impacts sampling properties of KM fit and log rank test.
checkresults Produce a graphical assessment of Monte Carlo experiment on fidelity of proportional hazards regression to the uniform ideal.
compareplot Plot resuts of simcode
compete.simulation Simulate from a competing risk model with correlated log normal errors, and plot various estimates.
convertbaselineltolr 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.
convertmtol Convert a polytomous regression to a conditional logistic regression.
convertstoml Convert a proportional hazards regression to a multinomial regression.
drawdiagram Draw diagram for toy PH example.
fixcoxph Remove observations from a proportional hazards regression, and return the fit of the reduced model.
gehan.wilcoxon.test 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.
heinzeschemper Simulate operating characteristics of repaired Cox regression and competitors.
inference Perform inference on conditional sample space.
lrapproximations 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.
network This function enumerates conditional sample spaces associated with logistic regression,
newllk Proportional hazards partial likelihood, using Breslow method for ties, excluding some observations.
PHInfiniteEstimates PHInfiniteEstimates: Tools for Proportional Hazards Estimation, and Inference on the Associate Parameters, when Other Parameters are Estimated at Infinity.
pllk Partial likelihood for proportional hazards
reduceLR Reduce a logistic regression with monotone likelihood to a conditional regression with double descending likelihood.
simcode Simulate Weibull survival data from a model, perform reduction to remove infinite estimates, and calculate p values.
simultaneouscoverage Calculate simultaneous coverage of pointwise confidence intervals.
summarizefits Summarize proportional hazards fits
summarizetable 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.
survregpredict Fit survival probabilties from a survreg object.
testcox Test size of asymptotic Cox tests.
voter.ml Subset of British elections data used in (Kolassa 2016). Data are from (Sanders et al. 2007).