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

# Tools for Inference in the Presence of a Monotone Likelihood

## Documentation for package ‘PHInfiniteEstimates’ version 2.9.5

- DESCRIPTION file

## Help Pages

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).