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riskRegression - Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

Implementation of the following methods for event history analysis. Risk regression models for survival endpoints also in the presence of competing risks are fitted using binomial regression based on a time sequence of binary event status variables. A formula interface for the Fine-Gray regression model and an interface for the combination of cause-specific Cox regression models. A toolbox for assessing and comparing performance of risk predictions (risk markers and risk prediction models). Prediction performance is measured by the Brier score and the area under the ROC curve for binary possibly time-dependent outcome. Inverse probability of censoring weighting and pseudo values are used to deal with right censored data. Lists of risk markers and lists of risk models are assessed simultaneously. Cross-validation repeatedly splits the data, trains the risk prediction models on one part of each split and then summarizes and compares the performance across splits.

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openblascpp

14.20 score 55 stars 50 dependents 1.3k scripts 17k downloads

prodlim - Product-Limit Estimation for Censored Event History Analysis

Fast and user friendly implementation of nonparametric estimators for censored event history (survival) analysis. Kaplan-Meier and Aalen-Johansen method.

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13.13 score 7 stars 517 dependents 1.7k scripts 161k downloads

Publish - Format Output of Various Routines in a Suitable Way for Reports and Publication

A bunch of convenience functions that transform the results of some basic statistical analyses into table format nearly ready for publication. This includes descriptive tables, tables of logistic regression and Cox regression results as well as forest plots.

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10.34 score 16 stars 52 dependents 282 scripts 16k downloads

pec - Prediction Error Curves for Risk Prediction Models in Survival Analysis

Validation of risk predictions obtained from survival models and competing risk models based on censored data using inverse weighting and cross-validation. Most of the 'pec' functionality has been moved to 'riskRegression'.

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7.96 score 36 dependents 647 scripts 13k downloads

SmoothHazard - Estimation of Smooth Hazard Models for Interval-Censored Data

Estimation of two-state (survival) models and irreversible illness- death models with possibly interval-censored, left-truncated and right-censored data. Proportional intensities regression models can be specified to allow for covariates effects separately for each transition. We use either a parametric approach with Weibull baseline intensities or a semi-parametric approach with M-splines approximation of baseline intensities in order to obtain smooth estimates of the hazard functions. Parameter estimates are obtained by maximum likelihood in the parametric approach and by penalized maximum likelihood in the semi-parametric approach.

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fortran

2.76 score 38 scripts 230 downloads