Package SvyNom. February 24, 2015
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1 Package SvyNom February 24, 2015 Type Package Title Nomograms for Right-Censored Outcomes from Survey Designs Version 1.1 Date Author Mithat Gonen, Marinela Capanu Maintainer Mithat Gonen Builds, evaluates and validates a nomogram with survey data and right-censored outcomes. Imports survival,rms,hmisc,survey License GPL-2 LazyLoad yes NeedsCompilation no Repository CRAN Date/Publication :30:01 R topics documented: SvyNom-package nona svycox.calibrate svycox.nomogram svycox.validate Index 8 1
2 2 SvyNom-package SvyNom-package Nomograms for right-censored outcomes with complex survey data Details Builds, evaluates and validates a nomogram with survey data and right-censored outcomes.
3 nona 3 Package: SvyNom Type: Package Version: 1.1 Date: License: GPL-2 LazyLoad: yes There are three functions for the user svycox.nomogram, svycox.validate, svycox.calibrate Author(s) Marinela Capanu and Mithat Gonen Maintainer: gonenm@mskcc.org References Marinela Capanu, Mithat Gonen (2015). Building a Nomogram for Survey-Weighted Cox Models Using R. Journal of Statistical Software, Code Snippets, 64(1), URL nona Gastric cancer case-control study Example dataset for the SvyNom package. Usage Author(s) Mithat Gonen, Marinela Capanu Examples
4 4 svycox.calibrate svycox.calibrate Checking the calibration of a nomogram for a survey-weighted Cox model Checks the calibration of a nomogram for a survey-weighted Cox model. Usage svycox.calibrate(.nom,.timept =.nom$pred.at,.ngroup = 5) Arguments.nom.timept.ngroup a nomogram object from svycox.nomogram the time point at which calibration will take place; defaults to the time value of the prediction axis in the nomogram number of groups to be formed for validation purposes Value returns a matrix of calibration values and plots them Author(s) Mithat Gonen, Marinela Capanu References Marinela Capanu, Mithat Gonen (2015). Building a Nomogram for Survey-Weighted Cox Models Using R. Journal of Statistical Software, Code Snippets, 64(1), URL Examples library(survey) library(rms) dd=datadist(nona) options(datadist="dd") dstr2=svydesign(id=~1, strata=~group, prob=~inv_weight, fpc=~ssize, data=nona) mynom=svycox.nomogram(.design=dstr2,.model=surv(survival,surv_cens)~ecog+liver_only+alb+hb+age+ Differentiation+Gt_1_m1site+lymph_only,.data=noNA, pred.at=24, fun.lab="prob of 2 Yr OS") svycox.calibrate(mynom)
5 svycox.nomogram 5 svycox.nomogram Builds a nomogram for a survey-weighted Cox model Builds a nomogram for a survey-weighted Cox model. Usage svycox.nomogram(.design,.model,.data, pred.at, fun.lab) Arguments.design.model.data pred.at fun.lab represents a survey design object obtained with the package "survey" indicates a Cox model specification contains the data on which the model is to be fit (can not contain NAs) specifies the time point at which the nomogram prediction axis will be drawn designate the label of the prediction axis Details In addition to the inputs, this function expects the following: 1) the input dataset (.data) cannot contain NAs. You can accomplish this using the na.omit function. See example. 2) datadist must be set. See examples and the documentation for the rms package. 3) survey design must have been saved in.design All of these requirements are explained in Capanu & Gonen (2015) in detail Value A list including elements nomog preds A nomogram object predicted values from the model In addition to what is listed below, the design and the fitted survey weighted Cox model (svy.cox), as well as the timepoint at which the nomogram prediction axis will be drawn (pred.at) are stored Author(s) Mithat Gonen, Marinela Capanu References Marinela Capanu, Mithat Gonen (2015). Building a Nomogram for Survey-Weighted Cox Models Using R. Journal of Statistical Software, Code Snippets, 64(1), URL
6 6 svycox.validate Examples library(survey) library(rms) dd=datadist(nona) options(datadist="dd") dstr2=svydesign(id=~1, strata=~group, prob=~inv_weight, fpc=~ssize, data=nona) mynom=svycox.nomogram(.design=dstr2,.model=surv(survival,surv_cens)~ecog+liver_only+alb+hb+age+ Differentiation+Gt_1_m1site+lymph_only,.data=noNA, pred.at=24, fun.lab="prob of 2 Yr OS") plot(mynom$nomog) svycox.validate Validating a nomogram for a survey-weighted Cox model Validates a nomogram for a survey-weighted Cox model using bootstrap. Usage svycox.validate(.boot.index,.nom,.data) Arguments.boot.index.nom.data a matrix of bootstrap sample indicators with the number of rows the same as the number of rows in the data on which the nomogram was created and the number of columns being the number of bootstrap samples a nomogram object returned from svycox.nomogram contains the dataset on which the validation will take place Details Note that generating the bootstrap sample is design dependent and it is not part of the function. The user has to generate the bootstrap samples consistent with the design used. An example of how the bootstrap sample was generated for the dataset is presented in the reference below. Value prints the estimated optimism and returns the vector of optimism values for each bootstrap sample which can be used to summarize the validation with the measure of choice References Marinela Capanu, Mithat Gonen (2015). Building a Nomogram for Survey-Weighted Cox Models Using R. Journal of Statistical Software, Code Snippets, 64(1), URL
7 svycox.validate 7 Examples bootit=200 library(survey) library(rms) dd=datadist(nona) options(datadist="dd") dstr2=svydesign(id=~1, strata=~group, prob=~inv_weight, fpc=~ssize, data=nona) mynom=svycox.nomogram(.design=dstr2,.model=surv(survival,surv_cens)~ecog+liver_only+alb+hb+age+ Differentiation+Gt_1_m1site+lymph_only,.data=noNA, pred.at=24, fun.lab="prob of 2 Yr OS") cases=which(nona$group=="long") controls=which(nona$group=="<24") boot.index=matrix(na,nrow(nona),bootit) for(i in 1:bootit){ boot.index[,i]=c(sample(cases,replace=true),sample(controls,replace=true)) } myval=svycox.validate(boot.index,mynom,nona)
8 Index Topic nomogram nona, 3 svycox.calibrate, 4 svycox.nomogram, 5 svycox.validate, 6 Topic package SvyNom-package, 2 Topic survey nona, 3 svycox.calibrate, 4 svycox.nomogram, 5 svycox.validate, 6 Topic survival nona, 3 svycox.calibrate, 4 svycox.nomogram, 5 svycox.validate, 6 nona, 3 svycox.calibrate, 4 svycox.nomogram, 5 svycox.validate, 6 SvyNom (SvyNom-package), 2 SvyNom-package, 2 8
Memorial Sloan-Kettering Cancer Center
Memorial Sloan-Kettering Cancer Center Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series Year 2011 Paper 23 Building a Nomogram for Survey-Weighted Cox
Journal of Statistical Software
JSS Journal of Statistical Software February 2015, Volume 64, Code Snippet 1. http://www.jstatsoft.org/ Building a Nomogram for Survey-Weighted Cox Models Using R Marinela Capanu Memorial Sloan-Kettering
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