Level plots for risk prediction models
Level plots for predicted risks
riskLevelPlot( object, formula, data = parent.frame(), horizon = NULL, cause = 1, ... )
object |
risk prediction model object |
formula |
formula |
data |
data |
horizon |
time point |
cause |
cause of interst |
... |
passed to lattice::levelplot |
Level plots for predicted risks
Thomas A. Gerds <tag@biostat.ku.dk>
# ---------- logistic regression -------------------- expit <- function(x){exp(x)/(1+exp(x))} partyData <- function(N){ Age <- runif(N,.5,15) Parasites <- rnorm(N,mean=3.5-0.03*Age) Fever <- factor(rbinom(N,1,expit(-3.5-.3*Age+.55*Parasites+0.15*Age*Parasites))) data.frame(Fever,Age,Parasites) } d <- partyData(100) f <- glm(Fever~Age+Parasites,data=d,family="binomial") riskLevelPlot(f,Fever~Age+Parasites,d) if (requireNamespace("randomForest",quietly=TRUE)){ rf <- randomForest::randomForest(Fever~Age+Parasites,data=d) riskLevelPlot(f,Fever~Age+Parasites,d) riskLevelPlot(rf,Fever~Age+Parasites,d) } # ---------- survival analysis -------------------- # --simulate an artificial data frame # with survival response and three predictors library(survival) library(prodlim) set.seed(140515) sdat <- sampleData(43,outcome="survival") # -- fit a Cox regression model survForm = Surv(time,event) ~ X8 + X9 cox <- coxph(survForm, data = sdat,x=TRUE) # --choose a time horizon for the predictions and plot the risks timeHorizon <- floor(median(sdat$time)) riskLevelPlot(cox, survForm, data = sdat, horizon = timeHorizon) # ---------- competing risks -------------------- # -- simulate an artificial data frame # with competing cause response and three predictors library(cmprsk) library(riskRegression) set.seed(140515) crdat <- sampleData(49) # -- fit a cause-specific Cox regression model crForm <- Hist(time,event)~X8+X9 csCox <- CSC(crForm, data=crdat) # -- choose a time horizon and plot the risk for a given cause timeHorizon <- floor(median(crdat$time)) riskLevelPlot(csCox, crForm, data = crdat, horizon = timeHorizon, cause = 1)
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