nomogram.plot: Nomogram plot by rms

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Nomogram plot by rms

Description

Nomogram plot by rms

Usage

nomogram.plot(fit = NULL, data = NULL, fun.list = NA, lp = F)

Arguments

fit	rms model
data	The data used to build the model
fun.list	an optional function to transform the linear predictors, and to plot on another axis. If more than one transformation is plotted, put them in a list, e.g. list(function(x) x/2, function(x) 2*x). Any function values equal to NA will be ignored.
lp	线性预测If fun.list is NA, lp will be TRUE. Set to FALSE to suppress creation of an axis for scoring X beta

Examples

# Logistic model
data(LIRI)
res = loonR::build.logistic.model(LIRI[,3:5], LIRI$status, rms = T, scale = F)
f1 = list(Risk = loonR::logit2prob)
loonR::nomogram.plot(res$model, res$data, lp = T)
loonR::nomogram.plot(res$model, res$data, f1, lp =F)

# Survial model
res = build.psm.regression.model(LIRI[,3:5],LIRI$status, LIRI$time, scale = F)

surv <- Survival(res$model) # This would also work if f was from cph
surv_100 <- function(x) surv(100, lp = x)
surv_300 <- function(x) surv(300, lp = x)

med <- Quantile(res$model)
med_f <- function(x) med(lp=x)

f.list=list(
  `Median Survival Time`= med_f,
  `Probability of 100-day Survival`=surv_100,
  `Probability of 300-day Survival`=surv_300
)
nomogram.plot(res$model, res$data, fun.list = f.list, lp =F)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.