TotalPoints.rms: Caculate Total Points for nomogram Picture

In yikeshu0611/nomogramFormula: Calculate Total Points and Probabilities for Nomogram

Description

Compared with points_cal() command, TotalPoints.rms() is suit for more complexed condition. Since this command is based on formula from 'rms' package, it may be also more accurate. However, formula for each variable can not be caculated.

Usage

TotalPoints.rms(rd, fit, nom, kint = NULL)

Arguments

rd	raw data
fit	regression result in 'rma' package
nom	nomoram() command result
kint	number of intercept. Default is to use fit$interceptRef if it exists, or 1.

Value

a dataframe contains rawdata and total points

Examples

library(rms)
n <- 1000    
set.seed(17) 
d <- data.frame(age = rnorm(n, 50, 10),
                blood.pressure = rnorm(n, 120, 15),
                cholesterol = rnorm(n, 200, 25),
                sex = factor(sample(c('female','male'), n,TRUE)))

d <- upData(d,
            L = .4*(sex=='male') + .045*(age-50) +
              (log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male')),
            y = ifelse(runif(n) < plogis(L), 1, 0))

ddist <- datadist(d); options(datadist='ddist')

f <- lrm(y ~ lsp(age,50) + sex * rcs(cholesterol, 4) + blood.pressure,
         data=d)
nom <- nomogram(f)
TotalPoints.rms(rd = d,fit = f,nom = nom)

yikeshu0611/nomogramFormula documentation built on Dec. 25, 2019, 11:36 a.m.