pmodel: Personalised model

In model4you: Stratified and Personalised Models Based on Model-Based Trees and Forests

Description

Compute personalised models from cforest object.

Usage

pmodel(
  x = NULL,
  model = NULL,
  newdata = NULL,
  OOB = TRUE,
  fun = coef,
  return_attr = c("modelcall", "data", "similarity")
)

Arguments

x	cforest object or matrix of weights.
model	model object. If NULL the model in x$info$model is used.
newdata	new data. If NULL cforest learning data is used. Ignored if x is a matrix.
OOB	In case of using the learning data, should patient similarities be computed out of bag?
fun	function to apply on the personalised model before returning. The default coef returns a matrix of personalised coefficients. For returning the model objects use identity.
return_attr	which attributes to add to the object returned. If it contains "modelcall" the call of the base model is returned, if it contains "data" the data, and if it contains "similarity" the matrix of similarity weights is added.

Value

depends on fun.

Examples

library("model4you")

if(require("mvtnorm") & require("survival")) {
  
  ## function to simulate the data
  sim_data <- function(n = 500, p = 10, beta = 3, sd = 1){
    
    ## treatment
    lev <- c("C", "A")
    a <- rep(factor(lev, labels = lev, levels = lev), length = n)
    
    ## correlated z variables
    sigma <- diag(p) 
    sigma[sigma == 0] <- 0.2
    ztemp <- rmvnorm(n, sigma = sigma)
    z <- (pnorm(ztemp) * 2 * pi) - pi  
    colnames(z) <- paste0("z", 1:ncol(z))
    z1 <- z[,1]
    
    ## outcome
    y <- 7 + 0.2 * (a %in% "A") + beta * cos(z1) * (a %in% "A") + rnorm(n, 0, sd)
    
    data.frame(y = y, a = a, z)
  }
  
  ## simulate data
  set.seed(123)
  beta <- 3
  ntrain <- 500
  ntest <- 50
  simdata <- simdata_s <- sim_data(p = 5, beta = beta, n = ntrain)
  tsimdata <- tsimdata_s <- sim_data(p = 5, beta = beta, n = ntest)
  simdata_s$cens <- rep(1, ntrain)
  tsimdata_s$cens <- rep(1, ntest)
  
  ## base model
  basemodel_lm <- lm(y ~ a, data = simdata)
  
  ## forest
  frst_lm <- pmforest(basemodel_lm, ntree = 20, 
                      perturb = list(replace = FALSE, fraction = 0.632),
                      control = ctree_control(mincriterion = 0))
  
  ## personalised models
  # (1) return the model objects
  pmodels_lm <- pmodel(x = frst_lm, newdata = tsimdata, fun = identity)
  class(pmodels_lm)
  # (2) return coefficients only (default)
  coefs_lm <- pmodel(x = frst_lm, newdata = tsimdata)
  
  # compare predictive objective functions of personalised models versus
  # base model
  sum(objfun(pmodels_lm)) # -RSS personalised models
  sum(objfun(basemodel_lm, newdata = tsimdata)) # -RSS base model
  
  
  if(require("ggplot2")) {
    ## dependence plot
    dp_lm <- cbind(coefs_lm, tsimdata)
    ggplot(tsimdata) +
      stat_function(fun = function(z1) 0.2 + beta * cos(z1), 
                    aes(color = "true treatment\neffect")) +
      geom_point(data = dp_lm, 
                 aes(y = aA, x = z1, color = "estimates lm"), 
                 alpha = 0.5)  +
      ylab("treatment effect") + 
      xlab("patient characteristic z1")
  }
}

model4you documentation built on Jan. 20, 2021, 5:09 p.m.