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Last data update: 2014.03.03

R: Get model data

getModelData4Forestplot

R Documentation

Get model data

Description

A helper function for forestplotCombineRegrObj. Extracts the data from the regression model fits and returns a list with model data gathered by the function prGetFpDataFromFit

Usage

getModelData4Forestplot(regr.obj, exp = TRUE, variablesOfInterest.regexp,
  ref_labels, add_first_as_ref)

Arguments

`regr.obj`	A list with all the fits that have variables that are to be identified through the regular expression
`exp`	Report in exponential form. Default true since the function was built for use with survival models.
`variablesOfInterest.regexp`	A regular expression identifying the variables that are of interest of comparing. For instance it can be "(score\|index\|measure)" that finds scores in different models that should be compared.
`ref_labels`	If add_first_as_ref is TRUE then this vector is used for the model fits.
`add_first_as_ref`	If you want that the first variable should be reference for that group of variables. The ref is a variable with the estimate 1 or 0 depending if exp() and the confidence interval 0.

Examples

org.par <- par("ask" = TRUE)

# simulated data to test 
set.seed(10)
ftime <- rexp(200)
fstatus <- sample(0:1,200,replace=TRUE)
cov <- data.frame(
  x1 = runif(200),
  x2 = runif(200),
  x3 = runif(200))

library(rms)
ddist <- datadist(cov)
options(datadist = "ddist")

fit1 <- cph(Surv(ftime, fstatus) ~ x1 + x2, data=cov)
fit2 <- cph(Surv(ftime, fstatus) ~ x1 + x3, data=cov)

forestplotCombineRegrObj (
  regr.obj = list(fit1, fit2),
  variablesOfInterest.regexp = "(x2|x3)",
  reference.names = c("First model", "Second model"),
  new_page = TRUE)

modifyNameFunction <- function(x){
  if (x == "x1")
    return ("Covariate A")
  
  if (x == "x2")
    return (expression(paste("My ", beta[2])))
  
  return (x)
}

forestplotCombineRegrObj (
  regr.obj = list(fit1, fit2),
  variablesOfInterest.regexp = "(x2|x3)",
  reference.names = c("First model", "Second model"),
  rowname.fn = modifyNameFunction,
  new_page = TRUE)

par(org.par)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(Greg)
Loading required package: forestplot
Loading required package: grid
Loading required package: magrittr
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Greg/getModelData4Forestplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getModelData4Forestplot
> ### Title: Get model data
> ### Aliases: getModelData4Forestplot
> ### Keywords: internal
> 
> ### ** Examples
> 
> org.par <- par("ask" = TRUE)
> 
> # simulated data to test 
> set.seed(10)
> ftime <- rexp(200)
> fstatus <- sample(0:1,200,replace=TRUE)
> cov <- data.frame(
+   x1 = runif(200),
+   x2 = runif(200),
+   x3 = runif(200))
> 
> library(rms)
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, round.POSIXt, trunc.POSIXt, units

Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

> ddist <- datadist(cov)
> options(datadist = "ddist")
> 
> fit1 <- cph(Surv(ftime, fstatus) ~ x1 + x2, data=cov)
> fit2 <- cph(Surv(ftime, fstatus) ~ x1 + x3, data=cov)
> 
> forestplotCombineRegrObj (
+   regr.obj = list(fit1, fit2),
+   variablesOfInterest.regexp = "(x2|x3)",
+   reference.names = c("First model", "Second model"),
+   new_page = TRUE)
> 
> modifyNameFunction <- function(x){
+   if (x == "x1")
+     return ("Covariate A")
+   
+   if (x == "x2")
+     return (expression(paste("My ", beta[2])))
+   
+   return (x)
+ }
> 
> forestplotCombineRegrObj (
+   regr.obj = list(fit1, fit2),
+   variablesOfInterest.regexp = "(x2|x3)",
+   reference.names = c("First model", "Second model"),
+   rowname.fn = modifyNameFunction,
+   new_page = TRUE)
> 
> par(org.par)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>